diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv new file mode 100644 index 0000000000000000000000000000000000000000..5ab5ecb459c80f2de9af671b46b5b37d32c09326 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv @@ -0,0 +1,1987 @@ +Orthogroup Duplications (all) Duplications (50% support) +OG0000000 33 27 +OG0000001 22 22 +OG0000002 17 15 +OG0000003 16 14 +OG0000004 13 8 +OG0000005 19 16 +OG0000006 9 6 +OG0000007 10 6 +OG0000008 8 8 +OG0000009 5 3 +OG0000010 8 8 +OG0000011 6 5 +OG0000012 5 3 +OG0000013 6 6 +OG0000014 4 2 +OG0000015 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b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv new file mode 100644 index 0000000000000000000000000000000000000000..8825eb1ab1b02802d79a5f1299810d19c85e8f39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv @@ -0,0 +1,10 @@ +Species Tree Node Duplications (all) Duplications (50% support) +N1 36 20 +AS2 135 135 +TT9 20 20 +N2 44 22 +SA211 36 36 +KBS0714 41 41 +N0 31 9 +KD337_16 113 113 +N3 9 9 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv 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b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv new file mode 100644 index 0000000000000000000000000000000000000000..903f730aff42336ba18435b432688ccfd9072d3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv @@ -0,0 +1,6 @@ + AS2 KBS0714 KD337_16 SA211 TT9 +AS2 0.0 2028.0 2012.0 2038.0 2029.0 +KBS0714 1989.0 0.0 1886.0 2044.0 2053.0 +KD337_16 1989.0 1926.0 0.0 1915.0 1949.0 +SA211 1978.0 2051.0 1881.0 0.0 2070.0 +TT9 1949.0 2022.0 1895.0 2053.0 0.0 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv new file mode 100644 index 0000000000000000000000000000000000000000..2ff0a551430f3acf8f6df37a93db044b3e321642 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv @@ -0,0 +1,6 @@ + AS2 KBS0714 KD337_16 SA211 TT9 +AS2 0.0 9.0 14.0 13.0 10.0 +KBS0714 8.0 0.0 3.0 8.0 8.0 +KD337_16 13.0 3.0 0.0 5.0 3.0 +SA211 14.0 9.0 4.0 0.0 4.0 +TT9 7.0 6.0 2.0 6.0 0.0 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one.tsv 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b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv new file mode 100644 index 0000000000000000000000000000000000000000..c75ad2fa0f175def7011d075524730c23cb79795 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv @@ -0,0 +1,6 @@ + AS2 KBS0714 KD337_16 SA211 TT9 +AS2 0.0 31.0 58.0 27.0 13.0 +KBS0714 77.0 0.0 59.0 25.0 11.0 +KD337_16 81.0 26.0 0.0 20.0 13.0 +SA211 79.0 24.0 49.0 0.0 12.0 +TT9 82.0 30.0 55.0 24.0 0.0 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv new file mode 100644 index 0000000000000000000000000000000000000000..6e9bc2b172b44ac1196602c7bfb8abdf7e1c6523 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv @@ -0,0 +1,6 @@ + AS2 KBS0714 KD337_16 SA211 TT9 +AS2 0.0 1819.0 1754.0 1819.0 1824.0 +KBS0714 1819.0 0.0 1763.0 1960.0 1960.0 +KD337_16 1754.0 1763.0 0.0 1778.0 1808.0 +SA211 1819.0 1960.0 1778.0 0.0 1997.0 +TT9 1824.0 1960.0 1808.0 1997.0 0.0 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Statistics_Overall.tsv b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Statistics_Overall.tsv new file mode 100644 index 0000000000000000000000000000000000000000..133441e0e119915a2a93f78c75e507a6fe592e35 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Statistics_Overall.tsv @@ -0,0 +1,53 @@ +Number of species 5 +Number of genes 11758 +Number of genes in orthogroups 11058 +Number of unassigned genes 700 +Percentage of genes in orthogroups 94.0 +Percentage of unassigned genes 6.0 +Number of orthogroups 2370 +Number of species-specific orthogroups 41 +Number of genes in species-specific orthogroups 98 +Percentage of genes in species-specific orthogroups 0.8 +Mean orthogroup size 4.7 +Median orthogroup size 5.0 +G50 (assigned genes) 5 +G50 (all genes) 5 +O50 (assigned genes) 1017 +O50 (all genes) 1087 +Number of orthogroups with all species present 1709 +Number of single-copy orthogroups 1563 +Date 2026-05-15 +Orthogroups file Orthogroups.tsv +Unassigned genes file Orthogroups_UnassignedGenes.tsv +Per-species statistics Statistics_PerSpecies.tsv +Overall statistics Statistics_Overall.tsv +Orthogroups shared between species Orthogroups_SpeciesOverlaps.tsv + +Average number of genes per-species in orthogroup Number of orthogroups Percentage of orthogroups Number of genes Percentage of genes +<1 600 25.3 1764 16.0 +'1 1753 74.0 8972 81.1 +'2 8 0.3 93 0.8 +'3 3 0.1 49 0.4 +'4 1 0.0 23 0.2 +'5 3 0.1 79 0.7 +'6 1 0.0 32 0.3 +'7 0 0.0 0 0.0 +'8 0 0.0 0 0.0 +'9 1 0.0 46 0.4 +'10 0 0.0 0 0.0 +11-15 0 0.0 0 0.0 +16-20 0 0.0 0 0.0 +21-50 0 0.0 0 0.0 +51-100 0 0.0 0 0.0 +101-150 0 0.0 0 0.0 +151-200 0 0.0 0 0.0 +201-500 0 0.0 0 0.0 +501-1000 0 0.0 0 0.0 +'1001+ 0 0.0 0 0.0 + +Number of species in orthogroup Number of orthogroups +1 41 +2 249 +3 130 +4 241 +5 1709 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv new file mode 100644 index 0000000000000000000000000000000000000000..3d820f01dcacd6eec62cd6850653591ae87fcc02 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv @@ -0,0 +1,100 @@ + AS2 KBS0714 KD337_16 SA211 TT9 +Number of genes 2623 2252 2432 2257 2194 +Number of genes in orthogroups 2300 2192 2205 2203 2158 +Number of unassigned genes 323 60 227 54 36 +Percentage of genes in orthogroups 87.7 97.3 90.7 97.6 98.4 +Percentage of unassigned genes 12.3 2.7 9.3 2.4 1.6 +Number of orthogroups containing species 2108 2095 2035 2104 2096 +Percentage of orthogroups containing species 88.9 88.4 85.9 88.8 88.4 +Number of species-specific orthogroups 13 1 26 1 0 +Number of genes in species-specific orthogroups 30 2 61 5 0 +Percentage of genes in species-specific orthogroups 1.1 0.1 2.5 0.2 0.0 + + +Number of genes per-species in orthogroup Number of orthogroups Number of orthogroups Number of orthogroups Number of orthogroups Number of orthogroups +'0 262 275 335 266 274 +'1 1983 2044 1923 2056 2065 +'2 98 36 84 32 21 +'3 16 7 18 4 2 +'4 4 2 7 2 2 +'5 2 4 1 6 3 +'6 1 1 0 1 2 +'7 1 0 1 2 0 +'8 1 0 0 0 0 +'9 1 0 0 0 0 +'10 0 0 0 0 1 +11-15 0 0 0 1 0 +16-20 1 0 1 0 0 +21-50 0 1 0 0 0 +51-100 0 0 0 0 0 +101-150 0 0 0 0 0 +151-200 0 0 0 0 0 +201-500 0 0 0 0 0 +501-1000 0 0 0 0 0 +'1001+ 0 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups +'0 11.1 11.6 14.1 11.2 11.6 +'1 83.7 86.2 81.1 86.8 87.1 +'2 4.1 1.5 3.5 1.4 0.9 +'3 0.7 0.3 0.8 0.2 0.1 +'4 0.2 0.1 0.3 0.1 0.1 +'5 0.1 0.2 0.0 0.3 0.1 +'6 0.0 0.0 0.0 0.0 0.1 +'7 0.0 0.0 0.0 0.1 0.0 +'8 0.0 0.0 0.0 0.0 0.0 +'9 0.0 0.0 0.0 0.0 0.0 +'10 0.0 0.0 0.0 0.0 0.0 +11-15 0.0 0.0 0.0 0.0 0.0 +16-20 0.0 0.0 0.0 0.0 0.0 +21-50 0.0 0.0 0.0 0.0 0.0 +51-100 0.0 0.0 0.0 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 0.0 + +Number of genes per-species in orthogroup Number of genes Number of genes Number of genes Number of genes Number of genes +'0 0 0 0 0 0 +'1 1983 2044 1923 2056 2065 +'2 196 72 168 64 42 +'3 48 21 54 12 6 +'4 16 8 28 8 8 +'5 10 20 5 30 15 +'6 6 6 0 6 12 +'7 7 0 7 14 0 +'8 8 0 0 0 0 +'9 9 0 0 0 0 +'10 0 0 0 0 10 +11-15 0 0 0 13 0 +16-20 17 0 20 0 0 +21-50 0 21 0 0 0 +51-100 0 0 0 0 0 +101-150 0 0 0 0 0 +151-200 0 0 0 0 0 +201-500 0 0 0 0 0 +501-1000 0 0 0 0 0 +'1001+ 0 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of genes Percentage of genes Percentage of genes Percentage of genes Percentage of genes +'0 0.0 0.0 0.0 0.0 0.0 +'1 75.6 90.8 79.1 91.1 94.1 +'2 7.5 3.2 6.9 2.8 1.9 +'3 1.8 0.9 2.2 0.5 0.3 +'4 0.6 0.4 1.2 0.4 0.4 +'5 0.4 0.9 0.2 1.3 0.7 +'6 0.2 0.3 0.0 0.3 0.5 +'7 0.3 0.0 0.3 0.6 0.0 +'8 0.3 0.0 0.0 0.0 0.0 +'9 0.3 0.0 0.0 0.0 0.0 +'10 0.0 0.0 0.0 0.0 0.5 +11-15 0.0 0.0 0.0 0.6 0.0 +16-20 0.6 0.0 0.8 0.0 0.0 +21-50 0.0 0.9 0.0 0.0 0.0 +51-100 0.0 0.0 0.0 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 0.0 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001022.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001022.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad8c272345db0d062308c31a69758e498a9ec3bd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001022.fa @@ -0,0 +1,57 @@ +>ACLBLIBL_01533 +MTDRPAFSSPRGGSTVGPAPGLPDARIRGLLLLVLVLLGGLALRLVYVQGVDPTGQAAAA +MDKRLTHQETLPERGSILDRDGDVLASSVRRYDMVVDQRLVKDFNEWDREARKTVLVDVD +SRLASLAEVLELPEEQVREATIGSRPYNVVKRSVTPEMRDAAMALKVPGLLAEPVDRRVY +PNGSVAGSIVGFMGGDGTPLEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAV +DGADLRLTLDKDAQWFAQETMGALAAEHDAEWANAVVLDAKTGDVLVMADSTTVDPADPE +GTEPYFRSSTVMSTPYEPGSTGKALPIAAALDAGAVTATDGYTVPSSQEFDGQTIRDFAP +HETYDMTVAGIFARSYNTGTVQVAEEISDELRYEYMRSFGVGKPIDLGLPRTAGGVLVPP +GEWDGRQRLTTAFGQGYTQTTLHTAQMYQAMANGGVMEPARLIDATVDGDGAEKRWEPAA +EPHRVVSEATAADMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGRYDGYNFGF +TAVAPLDDPRFVVSVSMHRPPSQLGSRAVTSAAAQIMEHMLRQADVPADGAAPQDYDVFV +DDPQDRPW +>MOLHKGIG_01360 +MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV +LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS +RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE +LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL +AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA +LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA +EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT +AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ +GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSMHRPPSKQ +GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW +>NAFOICDF_01428 +MPVSRSRVSGAGSRTAPPIGTARVRSRTVLLLLLALVTVLGLRLVWVQGIDASGAAATAM +SERLKTQEIRPERGAITDRDGAVLASTVRRYDIVVDQRLVKDFKEWDAEKRQSVLVSIDS +RLSSLAEALGMSEDEVRAAAIGDRPWAVLKRSVTPEVRDRVLALKVPGVLADAVDRRTYP +SGAVAGSLVGFMSSDGTPLEGLEKSQDAVLSGTPGTRTFEVGATGIRIPNAPEDVTPAVD +GATLRLTLDKDAQWYAQEAMARLADTYSAQWANAVVMDAKTGEVLALADSATVDPGDPQA +ADARARTPGVVYTPYEPGSTGKTATMAAALDMGLVTPETGLEVPDRLELKGQPPIRDASP +HETYTMTVAGVYARSYNTGTVMVAEKMSDEQRYEYMRSFGIGRPIDLGLPQPARSVLAAP +GDWDGRQRLVTAFGQGYTVTTLHTAQMFQAIANGGVLEPARLIAATVGADGTEHRWDPGV +ASRRVVSEQTAEEMLRMMETVVTQGTSTVAQLPGYRVGGKSSTAQVAGETGTYDGYNYGF +TAVAPLDDPRYVVSVSMNRPSAGGSSKVVAAAAADVMQHMLRQGGVPPGGAEPDDYRVFV +DDPQERPW +>MHAAABBN_01080 +MRTRILLLLVLVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV +LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS +RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE +LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL +AAEYDAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA +LPIAAAVDAGKVTATDGFTVPSSQDFDGQTIKDFSPHPTFDMTVAGIYARSYNTGTVQIA +EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEKWDGRQRLTTAFGQGYTQTTLHT +AQMYQALANGGVLIPARLIDATVDGEGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ +GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNFGFTAVAPLDDPRFVVSVSMHRPPSKQ +GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW +>LFPAFLNI_01315 +MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV +LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS +RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE +LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL +AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA +LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA +EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT +AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ +GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSLHRPPSKQ +GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001196.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001196.fa new file mode 100644 index 0000000000000000000000000000000000000000..d643c8b6e99611c435852cd3ea8e3bf0704ba53b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001196.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_01727 +MRTTELAAPPSLAGLYARAAGQAAKDALTRRSRPAVLPEREVVVTGHRIPRAAVAAWRDA +VGPADPAALPSVLVHTQVFGAAMELMADPEFPLPLPGMVHLTNTVLHRRPVPAETALRVT +ARAVGLVPHHAGTAVDVAVTVEGPHPAGGEAVLWEGVSRYLAKGVHLTGLRPERPAREEF +TAPARTAEWRLGAGAGRRYADVSGDWNPIHLTGVSARLFGMKGAIAHGMLLAARMLQGRE +PAAGGFRWEIEFDAPVVLPGTVAVRYEPADGQGTRVIGWDGRRCRRHFTGRIAPLAD +>MOLHKGIG_01163 +MQTTQLSAPPSLGRLYVRAAGRAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVTAWRGA +VGSANPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVAAETALRVT +ARAVGLVPHHAGTAVDVVVTVEGPGDDGEEALLWEGVSRYLAKGVHLSGLRPERPARPDF +VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE +PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVWGWDARRRRPHFSGEITPLEP +>NAFOICDF_01624 +MHTRTESSMPALAGLYRRAAGQALADAARRRTRPAELPDERLVVEGHRIPERALRRWQAE +IGPVDPASVPSVLVHTQVFGAAMALMAEPDFPLPLPGMVHLTNAVEHRRPVAAGEALDVT +ARAVGLVPHHAGTAVDLQVAVREAGETDDAPAAWEGVSRYLARGVHLAPLRPERPERPEF +TPPAPTAQWMFDGGAGRRYAEVSGDWNPIHLSALSARAFGQRRAIAHGMLLAARMLNRRE +PRAAAFGEGFGWDVEFHAPVVLPARVAVRYEAAADGSTRVSAWDPRRGRPHLDGRIRHAR +P +>MHAAABBN_00882 +MQTTQLSAPPSLARLYARAARQAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVSAWRGA +VGSADPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVAAETPLRVT +ARAVGLVPHHAGTAVDVVVTVEGPGDDGEEALLWEGVSRYLAKGVHLSGLRPERPARPDF +VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE +PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVWGWDARRRRPHFSGEITPLEP +>LFPAFLNI_01113 +MQTTQLSAPPSLGRLYVRAAGRAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVTAWRGA +VGSADPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVPAETALRVT +ARAVGLVPHHAGTAVDVVVTVEGPGDDGGEALLWEGVSRYLAKGVHLSGLRPERPARPDF +VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE +PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVYGWDARRRRPHFSGEITPLES diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001324.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001324.fa new file mode 100644 index 0000000000000000000000000000000000000000..e1c9346972f207aed64acb08c8ba351433580d47 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001324.fa @@ -0,0 +1,48 @@ +>ACLBLIBL_01904 +MVLDVEGDRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQL +EERLADLADRLPERLSLHVNGCPNSCARIQTADIGLKGQLLPDDDGGQTPGFQIHLGGGL +ASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFARWAHRVDEEALR +>MOLHKGIG_00985 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG +FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL +RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG +SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK +ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP +VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS +VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY +VERVVRRYDEQREPGETFARWAHRVDEEALR +>NAFOICDF_01851 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAREG +FDSIPSDDLHGRFRWWGLYTQRKQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL +RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG +SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK +ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP +VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS +VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY +VERLVRRYDEQREPGETFARWAHRVDEEALR +>MHAAABBN_00699 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTTPLNHNEEFKQQDDGLNVRERIEQVYAREG +FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL +RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG +SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK +ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP +VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS +VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY +VERLVRRYDEQREPGETFARWAHRVDEEALR +>LFPAFLNI_00928 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG +FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL +RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG +SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK +ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP +VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS +VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY +VERVVRRYDEQREPGETFARWAHRVDEEALR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001543.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001543.fa new file mode 100644 index 0000000000000000000000000000000000000000..184b93090b01a3c91d5c50b6005c400ed287d764 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001543.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_02260 +MTPGTRLSTPPKLKKGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD +LILPDFDYIRDRMDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE +HRIKPRTRVVKEDEIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL +DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF +SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYKDD +EVVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG +ANVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN +VILAGNGTVVDMTDGLVKVVGEVDCGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV +VNRQTGSIVSGPDIHARGVAEDEKVFEDIKPKIARALEEAVQSSKDHTAHQLQQVVRRTV +GTWVNRKLRRRPMIIPVVLEA +>MOLHKGIG_00694 +MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD +LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE +HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL +DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF +SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD +EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG +ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN +VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV +VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV +GTWVNRKLRRRPMIIPVVLEA +>NAFOICDF_00464 +MTRSSRNSSSRRRGGGQSRRPRSSGAPGQLAKGGLRITPLGGLGEIGRNMTVFEHQGKLL +IVDCGVLFPEDHQPGIDVILPDFTSIRDRLQDVVGVVLTHGHEDHIGGVPYLLKERPDIP +LIGSELTLAFIEAKLKEHKIVPKTHMVVAEDKRHMGPFELEFVAVNHSIPDALAVAIRTE +AGLILHTGDFKMDQFPLDRRITDLRHFARLGEEGVDVFLTDSTNAEVPGFTISERELTPA +IDHVFRTAPKRIIVSSFASHVHRIQQVLDAAHASGRKVAFVGRSMVRNMGIAGDLGYLKI +PKGLVVDFKKLQDMPDEKIALISTGSQGEPMAALGRMANQTHQIKLNKGDTVLLASSVVP +GNETSITGIINKFTDMGVNVVHKGNAKVHVSGHASAGELVYCYNIVQPRNVMPVHGEAAH +LHANAELAKKTGLPEDRVFITKDGDVLDLVDGRVSVAGKVEAGLVYVDGDTIGKVTEGTL +EERRTMQEAGVVTVVAIVDPDTNQLAEPLEFMTKGFIQDASVFKGAAEKVKSALSRSNVQ +DIDDIEKLERVIGDAVTRHLERAYRRAPLVTVVVVDA +>MHAAABBN_00431 +MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD +LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE +HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL +DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF +SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD +EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG +ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN +VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV +VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV +GTWVNRKLRRRPMIIPVVLEA +>LFPAFLNI_00664 +MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD +LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE +HRITPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL +DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF +SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD +EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG +ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN +VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV +VNRQTGTIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTA +GTWVNRKLRRRPMIIPVVLEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001655.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001655.fa new file mode 100644 index 0000000000000000000000000000000000000000..8eb116188ee3ba87c3b4e3ba5a38973d5ce84353 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001655.fa @@ -0,0 +1,16 @@ +>ACLBLIBL_02465 +MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRLAEPHTYDLCAEHARRTTAPRGWEVLR +LELPGHYEAVAPDGTVHTVPTAPRAVPAAPPADVASRPSLAAPRPAPAVPPVDADEPEAP +APPTRPGLRLVRDDDPLPPA +>MOLHKGIG_00482 +MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR +LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD +>NAFOICDF_02349 +MRRCSKTGCQEPAEATLTYNYAGSQVVIGPLAQRAEPHAYDLCAAHAARTTAPRGWEVLR +LAPAAPAAPGVAAPTHPALRLVTDPVEGTAG +>MHAAABBN_00200 +MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR +LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD +>LFPAFLNI_00482 +MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR +LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001889.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001889.fa new file mode 100644 index 0000000000000000000000000000000000000000..a1741866290b7f1887b3ce3f074ee6fdcd71da5c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001889.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01875 +MDETPEPPRTRRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY +NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEAPVVAALRAWARSYRDVFAAHPPLIPL +IATLPIEGAPSTQRVYETVCAVLARTGLAPGQVLARVIALESFIYGSAYDVDAPADIFEV +AGAQERLPAFGAAAEAFREGGGTRATGARNPYADAPFEEGLDLLLAGLDD +>MOLHKGIG_01013 +MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY +NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL +IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV +AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD +>MHAAABBN_00727 +MAAVGRRLGVAPSALYNHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWA +RSYRDVFAAHPPLIPLIATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFI +YGSAYDVDAPADIFEVAGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLL +LAGLGD +>LFPAFLNI_00956 +MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY +NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL +IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV +AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002026.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002026.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff2b4056392c7fc18bd02680329b0d02b93435b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002026.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_01278 +MQRIIVIPDSFKGALSSREAGSAIAAGLASVTDAEVLVVPIADGGEGTVEAFVAAAGGAL +RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA +VSAGARRVIVGAGGSATTDGGTGAAAALGVRFLDVAGEEFVPTGDTLTRIARIDSTPARD +RLRDVDVEVMCDISNPLTGPQGAAHVFGPQKGADPAAVASLDTGLVHLAGLVERDLGVAI +DALPGSGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA +GKVPIGVAQAVRAADRAIPVIVLAGSVGQDADTLYDEGITAIVPIGRGPQDLATAIRRTA +EDLTATARDVGRLVMACSPARLTR +>MOLHKGIG_01618 +MQRIIVIPDSFKGALSSREAGSAIAAGLASVTDAEVLVVPIAYGGEGTVEAFVAAAGGAL +RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA +VSAGAGRVIVGAGGSATTDGGTGAAAALGVRFLDAAGEEFVPTGHTLTRIARIDSSPARD +RLRDVDVEVMCDISNPLTGSQGAAHVFGPQKGADPASVASLDTGLVHLAGIVERDLGVAI +DALPGSGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA +GKVPIGVAQAVRAAGRAIPVIVLAGSVGQDTDTLYDEGITAIVPIGRGPQDLATAIRRTA +EDLTATARDVGRLVMACSPAGLRR +>NAFOICDF_01185 +MQSIIVIPDSFKGALSSREAGSAIATGLASATDAEVLVVPIADGGEGTVEAFVAAAGGAL +RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA +VSAGARRVVVGAGGSATTDGGTGAAAALGVRFLDVAGEEFVPTGDTLIRIARIDSTPARD +RLRDVDVEVMCDISNPLTGSQGAAHVFGPQKGADPASVASLDTGLVHLAGIVERDLGVAI +DALPGAGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA +GKVPIGVAQAVRAAGRAIPVIVLAGSVGQDADILYDEGITAIVPIGRGPQDLATAIRRTA +EDLTATARDIGRLVMACSPAGLTR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002033.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002033.fa new file mode 100644 index 0000000000000000000000000000000000000000..b3ddd6e958a6e4c697885248bc29e5c2bfc4a7a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002033.fa @@ -0,0 +1,9 @@ +>ACLBLIBL_01992 +MTATTHTLLRAEGFSCPSCVRKIEKAVDALPGVTGSKVHFETQRIEVDHDAERTSVQDLV +DAVDRVGYRARPSVF +>MOLHKGIG_00945 +MTATTHILLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV +EAVAKVGYTARPSAF +>MHAAABBN_00664 +MTPTTRTLLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV +EAVAKVGYTARPSAF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002099.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002099.fa new file mode 100644 index 0000000000000000000000000000000000000000..49ed28daa659d09369e8a666cdc27f44b81f9565 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002099.fa @@ -0,0 +1,12 @@ +>MOLHKGIG_02217 +MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA +ELAEAFDLDVSTVHRQVAAAMKAGLVERVVDPDGGSARLHRPTEEGRARLAAELSSRADN +VAQIVSSWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRL +>MHAAABBN_01930 +MMQTSEGAWADPVRGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSVA +ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN +VAQIVASWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRP +>LFPAFLNI_02156 +MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA +ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN +VAQIVSSWPAEDVVEFSRLLRRFNEGAEARRGHPWPRPQTGPGAEDPRL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002142.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002142.fa new file mode 100644 index 0000000000000000000000000000000000000000..52a2829c456e846c10e862dbb8b03aa4f37f490c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002142.fa @@ -0,0 +1,11 @@ +>ACLBLIBL_00343 +MQRIVPNIWCDGTADAAAEFYLRAFAGLPGTAHVRTDRYPTEGLLDFQRPLAGKTLTQEL +DLAGHRFILVNAGDEFAPNPSISFFVNADPSRMDDPRGTLDALWAELTDGGRVLMDLGPY +PHSEHYGWVEDRHGVSWQLMLTDPAGDPRPVIIPQLMFCGPAQNRAAEALDHYLAVFDDA +TPGQRVTYGDMGHVPEGGPVEAGSIVFADARLRGEWVAAMDSAVAQDFTFTEGVSLMVQC +RDQAEIDRLWEALSAVPEAEQCGWLKDRWGVSWQIVPEDMGELMERPGAFEALLGMKKLV +IADF +>NAFOICDF_00477 +MSDAAAGAPQLISPFLWFHDGAEEALRYYVDVFPDSEIEEIQRYPDESLDPHYAGMAGKV +ISAWVRLGGVRFGALDGGPAFTLSEAVSFVVACRDQEEIDRYWAALSHVPEAEQCGWCKD +RFGVSWQIIPADMGRLLQSPAQIQAMMAMRKIEVAALEALA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002250.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002250.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7d7422fe695464c27745b8be169be504b88e124 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002250.fa @@ -0,0 +1,6 @@ +>ACLBLIBL_02639 +MLLAGVYFYAAAICTTIINDGGPGWLYLLVLVFVWNAFKFLWIGPVSLIQLISVRAGERR +ERQPVPSSR +>NAFOICDF_01770 +MLMFRLIWIASIHTRDLLHRYMPTNIVLGKLRTRRGLKWGVPAMLLTIPYLAVANILTIL +IDRGAPGWFHLLVLLFIWNAFKFLVTGPVSVVLLVRARTVERRDRRLLSRSPAPTV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000174.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000174.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd24b4f15222e84ce27d08d8cb123370ad6aa66f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000174.fa @@ -0,0 +1,69 @@ +>ACLBLIBL_00004 +MLGAHPHPDGAAVTYRVLRPLARTVTVVRTGDGERVELAHEHDGVFAGVARMPRVAGAAA +GDYRLEVAYETADGQTGPAQEQDDAYRHLPTLGELDLHLIGEGRHERLWEVLGARVVRTP +AGEAVGTAFAVWAPNARAVRVVGEHNGWDGRGHAMRSLGSSGVWELLVPGVGHGHRYKFE +ILGRDGRWRQKADPMARWTEVPPATASRVLESEYEFGDRTWMERRRTVDPHERPLSIYEV +HLGSWRPGLDYRELAEQLVEYVQWLGFTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGS +PDEFKHLVDALHRAGIGVIVDWVPAHFPKDEWALARFDGTPLYEHADPRRGEHPDWGTYV +FDFGRTEVRNFLVANALYWLAEFHIDGLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLE +AIDFLREVNATVYRVHPGVHMIAEESTAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLS +QDPVNRRWHHGQWTFSMVYAYSENYVLPLSHDEVVHGKGSLLTRIPGDRRHQLATLRAYY +GYMWAHPGKQLLFMGGEYGQPSEWSEAEGLDWPVSWDESHRGVQLTVRELNALYRSKPAL +WSQDHSPAGFEWVDGGDADGNTLVFLRHPAERVVPEARIDDDGAAVSAAEPGGAPLLCIT +NLSGSPRQGLRVGVPGAGSGPWSWTPTPPTSTGTAGGSRPGSPRC +>MOLHKGIG_00331 +MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT +VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY +RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN +GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA +SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG +FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHQAGIGVIVDWVPAH +FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID +GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNMTVYRLHPGVHMIAEES +TAFSGVTAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMVYAYSENYV +LPLSHDEVVHGKGSLLSRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE +GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL +RMPAAQVVPEPRIDDDGDAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT +DSTDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPHPDSTVTP +>NAFOICDF_00005 +MTSPTLSPQSVDPAVLAAVAEGLHHDPHAVLGAHPHPDGAAVTYRALRPFARAVTVVREG +DAARIELAHEADGVFAGVGALPRKAGVAAGDYRLEVVYPGADGEDVVELHDDAYRHLPTL +GELDLHLIGEGRHERLWEVLGARVRRAADGALVGTSFAVWAPNARAVRVVGDFNGWTGRT +HAMRSLGSSGVWELLVPGVEHGAAYKFEILGADGQWQQNADPMARWTEVPPATASRVMES +EFAFTDRDWMERRRAEDPHERPLSIYEVHLGSWRPGLSYVDLAEQLVEYVQWLGFTHVEF +LPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVNALHEAGIGVIVDWVPAHFPKDAW +ALGRFDGTALYEHPDPRRGEHPDWGTYVFNFGRTEVRNFLVANALYWLGEFHVDGLRVDA +VASMLYLDYSREDGQWTPNALGGNHDLEAISFLQDVNATVYRVHPGILMIAEESTAFSGV +SAPVSAGGLGFGKKWNMGWMHDTLAYLSEDPVNRRWHHDQWTFSMAYAYSENYVLPLSHD +EVVHGKGSLLARIPGDHRQKLATLRAYFAYMWAHPGKQLLFMGGEYGQPSEWSEERGLDW +AASWDESHRGVQLTVRELNALYRAKPALWSADHSPQGFTWVDGGDADGNTLVFLRRPGAG +VEGAPLLCITNLSGGTRQGLRVGVPSSGEWTVVLDTDSTDFHGDGRREQAGQLEVIEAED +GQWQGQPAYLTLNVPPLTTLWLQPDED +>MHAAABBN_00047 +MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT +VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY +RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSAGEAVGTAFAVWAPNARAVRVVGDHN +GWDGRTHAMRSLGSSGVWELLVPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA +SRVLESDYAFGDRTWMERRRLTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG +FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH +FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID +GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES +TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHEQWTFSLVYAYSENYV +LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE +GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL +RMPAAQVVPETRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT +DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTTATP +>LFPAFLNI_00338 +MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT +VVRAGDGQRVELMHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY +RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN +GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA +SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG +FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH +FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID +GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES +TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMAYAYSENYV +LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE +GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFSWVDGGDADGNTLVFL +RMPAAQVVPEPRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT +DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTASTP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000176.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000176.fa new file mode 100644 index 0000000000000000000000000000000000000000..f12a5c9fb7c59e8bacc96d643e367ec0714fe668 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000176.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00009 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGKGPTPKAEDRVYHKAYRAKQLSERSAA +KRGGPVRPSRPKLTDETVSGRNPVVEALRAGIPAKALHVAVRIEMDDRVKEALRLCLEQG +VPVMENTKPELDRLSGEAIHQGLVLQIPPYEYADAMTLATDALEKHEKGHLRTPPLLIAL +DGITDPRNLGAIIRSGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLNTT +LVELHRAGYFVLGLDGGGDVSLPGLSLATEPLVLVVGAEGKGLSRMVREHCQQIVSIPIN +SDMESLNASMAVGISLYEISVQRAGGR +>MOLHKGIG_00326 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE +QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI +ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN +TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP +IDSTMESLNASMAVGISLYEISVQRAGGR +>NAFOICDF_00007 +MSTAPRSGGSRAPKGKKGPQKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KHGGGRVPVRDQVRGRVKLTDETVSGRNPVVEALRAGIPAKALHVATRIEVDDRVKEALR +LCAENKVPVMENTRPELDRMSGEAVHQGLVLQIPPYQYADALTLGREAMEAQEKGHLRTP +PLLIALDGITDPRNLGAIIRSASAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA +GNLNTTLVELHRMGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI +VSIPIQSEMESLNASMAVGISLYEIAVGRAGGRPVAS +>MHAAABBN_00042 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE +QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI +ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN +TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP +IDSTMESLNASMAVGISLYEISVQRAGGR +>LFPAFLNI_00333 +MSTAPRSGGSRKPKGKKGPVKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE +QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI +ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN +TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRLVREHCQQIVSIP +IDSTMESLNASMAVGISLYEISVQRAGGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000178.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000178.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ea70f0a50f87db30570711216fa8a10758f50d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000178.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00012 +MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL +RVTSVRNVTDIDDKILDRSAASHEEGFEPSALYPAREPWWALAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLVERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKEGEPATAVWTSPWGAGRPGWHLECSAMATKYLGAQFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVAYGGEKMSKSVGNTISPEEMLGM +ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFTARARTAGAVPPAVDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAAQDLESAAARLTEVEAMTAVLGLDDV +PEGDGDGTGPAADALDSLVRSQIEARAQARAEKDWAAADRIRDALAAAGVVVEDGADGAT +WRLAD +>MOLHKGIG_00325 +MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILERSAASHEAGFEASDLYPAREPWWALAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARLWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD +>NAFOICDF_00008 +MAQRFYDTRSAEIRDFVPLVPGQASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL +RVTSVRNVTDIDDKILDRSAASQEPGFEPSEMYPADEPWWALAFRFENAFDAAYLALGVR +RPTYEPRATGHVPEMLALIERLIERGHAYPAADGSGDVYFDVRSWDRYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKEGEPVTAVWSSPWGAGRPGWHLECSAMSTKYLGGEFD +VHGGGLDLRFPHHENELAQSAAAGDPFARFWLHNGLVTYQGEKMSKSVGNTISPQEMLAM +ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFVQRAAAALGAPELTAPLAEHV +PAAFRAAMEDDLAVPQALAVLHEAVRAGNSALAAGDDAAARARLAEVAAMTAVLGLDDVP +EASAGGSGPEAAALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGAQGATW +HLAG +>MHAAABBN_00040 +MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILERSAASYEAGFEASDLYPAREPWWGLAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD +>LFPAFLNI_00332 +MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILDRSAASHEAGFEASDLYPAREPWWALAYRFERAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLIERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGAEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRTAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDLLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000180.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000180.fa new file mode 100644 index 0000000000000000000000000000000000000000..caab701df11c3c21491f18077aee64db14b2f238 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000180.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_00014 +MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD +VVDSEGLEEVVEVLQAEQVEEPTNWSRRYKANLEKLASGDVKKVAEVVRDLWRRDQDRGL +SAGEKRMLSKARQVLVSELALAKKVTEEEAEGMLDQVLEG +>MOLHKGIG_00323 +MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD +VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL +SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG +>NAFOICDF_00010 +MPDTRGVFRVSVVESTDRKGAFHMVFEVGETVVYPHHGAARIEEIKTRTIKGEEKMYLKL +KVAQGDLTIEVPAENVDLVGVRDVVDDKGLEHVVEVLQAEHVEEPTNWSRRYKANLEKLA +SGDVNKVSEVVRDLWRRDHDRGLSAGEKRMLSKARQVLVSELALAKKVSEEEAEGMLDKV +LEG +>MHAAABBN_00038 +MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD +VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL +SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG +>LFPAFLNI_00330 +MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD +VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL +SAGEKRMLSKARQVLVSELALAKKVTEEEAEGRLDKVLEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000181.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000181.fa new file mode 100644 index 0000000000000000000000000000000000000000..56db1c80a5cead3525d5f22c631a7690efb4b9f5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000181.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00015 +MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIEYDASDGINGEEKDFLSYRNLA +LVGDGDSGPARLIGTLENLSDQAQTYTFQAEGGGSATVQVPAGETFKLEDDANQTVLERQ +DAWVGELLPVTVSGNGGQTELEVPLLGATQDHYRDLLPEGVSPSDEELGSHLDEETHDYG +GEH +>MOLHKGIG_00322 +MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA +LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE +GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG +EEH +>NAFOICDF_00011 +MKSVASRPARRRLAAGALALTAVLGATGCSAVSPVATGIQYSASDGVNATQTGFVEVRNL +GMVGEGASGPARLIGSLKNDSGADKTYTIAVQDGGQITVPVKAGETVKLEEQQLEVERSV +WPGQNAQATVSADGTQLQLGVPVLSATQEQYKEYLPAGQSADTEHLDEQTATYGEGEGEQ +H +>MHAAABBN_00037 +MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA +LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE +GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG +EEH +>LFPAFLNI_00329 +MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA +LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE +GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG +EEH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000183.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000183.fa new file mode 100644 index 0000000000000000000000000000000000000000..a9f230794863115b2d221cecaaa3b0099baf102c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000183.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00017 +MDPVIIGLLCGAVGLFIGVASMLAFRASERSRTVDLAVGEPTLAPGAAEVLAVVGRAYAV +VDDVDGVVRANPSAYALGLVRGHSLVQQQVKDLTRSVRAEGVIVERRLELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLAEAIGDAA +EDEEAVRRFASRLGIESRRLTALVQDIIEFSRLQAKDVVQDGRAVDLNAVVADAVDRLRL +TAEDRGITLRVGGRVDAVVHGDADQLMTAVRNLVDNAVRYSPEGTTVGIGLSSADGLAQV +TVTDQGIGISPEEQERVFERFYRVDSARSRQTGGTGLGLSIVKHVVINHGGEVSLWSQPG +RGSTFTIRLPEWEDDGAAVDGPPAASHVTERRGHRVTASAASPPRKESSA +>MOLHKGIG_00320 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWGDGVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA +>NAFOICDF_00013 +MDPVIIGLLCGAVGLLIGVASMLAFRASERSRTVDLSVEEPTLSPGAAEVLSVIGRSYIV +VDAVDGVVRANPSAYAMGLVRGHTLVPDALRELTGAVRADGVVRERQVDLPRDPRHQSSL +VVELRVAPLDDEYILVLAEDRTGAMRTEAMRHDFVVNVSHELKTPVGAISLLSEAIADAA +DDDDAVRRFARRLGVESTRLTALVQDIIEFSRLQAKDVVREGRSVDLNLVVAEAVDRVRL +TAEARGISIRAGGHVDTVVHGDPDQLMTAVRNLVDNAVRYSPDGTTVGVGLTSKDGLAQI +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWAQAPQTPDAGAPATVATLPERRGHRVAAAAAPARKEHSA +>MHAAABBN_00035 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWGDGVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA +>LFPAFLNI_00327 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWGDSVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000184.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000184.fa new file mode 100644 index 0000000000000000000000000000000000000000..356bc1ee72c9908d771b81e58c42cb3999a87406 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000184.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00018 +MRELYRADLERLGRDLTEIARLVHRAMIDAQEALESADVHGAERVISEDARIDRLQESLD +EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPAPVRPV +FTAMCDAAVDVAEETVLLLETQDLAHADRIHAVNEDVNALHASVFRFIAASDWTATPATT +TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWAYHRGSETSGP +>MOLHKGIG_00319 +MRELYRADLERLGRDLTEIARLVHRAVMDAQAALEAADVHGAERVISEDARIDQLQESLD +EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEPVRTV +FTAMCDAAVEVAQEVVLLLETQDLAHGDRIDALNEDVNALHVSVFRAIAAPDWSATPATT +TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS +>NAFOICDF_00014 +MRELYRADLERLERDLVGTARLVHRAVLDARAALDAADVHLAEQVISEDARIDLMQEGLD +EQAVRLLSLQAPVASDLRTVLATLRMSASLERMGDLARHIAQLTRLRYPEHVIPCDMRPL +FGSMTDAAVEVAQEVVLLLETQDLAHADRIHALNQVVNDHHVSVFRAIAAPSWGSPPATT +TDVTLASRYLERFTDHGLAVAAKARYLVTGESTRREGSAPA +>MHAAABBN_00034 +MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD +EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV +ITAMCDAAVEVAEEVLLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT +TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS +>LFPAFLNI_00326 +MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD +EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV +ITAMCDAAVEVAEEVVLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT +TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000185.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000185.fa new file mode 100644 index 0000000000000000000000000000000000000000..76a1ce2075386f11dbd0eaeb62893c88d7aa3508 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000185.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00020 +MVEKARRLSASTTPGRVRGPQGHITRGTTAAQRMRRVDRWLTDVHGALLRRTDRPLAVDL +GFGAEPVTAVEMFTRLRAVNPALELTGLEIDPARVARARERAGGVPGLSWAVGGFELPVP +RPPTVVRAFNVLRQYREEDVPAVWALLCAGLAEDGVLVEGTCSEDGRRATWVDLRRDGPA +SLTLALRLGSFERPSDVAARLPKALIHRHVPGEPVHRFLAEADAAWAAHAPLAAYGTRQR +WLASVAALREAGWPVLGGPRQWRRGEMSVRWEAVAPSS +>MOLHKGIG_00317 +MVEKARRLRARTTPGSVPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV +DLGFGGEPVTAVEMAERLRVQNPALELVGLEIDPARVARARERAGGLPGVTWAVGGFELP +VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRWAAWVDLRRDG +PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR +QRWLATVGTLRSGGWPVLGGPHQWRRGELSVRWAAVAPSS +>NAFOICDF_00016 +MVQKARRLTLPDGGRARPGARGGPQGHVTRGTTAPQRMRRVDRWVADVHGPLLRRTAAPL +LVDLGYGAQPWTAVEMLTRLRAVQPSAELVGLEIEPERVAHARATAPALPGLSWERGGFE +LATSRPPTVVRAFNVLRQYREEDVPAIWDLMASRMAPGGVVVEGTCSEDGRRAAWVDLRA +DGPASLTLAMRLGAFERPSDVAERLPKALIHRHVPGEPVHRLLADADAAWALHAPLGAYG +TRQRWIAMVRTLKDAGWPVLGRESRWRRGELTVRWDAVAPGVG +>MHAAABBN_00032 +MVEKARRLRARTTPGPGPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV +DLGFGAEPVTAVEMAQRLRVQNPALELVGLEIDPARVARARERAGDLPGVTWAVGGFELP +VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRRAAWVDLRRDG +PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR +QRWLATVGTLRAAGWPVLGGPHQWRRGELSVRWAAVAPSS +>LFPAFLNI_00324 +MVEKARRLRARTTPGPVPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV +DLGFGAEPVTAVEMAQRLRVQNPALELVGLEIDPARVARARERAGGLPGVTWAVGGFELP +VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRRAAWVDLRRDG +PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR +QRWLATVGTLRAAGWPVLGGPHQWRRGELSVRWAAVAPSS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000187.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000187.fa new file mode 100644 index 0000000000000000000000000000000000000000..8a0db764b0f5af801cd4fce99b7b440d248aace4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000187.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_00022 +MSTETEHRGLFVAVEGPDGSGKSTQARALVAALRAAGREAVLTREPGGSDLGETLRGLLL +DPAHAPVDPRTEALLFAAARAAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAVRGLGEE +WIARLNDWATDSLVPDLTVLIDVDAATAAARRTGRDGDGADRMEQETADQHEALRAAFLA +RAAAAPERYLVLDGALDPEELTARALARVTAEADAR +>MOLHKGIG_00315 +MSTQTEHRGLFVAVEGPDGSGKSTQARALTEVLRAAGHEVVLTREPGGSDLGETLRELLL +DPEHAPVDPRTEALLFAAARSAHAVRTLRPALARGALVVTDRYVDSSVAYQGAARGLGEA +RIAALNEWATDGLVPDLTVLIDVDAATAADRRERRAAGGEGAPDRMERETADRHEALRAA +FLARAAAAPERYLVLDGALPPQELTARALARVTAEAADR +>NAFOICDF_00018 +MSTPSPRPAPHPAPTPAADPADSPAAAAQGMPGRGLFVAFEGADGTGKSTQARAVAQALR +DAGREVVLTREPGGSDLGEAVRALLLDPAHAPVDARTEALLFAAARAAHVARTVRPALAA +GTVVLTDRYVDSSVAYQGEVRGLGAERVAELNDWATEGLVPDLTVLLDADAATAEARRAA +RHAGGGDAPDRMEQETAQAHGTLRAAFRARAAAAPHRYLVLDAAGAPEELTAAIAARVLT +AAADAARDGTGA +>MHAAABBN_00030 +MSTQTEHRGLFVAVEGPDGSGKSTQARALTEALRAAGHEVVLTREPGGSDLGETLRELLL +DPGHAPVDPRTEALLFAAARSAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAARGLGEA +RIAALNEWATDGLVPDLTVLIDVDAATAADRRDRRAAEGEGTPDRMERETADRHEALRAA +FLARAAAAPERYLVLDGALPPQELTARALARVTAQAADR +>LFPAFLNI_00322 +MSTQTEHRGLFVAVEGPDGSGKSTQARALTEALRAAGHEVVLTREPGGSDLGETLRELLL +DPGHAPVDPRTEALLFAAARSAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAARGLGEA +RIAALNEWATDGLVPDLTVLIDVDAATAADRRDRRAAGGEGSPDRMERETADRHEALRAA +FLARAAAAPERYLVLDGALPPQELTARALARVTAQAADR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000191.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000191.fa new file mode 100644 index 0000000000000000000000000000000000000000..cdd0a022cbc84a8c34ea106164c81e8e5389c086 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000191.fa @@ -0,0 +1,72 @@ +>ACLBLIBL_00029 +MSSLFRRHAVATAACTVLVLAPASAAPALAVETVAADETTISLLSFNDFHGALSSDFSGT +QFADTVEDYRTAFEAQHGERSVLLTSAGDLIGGSASVSNVQQDDPTIDVMNALGLSALAA +GNHEFDRGLDDLQDRVIPRAEFPVLAANFVDPDTLEPILASHAIFDVNGVSVAVIGAVPN +ELYATTTGAGLQGNTVLDMVEAVNGVAAELEASGAADVIVASYHEGAAGAGDLAAELGKR +EVFRSMVEDTHPAVDVIFNGHTHQLYQYETAGDGVARPVLQAGASGSNLAAVELTVDAAG +EVTAVASRLLDRSTQDPAEAAAESAVTAEVYAIEQEAVAVFEDMQSQVVADLDGSLTTDY +QKRLDEGGTWRAGGTRSAETTLGNWVADATKQTALNADPEVDLGVVNPGGLRSEILVDAF +TGGGTFSPKPADLIGKLTLGELLDVAPFGNSISYFDIPGSSIELALEQNWRDDVRTFTLG +WSENLTWTYDESRPQGEKVTGVWIDGEPLEQDAIYTVATQSFLADDTWVALGDPTAAPDG +YTAFATGREDFVDLGVLDTQAISDYARLQASAEGAVGPDFAKKGVPVSGAPETVAAGEEI +VLTLGDLVIDSDDAPAAAEVAVAFEAADGTVTELGSVTVPAGSEEVTLSGIAAPAEAGAG +ELRMTVRYADGTETIVRHALEVTASEAPVEPTEPTDPTVPADPSEPADPADPTVPADPSE +PADPADPSDPTDPAAPVEGDDDGDDRDEEHTVPSTVETGDASAWWLAGFGALLGAALLRG +RRALGLTASSTPAGR +>MOLHKGIG_00308 +MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT +QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA +GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN +ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR +AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG +EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY +QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF +TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG +WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG +YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV +GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG +ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKDADHPGKGRVK +GEDHPGKGRGVQRGAATHPVFSAQAWLTAAGLPR +>NAFOICDF_00025 +MSSIFSRRTAATLACTTLVLAPAAAPALAADASGERTISVLSFNDFHGALSEDFKGTQFA +DTVEDYRTAFEAQHGEGSTLLTSAGDLIGGSASVSNVQQDNPTIDVMNALGLASLTAGNH +EFDRGLDDLQGRVADRADFPVLSANFVDPNTKAPVLTSHKVFDVDGVRVAVIGASPNELY +ATTTGAGLQGNLVVDMVDAVNAVATGIEAADEADVIIASYHDGAAGAAADLSAELGNRAT +FDAMVERTVPAVDVIFNGHTHQLYQYQTDNGGVPRPIMQAAASGADLAAVELTVDAAGEV +TAVTPRMLPRSTQDPAEAAAESPVTARVYEIEQQAVDVFTDMQSQVIADLSGSITTDYAT +RIAAGMGWKAGGTRTAETTLGNWVADSLKHSVSAAEPGVDLGVVNPGGIRSELLVDQTNA +GGVFSPKPEQLVGKLTMGEVMDVAPFGNTLTYFDLPGSSIKEALEQNWRDGERTFTLGWS +SNLTWTYDDARAQGDKVTGVWIDGEPLQADRMYTVAAQSFLADDTWVKLGDPSKAPDGYT +AFATGRQGFVDLGVLDTTAVLSWARAQDAADGAAHPDYAKKGVPVTGAPASVEGGQDVVL +TLGDLVIDSDGAPAATAVDVAFQGADGAVTELGTVEVPAGQESVTLSGITAPQTAGAGEL +VMTVRYADGTTAVVRHALEVTASAAPVDPSTPAEPTQPGEPSDPAEPTTPGEPTPSAQPT +APVEPTAPVEPSAPAEPTAPVEPTAPAESPEPTPTAQPSTPAEPTAPTPSAPAEDGGEHA +VPGKVQTGDQAIWLVAALGALGAGALVAVRRRAAAR +>MHAAABBN_00023 +MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT +QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA +GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN +ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR +AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG +EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY +QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF +TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG +WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG +YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV +GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG +ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK +GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR +>LFPAFLNI_00315 +MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSGDYIGT +QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA +GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN +ELYATTTGAGLKGNEVLDEVAAVNAVADELAAQDAADVIVASYHDGAAGAGELAAERAAR +AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG +EVTGLTPRLLTRSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY +QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF +TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG +WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG +YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV +GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG +ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK +GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000192.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000192.fa new file mode 100644 index 0000000000000000000000000000000000000000..dead333f020c5cf6a40ba1cdb88310411dd913c2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000192.fa @@ -0,0 +1,84 @@ +>ACLBLIBL_00030 +MTQRTFRLSRPAVALAALTLLAPAVVAGPAHAAPTGDGLVINEVYTNGGSANAVFTHKFV +ELYNPTDTPISLDGWSLQYRSATGTAAPNGVVALSGTVPAKGHFLIQGGSNGTTGAALPR +PDLNAGGAFNPAGARGTVVLSDQAGALTALPVGSVTTGQAEGVADLLGYGTSNTFETAAA +GAPSSNSDPKSLTRTDGVDTDDNAADFTVTAQVTPTSSTGEAPVDPIPDPEPDPEPAPAL +TIAQIQGDGAATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGSAEDATPGASDGLF +VYSPDTVGSVALGDHVQVTGEAAEHYGLTQVRVGAAGVTPVAEPAAVAPTAVDFPLSEAD +REALEGMLLAPTGEWTVTDNYDLNQYGSLGIVPGTEPLPNPTSVAAPGAEAQAVAADNAS +RLIVLDDGASTNFMRSPGNENPLPYLDADRPVRVGAGLDFTTGVILDYRFDAWSFQPLGH +LTDATAAAVQPVAVEDTRPEEASPEAVGGNVSVGSFNVLNYFTALGQDFPGCRAYTDRFG +EPVTTNGCLPRGAYTPEAFARQQEKIAAAIDGLDASVVALEEIENSAKFDLDRDRALAHL +VDALNAQAGEQKWAYVASPADRPALSEEDVIRNAFVYQPAEVTPVGESVILRDEVNFDNA +REPLAQHFRAADGTEAGVAGTDFVAVTNHFKSKGGSGAAGDNADSGDGQGAYNGDRTRQA +QALVAFAEQVADDAGTDRVLLLGDFNAYEKEDPIRVLEEAGYVSQGALTGEYSYTFDGAV +GSLDGVYASPAASAVVTGQDIWMINANESVALEYSRHDYVAEDLYAPDQWRSSDHNPLLV +GLQLDAPVVEPEPQPGAGHPGKGKGLDKGAGHPGKGKGLDKGAGHPGHGRVPEAARP +>MOLHKGIG_00307 +MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE +LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA +DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG +APSANSDPKSLTRTNGVDTDDNSADFTVTGQVTPTNAAATGGEPTPEPEPQPTPSERITI +AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY +SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAADGVLPVAEPGAVAPTPVEFPLEEADRE +ALEGMVLAPQGDWTVTDNYSLNQYGSLGVVPGTKPLDNPTSVARPGAEAQAVAAANAQQL +IVLDDGASTNFMRSPGNQNPLPYLDADQPVRVGAGLEFSTGVILDWRFDAWSFQPLGHLT +DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCGAYRDRAGTP +VTTNGCLPRGAYTPEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE +ALNAQAGEQRWAYVASPSARPALADEDVIRSAFIYQPAEVTPLGESVILDDQTNFDNARE +PMAQLFRAADGTAEGAAGTEFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA +LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYVSQGALTGEYSYAFGGAVGS +LDGIYASPSAAAAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL +QLDAPVTEPTPEPEPEPTPGETCDGVTDPRGVPGKPANSVREWLRCIGATPGHGGDHPGK +GHGGDHPGKGRGPVRP +>NAFOICDF_00026 +MPTPRLRLVRTAATLAAATLLAPAVLALPAQASPAGDSLVINEAYTNGGSAGALFTHKFV +ELYNPTDQPISLDGWSLQYRSATGTTAPSTTVALSGTVPAKGHFLIQGGSNGATGAALPT +PDLTTSFNPAGTKGTIVLADQAGTVAGLPTGSVVTDQVAGVADVLGYGATNTFETAASGA +PAANSDPKSIARTGGADTDDNAADFTVAADVTPQNAAGGGTAPVDPVDPVDPTPAPAPSV +TVAEIQGTGATSPLEGRRVSTTGVVTAVYSTGGYDGFYIQTAGTGGAEDATPGASDGVFV +YAPAEVGSVTLGQTVTVTGDVAEYYGLTQVKAEAGGVRQAAEAGAPVTARELAFPLTEAE +KEAHEGELLAPAGAWTVTDNYDVNQYGSLGLAPGTSPLPNPTSVALPGADAQAVAADNAQ +RLIVLDDGASTNFFRSPGNQNALPYIDADAPARVGSAVDFRTPVILDYRYGAWSFQPLGH +LTDANKAEVQPVDIADTRPAEAVREDLGGNVTVGSFNVLNYFTTLGEDVPGCGYYADKDG +APVSTKGCLPRGAYTEEAFLEQQAKIATAINGMDTSVVALEEIENSEKFGLDRDHALAHL +VDALNAQAGYAKWAYVASPTVRPALADEDVIRSAFIYQPAEVTPVGESVILDDQVNFANA +REPMAQAFRVADGSAGGVVGTEFVAITNHFKSKGGSGATGDNVDTGDGQGAYNGDRTRMA +QALVAFAEQMKVQAGTDRVLLMGDFNSYEKEDPIRVLEAAGYISQGAKTGEYSYTFDGAV +GSLDGIYASPAADATVTGQDIWMINANESVAFEYSRDNYVGEEFYAPDQWRSSDHNPVLV +GLQLDAPAAPVVPTPGTRPTPPADQCALITSPRGAKASAGFSASEWMRCAGVHPGKGRGR +G +>MHAAABBN_00022 +MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE +LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA +DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG +APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI +AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY +SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE +ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL +IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT +DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGTP +VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE +ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE +PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA +LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS +LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL +QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH +GPEHPGKGRGPVRP +>LFPAFLNI_00314 +MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE +LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA +DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG +APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI +AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY +SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE +ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL +IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT +DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGNP +VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE +ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE +PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA +LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS +LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL +QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH +GPEHPGKGRGPVRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000193.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000193.fa new file mode 100644 index 0000000000000000000000000000000000000000..fab8dfe9c0f4adc9e2b84290fa69f1d18477e29e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000193.fa @@ -0,0 +1,61 @@ +>ACLBLIBL_00031 +MPDAQEAVRRLAVVGAGPRGVMLLERLLARLEGSAPGAHPARLRIDVVDPYPPGPGRVWR +TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVQRHQYPARAVY +GRYLRHLYQDVVAGLRARPEVADVVEHRAEVTALHPTPAGGARLELRDADGAASELAADA +VVLCLGHQPAELSPGQARMAAAARGRDDLHYQGPQIPSDVDWDTVEPGARVLVRGMGLNA +FDLLAQLTQGRGGVYRRTGDGPGRALAYEPSGREPRLHLMSRRGVPYLPKAEVDAFVPRG +VTLSYLSDAAVDALSARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF +LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYTAPFEDAVFASHEDYQRAV +ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRIAEDSRIRDVQGWFEPLVE +GLASGPPLWRVEQMLAVHRAGLLTWAGPVPVVDAEERAFSVRSPQVGAADSLGPAVVEGE +WLVEAMMPPNRVQAASSPLIRGMLDDGVAAAGTWEDEEGVRVPAPGFDVTGRPHRLRAAD +GAVHEDVYVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAVAQAVLAG +>MOLHKGIG_00306 +MSEPLVADRRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR +TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY +GRYLRHLYKDVVAGLRARPEVAEVVEHRAEATALHPRPDGGARLELRDPDGSVSVLDADA +VVLCLGHQPAELSPGQMRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA +FDLLAQLTQGRGGVYRRTGDGPGRALRYEPTGDEPRLHLMSRRGIPYLPKAEVDAFVPRG +VTLSYLSDAAVDALTARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF +LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV +ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE +GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLEPAVVEGA +WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD +GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAAAAVLAG +>NAFOICDF_00027 +MSPPSISEPTRAIAVVGAGPRGVMVLDRLLARLEAASEPRPTGSLAVHVVDPFPPGPGRV +WRPDQDPLLLMNTPAFFPTACAADNPGLAPSSVSLSFDQWRLARPDRAAGLERTDYPPRA +VYGRYLEDVVAAVLDALRARPEVVAVTVHAAQAVALRAAYEGGPVAAPESPSAWRLTLRP +VDGTPPRELQADVVVLCLGHQDAEPSAAQRRLGEAADASPALHYRGPHLPAELDVDGIAP +GATVLVRGMGLNAFDLQARLSEGRGGRFEPTGGEPGRALRYVPSGREPVLHLLSRRGLPY +LPKAAVDAFVPRGVRMSYLTDTEAEALVARHGQLDLAEHLWPLLHRDVVRAYYATLARVH +PERLGGPADAGRFVRELVGMFESAGRGAPVTARHGQELLHAFAPGMRFLDIRSWAAPFQG +AVFDDAAAYQEAVAGVLEQACGEAAAGEDSPFMQAVGTLHAGRLRIKAWIAQGLLTDASR +IRDVQGWFEPLVEGLASGPPLVRVEQMLALHRAGLLSWAGPGPQVEADAEAGVFRARSPQ +VGADDAVAPAVTEAAWLVEAMMPPSRVEAAATPLVRQMLADGVAAVGRWEDEDGALRSSS +GFDVTARPHRLRGADGTVREGVLVLGLQLSGVQWGTAIAAEAGADVRDRALFLADADAAA +RVALGG +>MHAAABBN_00021 +MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR +TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY +GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA +VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA +FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG +VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF +LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV +AELMEQTCVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRITEASRIRDVQGWFEPLVE +GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA +WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD +GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG +>LFPAFLNI_00313 +MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR +TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY +GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA +VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA +FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG +VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF +LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV +ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE +GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA +WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD +GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000194.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000194.fa new file mode 100644 index 0000000000000000000000000000000000000000..2d5c53c2c8311244bd058942308f57b668f3ca33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000194.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_00032 +MDRNMLDQLQNANVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ +TTADGITVPFDKAFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSNVDHDRDVRHDDGLRA +DAGTAGVAGTAGVAGVADRREDTVVDGDRRDVVDGDRRDLVDADRRDVVDGDRDSMVVKD +EHLQVGTERQATGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDI +EVTTYEETPVVNKTVEAEKVSLGKRQVQDTETVSEELRHEDVKIDGDATDRDLDGRTDRK +DRI +>MOLHKGIG_00305 +MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ +ITADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSYSVEHPAADHDGDVRR +DDVRTDAGTAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRRDVTDADSVVVKDEHLNV +GTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTY +EETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI +>NAFOICDF_00028 +MDRNALDQLQNGHVFSTDGEKIGSVGQVYLDDVTNEPTFVTVKTGLFGAKETFVPLQQAQ +TTTDGITVPFTKDFVKDAPNVDADGSLTPEEEQRIYEYYSMDYSAVDTHDRRDVRDAAAA +GTAGGVVTDRERRDVVDADRRDVVDNDRRDLVDGDADSVVVKDEKLNVGTERRATGRVRL +RKQSYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDIEVTTYEETPVVNKTVEA +EKVSLGKRTVQDTETVSEELTHEDVKIDGDDVDGRRR +>MHAAABBN_00020 +MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ +TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD +AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA +SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV +NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI +>LFPAFLNI_00312 +MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ +TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD +AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA +SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV +NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000195.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000195.fa new file mode 100644 index 0000000000000000000000000000000000000000..0d82f5885f0960981cdbc7a1252e4bdd05e9b837 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000195.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00051 +MEYLVPVLAVVLIGALAFAVSRWMSAARDRQTAGPRTPSGRPLEIGPERARQAAALLDED +AHRRVYGHIAQSRVMEAVRDYRAHTGRSLKDAVMDVQSLAVHPQVYSVPATEQEAPEEAE +VRDPRTRPTPPEPARDEAADGERQGTERADVVEEGADDPAADDEPRPEAESDLSAEEGRV +DDGAASGTEPRPGTSEPARADELTALTVPADWSAAPAEEEPPFEVEVMRGMDSVRLSSQD +LPPWLRDQLSAMVRDGNLESAAVQLSSHSQLSVPEAYELLRRMRERRGED +>MOLHKGIG_00303 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED +AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPAQEPDATSAGA +AGPVPADHEEPHRDDTAPAETPGPERPGQDSSGRGEPDAQTPDREPSDAVAEDDARQDTD +HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD +QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMREHRGEG +>NAFOICDF_00030 +MEYLVPILAVVVIGGITLLVARRLSGRSQAPTRSATGTGADTVEASPERARTAARRLDEA +THRAVYGHIAQGRPFEAVRDYRRATGRGVRDAILDIQSLTLHPQVWSLPVQAEPADDASP +AAADMPSGPPRGPSDGRGRDGESSARPRLRRAEPSEAGPAPDAEPAPGGDAAADPEADGA +TSRRPGRQAPEELTTLTVPEGWTADPAPEEPPFEVEVMRGEESVRLASQDLPPWLRDQLS +AMVRDGNLESAAVQLSSHSSLSVPEAFELLRRMKERREGRG +>MHAAABBN_00011 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED +AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV +AGPVPGGHGEPHRDDAAPADTPGPKRPGQDSSGRGEPDAQTPDRETSDAVAEDDARQDSD +HASAAPRPTAPSADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD +QLAAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG +>LFPAFLNI_00310 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED +AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV +AGPVPDDHGEPHRDDAAPAETPGPKRPGQDSSGRGEPDAQTPDREPSDAVAEDDAQQDTD +HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTDSVRLSSQDLPPWLRD +QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000196.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000196.fa new file mode 100644 index 0000000000000000000000000000000000000000..06b0faca6b2511774324e21742f582c765a7de2a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000196.fa @@ -0,0 +1,42 @@ +>ACLBLIBL_00053 +MPPQPPPAGPPAVPPSGPAPLAPGDPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSADL +GVGAHRAALLVSAGTLGLALSVVPWSMAGDRWGRRRAMVVSMVSASLFALAGVLAPTFEA +MLGLRLLEGMAHGGVAGLAVALLAEEVAPRAVATAAGTYIAGTTIGGLSGRLIALPVAEA +FTWRTGMLAVTVVGVACTAAFLAVTPQARRFTPSPTSVARLVRIVRGHLGSAELVAVYLQ +AALLMGGFVALYNFVGYRLLGPPFSWAPTAAGLVFLAYLAGTWSSPRAGRLAARFGRLPV +LTGATAAMAAGAALTLVPHPAVLVGALVLTTGAFFAAHSVASAWSGTAAPHGRAQSTSLY +NLAYYAGSSLFGWLGGVFHESHGWTGTVLMVVALALTALAIAVVVLRGRGTAPARCAGAV +RGAGRRGIRRISRGRLRRRRWPSGAGRARPRGPRGPAARASRPSAGRSRSRCPARRTPPA +WSAPRPG +>MOLHKGIG_00301 +MPPTTPPPPAGPPAVPPSGPAPAAPGEAAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLALSVVPWSVAGDRWGRRRAMVVSMVSASACALAGVLAPTF +EAMLRLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY +LQGALLMGGFVALYNFVGYRLLGPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR +>NAFOICDF_00031 +MPPALPAPLEPGTPLYRRLLLGLFLAGVATFAQLYAPQGLLPLVSSDLGVPSHRAALLVS +AGTLGLALSVVPWSLAGDRWGRRPVMVASLVSASVLALVGVFMPSIELLMGMRLLEGMAH +GGVAGLAVTLLAEEVAPRVVPVAAGTYVAGTTLGGLSGRLLAMPVGEWAGWRAGMLAVTA +AGAACTVAFLFVTPPARRSTPVRLSLARLGRIIGGHLRTPGLVALYLQAALLMGGFVALY +NYIGYTLLAPPFGWPPTAVGLVFLAYLAGTWSSPRAGRLAVRVGRLKVLTGSTALMAVGV +VLTLVPSPFVLVPALVVATGAFFAAHSVASGWAGTAAPTGRAQSTSLYNLAYYAGSSLFG +WLGGVFHEGVGWAGTVFMVAGLAAVALVVALVVLRGREDAGPPPPSAVAEGAAA +>MHAAABBN_00009 +MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF +EAMLGLRLLEGMAHGGVAGLAVALLAEEVVPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLTVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY +LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALVSAVVVLRGRGTAPAR +>LFPAFLNI_00308 +MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF +EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSAAALVRIVRGHLSSPELVVVY +LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000197.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000197.fa new file mode 100644 index 0000000000000000000000000000000000000000..0a87a21140b220b66e11510183c369750909dd0f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000197.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00054 +MTTSTSSLDLHESFKAYDVRGIVGETITADSVRAVGAAFVDVLGLAGETVLVGGDMRPSS +PAFMAAFAEGATRRGADVVDLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAKA +GAVPVSSDTGLYEIRDAAQALLDAGEIPAAEAVGTVTQQDILPAYAEYLRSLVDLSGVRP +LTVVVDAGNGMAGKTTPAVLGDAALDALPLRIEPLYFELDGTFPNHPANPLEPENLRDLQ +AAVVEHGADIGLAFDGDADRCFVVDEKGAPVSPSAITALVARREIARAKGEGEETPVVIH +NLITSRAVPELVAADGGRAVVTRVGHSFIKAVMAEESAVFGGEHSAHYYFRDFFNADTGM +LAAMHVLAALGEQDQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPTVGEGAG +EGRAVHEDFAGVDTAVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEAIR +DAVLAIVRAER +>MOLHKGIG_00300 +MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS +PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA +GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR +LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ +AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH +NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM +LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGVG +EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR +DAVLAIVRAER +>NAFOICDF_00032 +MVTLRPGRIIDRVTTAADAINLRDSFKAYDVRGIVGETITAETVRAVGAAFVDVLGLAGQ +TVLVGGDMRPSSPEFIEAFAEGATRRGGNVQRIGLISTDMLYYAAGVEQAAGVMFTASHN +PAAYNGMKMAKAGAVPVSSDTGLYEIRDVAQGYLDAGEIPAADAQGSVTESDILTGYAEY +LRSLVDLSGIRPLKVVVDAGNGMAGKTTPAVLGGEVLEALPLEITPLFFELDGTFPNHPA +NPLEPENLRDLQRAVVEHGADIGLAFDGDADRCFVIDEQGEPVSPSAVTALVARREIARA +KASGEETPVIIHNLITSRAVPELVSADGGRAVQTRVGHSFIKAVMASEGAVFGGEHSAHY +YFRDFFNADTGMLAAMHVLAALGEQDGPLSTLGAEYEPYVASGEINSQVEDKDAAVAAVL +ARFAPQAADGGESGTAVEDAVAGTSTSVLRMDGTTVSAADGSWWFNLRPSNTEPFLRYNG +EAKDRATMETVRDAVLAIVRAPR +>MHAAABBN_00008 +MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS +PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA +GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR +LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ +AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH +NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM +LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGAG +EGRAVHEDFAGVATTVTRMDGTTIAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR +DAVLAIVRAER +>LFPAFLNI_00307 +MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS +PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQASGVVFTASHNPAEYNGMKMAQA +GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETTGTVTEEDILPGYAAYLRSLVDLTGVRR +LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ +AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAVTALVARREIARAKADGEQTPVVIH +NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM +LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVEDKDAAVAAVVAQFAPAVGEGVG +EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR +DAVLAIVRAER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000198.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000198.fa new file mode 100644 index 0000000000000000000000000000000000000000..c2c42822813b8eeb7c073177195440a23b6facfe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000198.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_00055 +MDTTQHPDAGPLPSESTAPIGPYGSGAAAPGAAAAREPELHAEALAVLRRLVDRPDAQFK +DGQFEAIEALVAHRRRALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQV +AAAARAGVRAVSVSSANATQWDEVRARLAADEVDVLLISPERLTNPRFREEQLPDLVARM +GLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPSTGPRAVPVLATTATANARVVGDVVEQ +LGVDSAQDVFVLRGSLARASLRLGVLRMPSPAARLAWLLDHLEDLPGSGIVYALTVSAAE +DTARALREAGHEAVAYTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVH +FGAPSSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLQALA +QHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWVYDAQRYARVA +EARRAEERLMLDYQTTDTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDTSARERAE +AALRRTGVPIEPRRMWPSGMDRLGVPVKGRMAPEIQAEEGRALARLTDLGWGTVLRELLD +KEDAPVPEDVLQGAVGVLAGWGWQTRPIAVVAMPSRTRPLLVGSFAEGIARIGRLPFLGS +LEHARGGPTAGPGGNSAYRLGSVHGRFEVPEAMAHLLRTASDAGRHGPVLLVDDLVDSRW +SLAEASRVLREAGAQGVLPLVLAQAG +>MOLHKGIG_00299 +MDATSHPDAGPRLPETSVPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR +RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS +ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG +HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP +LARASLRLGVLRMPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA +YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG +RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV +RIKRTALELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT +TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM +WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV +DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN +SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ +GVLPLVLAQAG +>NAFOICDF_00033 +MSTSPQDPARPAAVADPALYAEALGVLRALVGRPDAEFKDGQYEAVEALVAHRRRALVVQ +RTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAASLSSANATEW +EDVRRSLEADEVDVLLISPERLTNPRFRDEQLPDLVSRMGLLVVDEAHCISDWGHDFRPD +YRRIRDLIRLLPSSGPRAVPVLATTATANARVVQDVVEQLDVESRQDVFVLRGPLARASL +RLGVLRLPSPAARLAWLLQHLGELPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRTD +PEQRARIEQDLKDNRVKAVIATSALGMGFDKPDLTFVVHLGAPSSPVAYYQQVGRAGRGT +DHADVLLLPGQEDRAIWEYFATASMPDEVQARAVLEALEESGGAMSVAALEPVVSVKRTA +LELLLKVLSVDGAVERVGGGWRATGSPWTYDAERYARVAEARRAEERLMLDYQTTQTCRM +EFLARTLDDPTAAPCGRCDVCAGPWYPTGWDGAAREQADRALRRTGVPLEPRRMWPSGMD +RLHVPVKGRISPAEQAEEGRALARLTDLGWGSRLRELLAAPDAPVPEEVLQAAVRVLAEW +GWQERPIAVVAMPSRGRPQLVDSLARGLAGQGRLPFLGPLELVGGGPTAGPGGNSAYRLA +SVHGRFAVPEGMARMLATAPDAGRHGPVLLVDDLADSRWSLAEAARVLRGTGAQGVLPFV +LAQNG +>MHAAABBN_00007 +MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR +RALVVQRTGWGKSAVYFVASLLLRARDAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS +ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPGLVARMGLLVVDEAHCISDWG +HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP +LARASLRLGVLRMPSPAARLAWLLDHLADLPGSGIVYALTVSAAEDTARALREAGHEVVA +YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG +RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV +RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT +TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM +WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV +DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN +SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ +GVLPLVLAQAG +>LFPAFLNI_00306 +MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR +RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS +ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG +HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP +LARASLRLGVLHLPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA +YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHLGAPGSPVAYYQQVG +RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPDV +RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT +TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM +WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV +DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN +SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ +GVLPLVLAQAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000201.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000201.fa new file mode 100644 index 0000000000000000000000000000000000000000..f93057340cd9fcb0c0ea9735618dc7d373bb11c0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000201.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00060 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLRENGLVPDAIVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYHADAAKALAIVNETEETTRSLLVVGHMPWVQN +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWVELDGRDAALTHFVVPGR +>MOLHKGIG_00294 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHGLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR +>NAFOICDF_00039 +MSPADAKTLVLLRHAKADWPAGVDDHDRPLAPRGHAQAPAAGDWLLEHGIAPEAAVVSDA +LRTRQTWVWVAQRLGERAPTAYLDRRLYEADAARALAVVNETEETVRSLIVVGHMPWLQN +LGMRLMSLDSDQDAALEMAEHLPTLGLQVFRVDTPWAELDGRDAALTHFAVPGR +>MHAAABBN_00002 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHDLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR +>LFPAFLNI_00301 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPTAGDWLREHDLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000202.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000202.fa new file mode 100644 index 0000000000000000000000000000000000000000..687b74db8edabb2ae6ea5a76034e348bca3e5e58 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000202.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00061 +MGQSAGYVHISVRNAQRRADGMSRRGQARADLRLAGGTDAPAAQTAPTPVLAPNGIPGPQ +AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGSESHAAVALAPSGA +EGRDLEVVRQVLGDPTVQGGAHPDLAQAPAPVSTREPGVLIDLSRREVQLDGESLNLTYK +EFELLNYLVENGERTVGREELLEALWHNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR +GQGYRFYRHPEVVVWAAPEYSI +>MOLHKGIG_00293 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ +AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA +EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK +EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR +GQGYRFYRHPEVVVWAAPEYSI +>NAFOICDF_00040 +MGETAGYVHISVRNAQRRANVSRARRGDLRLAGGTSHEPTPPQTAPTPVLAPSGIPGPQA +VARENEARGFVIYVGMDELMASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGAA +GRDLEVVRQVLGDPTVQGAARPDLAQAPAPVSTRQPGVLIDLSRREVQLDGEALNLTFKE +FELLNYLVENGERTVGREELLDALWKNSDEVPNERTIDVHIRRLRAKLGRLANTVRTVRG +QGYRFYRHPEVVVWAAPEYSI +>MHAAABBN_00001 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ +AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA +EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK +EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR +GQGYRFYRHPEVVVWAAPEYSI +>LFPAFLNI_00300 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ +AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA +EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK +EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR +GQGYRFYRHPEVVVWAAPEYSI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000203.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000203.fa new file mode 100644 index 0000000000000000000000000000000000000000..91a355bfc5d721ffed91a70ffba58563085930f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000203.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_00062 +MRVHLVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVEIQTPVAT +TTGLRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD +LSGRHVFVLDPMLATGGTLIESIRFLYERGAARVTCICLLGAPEGIARLEESLGDVEVDL +YLAAQDERLDENAYIVPGLGDAGDRLYGLAE +>MOLHKGIG_00292 +MDGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE +>NAFOICDF_00041 +MRLHVVDHPLVAHKLTVLRDERTPSMIFRQLTEELVMLLAYEATRGVAVTEVEVKTPVAT +TVGTTLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD +LTGRHVFVLDPMLATGGTLIEAIRFLYERGAERVTCLCLLGAPEGVARLEEALGDVDVEL +YLAAVDERLNEKSYIVPGLGDAGDRLYGLAE +>MHAAABBN_02315 +MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE + +>LFPAFLNI_00299 +MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000207.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000207.fa new file mode 100644 index 0000000000000000000000000000000000000000..38116c293aafea5a9c581b6e1f5efed70adf631b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000207.fa @@ -0,0 +1,47 @@ +>ACLBLIBL_00069 +MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPP +AGRPAARPLTLVSHLKMEGRWLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVP +TDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTARPERPVGLALLDQRTTCGIG +NIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP +DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAA +GRRRTGCTGTTAPPACAAAGACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYA +ERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAGGRGSRLAPLTDARSKPAVPF +AGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG +RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVT +TQVAEGASRFGVVSSDADGRVTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSAS +EEQVDDDDPAGAQLGDYGETIIPALVERGRVHEFRHEGYWKDVGTIDAYYQAHMALLRGD +GLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGVVVEAGAT +VHRSVLLGSATVPAGARLDAVIADVGARIPEGATGQTKPGPGNITVLTPDDRSTAEGDET +TGHA +>MOLHKGIG_00284 +MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR +DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL +LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA +VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS +LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLIT +NPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGVVVAAGATVRGSLLLGDCEVP +AGAVLDTVVVDVGGAVPAREVTGRAAPAEEVVVLTPQDRGPAEDETTGSGRPGRSD +>NAFOICDF_00049 +MADPFPKDPAGSTVALVLAGGRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLK +DVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEGREEEGFSAGNGHALAQQVPI +LRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA +VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASS +LGDYGETIIPAFVERGRVREHRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLT +NPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGVVVERGAHVRRSVLFGECIVP +RGARLDAVIADVGAHIPAEEVGRSRPGPGNLTVLTPATRDPDSEDETTGGAAAKDG +>MHAAABBN_02306 +MADPFPTDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR +DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL +LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA +VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS +LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT +NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP +SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD +>LFPAFLNI_00290 +MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR +DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL +LEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA +VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS +LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT +NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP +SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000209.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000209.fa new file mode 100644 index 0000000000000000000000000000000000000000..34c148b45945ebecef2b70c17784567226b39f3d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000209.fa @@ -0,0 +1,74 @@ +>ACLBLIBL_00072 +MQDPSSESHAALERLRGAPKPVPAPEEAAGAPRTPDQDDDGAATAEDPVPAAARTPADDP +APAPSPSPPQDAETAPAPDASPASDADAPADVEADVEAPRPARRATPPRPRRPRPDLPPR +PAPPRARPAHRLSPRRPMRGACARAAARTSTRRWSGRAPPAPPRSSAPRRDLSDILDRLG +SPDLARFTAPLVGTVERILPAPGADPQKAAQAARRREEAEARRRARLQSGRERAAESARR +RAAEHDRLAAEAAEREAALRDDDARSEARRADEEAAAAKEACRQERLRERRTAGRAAAEE +RARLAAEAVEADRERERREAEEAAAAAAREEAALQARLQEEARARRERAEQEERLAQERA +AEEARLAQAARIARRRREEERERQRREAERRRRLAQEAKARAAADQEKRRQQEQERRRRE +AKVAEERARVQAERRAREEAELAERERRRLEAEAEAERRRQAQEAERRRREAERAEAERR +ARAEEAERRRREAEEAARRAAEARRLHAERTRAHTVLHAERALAQARLLEDRARDAERRA +AEEEARRLREHQDRESRALYRAARELEGPEVIPAASQRPLLARPEEGLTDEELVARARQA +LPEWRHRQRLATKARAVGAETAAGRSAGPPTGPVPLIPGYTPAAPEEPAGPATVRDRRGQ +LVLTLAWAAFVLAGVWGLGLFRFVPGLDALDAGPYPAAGDGRHGSGATVFSLFPLHPVIW +PVLWLLTGLHVARQWGPGQGAAPRHRRTRGPMAGTLLALALWFPLTVLVPWGLESVLWLV +ALALMLGAVRRLGARPAAGRLARLAEDGAPGALLGTLLAGAPTALAATLHAWGVHVGRFP +TELVAALVLLTLLPGAVRLVLGGRGRMGVAVGMAWTLLCLALPRLLPSPLGAQQSAWVGF +AAAFGALLLLTAAAVRRSWVRQIERDAARRPPPAVA +>MOLHKGIG_00281 +MQDASSESRAALERLRAASAPRPDDAETRAPAARPRRALAAPGEISRRDLRRHERALRSG +RSETAAERRVREDHRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV +GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRAAEHERPVAEAAAAAQARDAA +RARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEEKARAAAEAEA +RRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERR +RLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLHAERALAQARL +LEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADRPLLSDPEERL +TDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIPGYTPAPPEEP +AGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGAS +VFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLALALWFPLAVL +APGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLLAGAPTAVGAA +LHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLLCLALPRLLPS +PLGAQQSVWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA +>NAFOICDF_00058 +MTSQDDDAPRPAPPAPRHAARPRRALAEPGRLAPEQLERHTRRLRGEPLPPETPEEAAAR +AGRRHDLAAALDRLPAESAPAAPRPRADLSDLLDRIGTPDLARFADPLLGTVGRILPSGP +SPERAAAAARRRAEHEGRRRAERAAGRARAAEAARRRAEETARREAEAAERARAARTVEE +SRAEAVRAAEDAAREAERHRAERLRERREAARAAAADKARRVAEAAERARVEEEALLAVE +ADAQAREVAAAQAEPDALARERRERADQEERRRRAALLARRRRDEERRRRRREAERARRE +AEEQRERAARAERSAAEAARRRQAEEAAEAERRQMAVEAARARAEAERLAQEAARERRRR +IAAARALPRTVAARHIAAGTAAEDRRRQAAARASEEAARVLAAHHDRETRALMAAARELD +GPDVVPPAHLRPLLADPAEGLDDAALLERARAALPQWRRTGRLLTKADAVRAQTAHGAAD +GTGPATGAFPIVPGYVPPSGPPEPRAPATREDRRHQLELTGAWLLFVLASAWGLGLFRLV +PGLRVVDQGSYTAAHGGRYAFTTSVLSLFPLHPAVWPVLWLALGVYVAHQWGPGQGAAAR +QRQTRRSVAGALALTALWFPLAVLVPWGLEFMVWLAALALMIRVMRGLTAVPARTRAAQT +CTDGVLGGFLGLLLAAAPTTLASPVAATGVFWGWFPSALVAAALLWAVVLTGARLALQDR +GRLGLALGMAWTLLCLALPRLLPSPLGAWQSAWVGLSAVAGGLGVLLLVVVRRTWVREIE +EQAAAAPQGVPAGRVNGR +>MHAAABBN_02296 +MQDASSESRAALERLRDASAPRPDDDATRAPAERPRRALAAPGEISRRDLRRHERALRSG +RPETAAERRVREDRRADVHRAMDRLRTPGAPAQQRPRRDLSEILDRLGSPDLARFTDPLV +GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRERAAEAARRRAAEHERPVAEA +AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE +KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER +RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAYTVLH +AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR +PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIP +GYTPAPPEEPAGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT +ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLA +LALWFPLAVLAPGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLL +AGAPTAVGAALHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLL +CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA +>LFPAFLNI_00280 +MQDASSESRAALERLRGASAPRPDDDATRAPAARPRRALAAPGEISRRDLRRHERALRSG +RPETAAERRVREDRRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV +GTVERILPAPGRDPEKAAEAARRRAAAEERRRARLRAGRERAAEVARRRAAEHERLAAEA +AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE +KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER +RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLH +AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR +PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVQAEATAHSSAGPVTGALPLIP +GYTPAPPEEPAGSPTRADRRGQTLLTVAWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT +ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGPGQGASPRHRRIRGAVAGTLLA +LALWFPLAVLAPGGLDVVPWLLALVLMLRVVRRLGARPAARRLARVAEDGALGVLLGTLL +AGAPTAVGAALHAWGVHVDWFPTELLALLVLMALLLAALRLVLGGRGRLGVALGMAWTLL +CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000210.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000210.fa new file mode 100644 index 0000000000000000000000000000000000000000..585627924efda4d6aca3c4431a55a1367005292b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000210.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00073 +MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAATGRLDVLRRDGGRWVPVPAGPGR +>MOLHKGIG_00280 +MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR +>NAFOICDF_00059 +MPSYRARLQIGDVLPGHRPEEVLDTAEAAIGATHEVAAKDVEVVARVPRIVLRFTVPAAH +RAAEDAEAAAVAGRMAEAVADVATVGRLDVLRREGGRWLPVSAR +>MHAAABBN_02295 +MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR +>LFPAFLNI_00279 +MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQASHVLAAKDIEVVARVPRIVLRFTVHGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGPGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000212.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000212.fa new file mode 100644 index 0000000000000000000000000000000000000000..d45c80a5ae28d9d841c08e11fcb7c7e5bc3ca423 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000212.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_00076 +MAPMTGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV +KIAHGSVIRVRTDRQEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH +GLNLRSGSQLEDLFGMAERLYLLHEDVEGTLAALGLLTNLPWDGAVGRWKSIQAGLALAS +QILRDEGEHIVAANLGKRLHEADEVPSEPGRAARVLEVRQRQLNEPQLYDREISRALQAR +DAEAEYRWRRARFAQLLYLRGRGGSETLTDADLDSRIARELGTLRGLARDLDAKAAARS +>MOLHKGIG_00277 +MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV +KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH +GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS +LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR +DAEAEYQWRRARFGQLLYLRARGGSETLTDADLDSRIARELGALRTLADELEAKAATRR +>NAFOICDF_00061 +MSDGGAEVAPIAGGYLRHLKAQDVRPGDSFLTRRGEPAPAVASTRVVRDDFGTPALVIAT +LVGGREVKIAHGSVIRVRTDRPEEVKAAADTAFSPVDAGSPESRIVAVGQRHLDDAELTA +TAARLSHGLNLRSGAQLEDVFGMAERMYLLHEDVEGTLTTLGLLTNLPWDGAVGRWKSIQ +AALGLAALILREDGDHITAANLGSRLKEADEVPSEPGRAARVLEVRQRQLDEPQLYDREI +SRALQARDAEAEFRWRRARFAQLLYLRGRGGSQTLTDQDLDSRIHRELGTLRQLAKRLAA +QAARA +>MHAAABBN_02292 +MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV +KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH +GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS +LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR +DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR +>LFPAFLNI_00276 +MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV +KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH +GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS +LILREEGEHIAAANLGRRLLEADEVPSEPGRAARVLEVRQRQLNEPPLYDREISRALQAR +DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000213.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000213.fa new file mode 100644 index 0000000000000000000000000000000000000000..05751168ece0fb861e4044edf25a82448e4ada0f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000213.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00080 +MSTPSAPQPAPSADAPPSGRPFLLIQTRPEDEAARAEEEAVRRLGGFAEHQLAALRLDRT +LDADPDARQDWAALVAGHAGVILSGSPYTSSVPQETKDELQVAVELELGRMLDAVLDADA +PFLGCCYGVGTLGAHAGGTVDGTHAEPAGPTDVTLTEAGAADPLLEGLPPRFTAYVGHKE +GLTVPPPGAVVLATGEACPTQMFRLGRRQYATQFHPELDQVGLVERLRIYLHHGYVDPED +AEDTFARIESTPAPVPPRILENFRRVFG +>MOLHKGIG_00275 +MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV +ATHGLDWEAELADVAAVILPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG +CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA +LPPGAVLLAAGTDCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT +VAGLAAVDPEHPRRILANFRTLFG +>NAFOICDF_00063 +MTETTAPAADAAAPRPFLLVQTRPEEDAAAAEAESVRRLGGYDDATLRVLRLDRRVLDAE +GEAHAGAVDWEAELADVAGVILPGSPFTGSDPEESKSDLQVAVEAELGRLMALVLARQTP +FLGCCYGVGTLGRAAGGVVDTTYRELPGPIDVALTSEGLRDPLLEGMPAEFAAYVGHKEA +VRELPPGAVLLATGQACPVQMFRVGEHLYATQFHPELDQAGLLERLEIYADHGYFAAHEA +DDMFAAIRAREAPIPPRILERFRAIYG +>MHAAABBN_02290 +MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV +ATHGLDWEAELADVAAVILPGSPFTGTDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG +CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA +LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT +VAGLAAVDPEHPRRILANFRTLFG +>LFPAFLNI_00273 +MTTPTGAVPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV +ATHGLDWEAELADVAAVVLPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG +CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA +LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT +VAGLAAVDPEHPRRILANFRTLFG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000217.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000217.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d1dd6e5ca7091a3334ecbb3a06c5b6b5bde93c5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000217.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00095 +MTENLPTAEPEYDVAAPLDTDFYLALGDVSDDEKEVWRRARAFALEPDVLPRIREAWDRH +EYPLDLVARLGAADLLRDGVPVDGLPEVSRVAAGLAMMELSRLDGSIATVAGVQGGLAMR +SIQLCGSDEQRAELLPAMSRGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLRGHKKW +IGNGAAGGVSVVWARSAEDEQVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV +PDADVLPEARSFKDTSRVLFATRVGVAWSALGQAVGCYEAAVQYAGQRIQFGRPLAAAQT +VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASLAKYSATRAARSIAANARDLLGG +NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>MOLHKGIG_00268 +MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH +EYPLDLVARLGQADLLRDGVPVDGLPEISRVAAGLAMMELSRLDGSIATMTGVQGGLAMR +SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW +IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV +PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS +VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG +NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>NAFOICDF_00066 +MTETLPTAEPDYSTITGPLDTDAYAVFAELPDEDLALARAARAFLTPEVQKRLQEAWDTG +EYPTELIAGLAEADLLRDGVAVEGKPAQSRLACGLAAMETSRIDGSLATVVGVQGGLAMR +SIEMCGSDEQKAKYLPAMDRGELFGAFALTEPTHGSDSVSLQTTATKVEGGWRISGHKKW +IGNGAAGGITVTWARSAEDGQVKGFIVQQDAEGYSAEVIRGKMSLRAIHQAHITYDDVFV +PDEDVMPGAQSFKNTAAVLFATRLGVAWAAVGHALGCYEAAVQYAKQRVQFGRPLAESQI +VQERLARMLSELTQVQLLVLRAARLEDAGKLTGPQASLAKYSATRTARSIAANARDLLGG +NGILLENEVGKHFADIEAIHTYEGTETVQALIVGRDITGVGAFA +>MHAAABBN_02281 +MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH +EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR +SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW +IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV +PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS +VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG +NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>LFPAFLNI_00266 +MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH +EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR +SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW +IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV +PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS +VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG +NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000219.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000219.fa new file mode 100644 index 0000000000000000000000000000000000000000..24e7d9acfc33ac4bffc258cdf266d2d034754fdd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000219.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00097 +MSTEQNSTQTPAYRAAHVPAGQDLGHRWSTRVADHEDPADRRAIRQIAELTFESSAEADL +VEELAGGGEGWLPQYSLVAMTASIPGTDLQSDPMGYGTLVRAHVGEAEVLALAPHGVLPE +HQGEGAGTAIVNALLQKAQGDGEKVVVVYGWPEYYAKFGFRPGVEHGVTAAFADQPEALQ +VLTLQDDAEVPSGEFRYPPAFGAENAQVAGRA +>MOLHKGIG_00266 +MSAEQNSTQTPGHRTAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL +VEALADGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE +HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHQASEHGVHAAFARQPEALQ +ILTLQDGAEVPAGEFRYPPAFGAENAQVAGR +>NAFOICDF_00068 +MSTEKGSTATPTYRAAHVPEGQDLGHRWSTRLAHHDDPADRRAVRQIAELTFESSAEADL +VEELVASGEGWLPQYSLMAMTASIPGTDLYSDPMGYGTLVRAHIDDAEVLALAPHGVLPE +HQGEGAGTALVNALLEKAQKDGEQAVVVYGWPEYYAKFGFRPAAEHGVTAAFATQPEALQ +VIALQEGAEIPSGEFRYPPAFGAENAQVAGR +>MHAAABBN_02279 +MSAEQNSIQTPGYRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL +VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE +HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPEALQ +VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR +>LFPAFLNI_00264 +MSAEQNSTQTPGHRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL +VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAQVLALAPHGVLPE +HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPDALQ +VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000220.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000220.fa new file mode 100644 index 0000000000000000000000000000000000000000..37374f658bdbfb1c6a23f4747c55cab5d4ae13c0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000220.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00098 +MDRMILINLKYTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYLLIEGF +TDEGAKAHVESPHFQEGIDAMRPLLASTPQIISEHVDAEGFGPMGELQID +>MOLHKGIG_00265 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID +>NAFOICDF_00069 +MILINLKFTVKPELADQWMDAVAKYIADVRSEPGNMFFEWYKPVEGGDNEFFLLEGFTDE +GAQAHVASPHFQEGIDAMRPLLQSTPQIISEQIGAEGFGPMGEIQID +>MHAAABBN_02278 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID +>LFPAFLNI_00263 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000226.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000226.fa new file mode 100644 index 0000000000000000000000000000000000000000..fb6ae5b4684a490ca41114804a5affa6f9497103 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000226.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00113 +MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKHGSELAEHKAVRTAAGLFDLSHMGEVRV +TGPQAGAMLDYALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEDGSEPDFMVV +PNAGNIAAVHTALNQRASGWDATVEDQSSTTSLVAVQGPKAEAILAQAMPEAAEQLAALK +YYGHLTLTVPTEAGDVTAVVARTGYTGEDGFELFLPASSTQEAGDRGSAVWNAVLKAAEA +ADVELTLCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVGFAVPASKEADFVGKAALVG +KDDAEEVLVGLRGEGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA +EGTSLQVDLRGRGEPFTVVATPFYRRER +>MOLHKGIG_00256 +MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV +TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV +PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK +YYGHLTLTVPTDAGDVTAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE +AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG +RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA +EGTSLQVDLRGRGEPFTVVATPFYRRER +>NAFOICDF_00081 +MTESTRNSPLHPVHEAAGASFTDFGGWNMPLKYGSELAEHKAVRESAGLFDLSHMGEVRV +SGPESGAMLDHALSSSISVLKPGRAKYALCLTDAGTVLDDLIVYRTDSGAEGEDQEFLVV +PNAGNISAVVTALTQRASGWDVEVHDESSTTALVAVQGPQSEAILARLMPASAQELAELK +YYGHVTLTVPTAAGDVQAVVARTGYTGEDGFELFLPASSTAEAGDRGSAVWSAVVKAAEE +AGIALTPCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVSFAVPASKEGDFVGKAALVG +KDEVEEVLVGLKGEGRRAARHGYSVLDADGAVIGEVTSGAPSPTLGHPVAMARIRREHAA +EGTSVQVDLRGRGEPFTVVPLPFYTRAR +>MHAAABBN_02270 +MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV +TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV +PNAGNIAAVHTALNQRASGWDAAVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK +YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE +AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG +RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA +EGTSLQVDLRGRGEPFTVVATPFYRRER +>LFPAFLNI_00255 +MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV +TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV +PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAEKILARAMPEAAAQLAELK +YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE +AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG +RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA +EGTSLQVDLRGRGEPFTVVATPFYRRER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000230.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000230.fa new file mode 100644 index 0000000000000000000000000000000000000000..498247e9866eb531d99480b92b42ee34c7b12381 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000230.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00122 +MDLSNQSAIVTGGASGLGHATARRLAEAGAAVVVVDLPDREGETLRADAVAALGPRARLV +TGDVTAEATAEEAVAAALEAGPLRVLVNCAGVATPGKLVGRGGPLSAEVLTRVLAINTVG +TVNFMSRAAAAMQGQEPQGEDRGVIVNTASVAAYDGQIGQIAYAASKGAVVSLTLPAARE +LAASQIRVVTIAPGLMETPMMAGLPEAAREALATKTPHPARLGRPEDYALLVEQIVANPF +LNGEVIRLDGAVRLEPK +>MOLHKGIG_00248 +MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDRERETVRADAVAALGPRARFV +TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG +TVAMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALTLPAARE +LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDHALLVEQIVSNPF +LNGEVIRLDGAVRLEPR +>NAFOICDF_00090 +MARRESLDLQGASAIVTGGASGLGHATARRLAAAGAAVVVVDLPDREGESLRADAVASLG +ERARFITGDVTAEATAEQAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLAAEALSRVL +AINVVGTVTMMARAAAVMKDQELWGEDRGVIVNTASVAAFDGQIGQIAYSASKGAVAALT +LPAARELAASQVRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGAPDDYALLVEQ +IVSNPFLNGETIRLDGAVRLEPR +>MHAAABBN_02260 +MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALGPRARFV +TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG +TVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVSLTLPAARE +LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQIVSNPF +LNGEVIRLDGAVRLEPR +>LFPAFLNI_00248 +MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALGPRARFV +TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG +TVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALTLPAARE +LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQIVSNPF +LNGEVIRLDGAVRLEPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000232.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000232.fa new file mode 100644 index 0000000000000000000000000000000000000000..73429300acea8a1ef42a5a2b91edb12a421ecfce --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000232.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00125 +MSDAQTTTTAGSAPQAGEGGDVLLEVRDGLARITLNRPRALNALTHVMVQEIDAALVAWA +ADPAVRGVLIRGAGEKGLCAGGDVVSLHASLTGGRFEEAAQFFRDEYRMNHRISAYPKPY +VAFMDGIVLGGGMGVSVHGSHRVATERTRAGMPETAIGFTPDVGGSYHLARAPFHAGRHL +AATSAHASGADAVALGLADAFVESARLDELEQAMADALGSLEAPSGDAGRDGVRDEAAFA +AADEVLARFAMAEGERPDSALAAGREWIEDAYGRQTAAEVLAALDERAAGGGEHADAARS +AAEAIRAKSPTAVAVAHEAQNRLAAHGQDLTVAEALRQEFTVGAHLMRAPDMPEGIRALL +VDKDKDPKWSPARLEDVTADAVATHFEPVEGVARLELS +>MOLHKGIG_00244 +MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW +AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP +YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH +LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD +EVLARFAVAEDAQPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE +AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK +DKDPTWSPARLEDVSTEDVAGHFEPVSGVDPLQLG +>NAFOICDF_00094 +MSEQTSTPQAAAEDEVLFEAADGVGVITLNRPKALNALSHGMVVAVREQLAAWEEDPAVR +AVVVRGAGERGLCAGGDVVSLHGMITTGRAAEAMGYFEDEYAMNHAISVYPKPYVAFMDG +FVLGGGVGVSAHGSHRVVTERTRIGMPETGIGFTPDVGGSWLLARAPRNLGRHLGLTSAF +ATGADALELGFGDVLVDSGDLDAIVAELRAEVGSAGDDADAAHAAVDAVLARHARPASEA +PLLADAEWLEPAYAHDRVEDVFAALEATAADHADEGVRTRAAEAAETVRAKSPTAVKVTL +EALRRLGDRAGGTGRREGVAAALEQEHTLASHLTRGHDMAEGIRAQLVDKDRNPQWSPAT +VEEVSDEAVAAHFGPGEDAPLRLR +>MHAAABBN_02256 +MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW +AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP +YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH +LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD +EALARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE +AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK +DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLQLG +>LFPAFLNI_00244 +MSDAQTTATTAPAAAQEGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW +AADPAVRGVLIRGAGEKGLCAGGDVVSLRSSLLAGRFAEAEEFFRDEYAMNERIAAYPKP +YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH +LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD +EVLARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE +AIRTKSPTAVAVAHEAQRRLAARGADLAVADALRQEFTIGTHLMREPDMAEGIRALLVDK +DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLELG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000233.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000233.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a98d47c5db89a8d0db19043ec8c3815513c1d6d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000233.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00128 +MRWHGDRAAASGVTALTNILGHPIICDAAGRGRSASVLTVQNSLRPAADSPTGPRAHASG +RTEQLFGIRRHAAMPERDGALNPAAFEAGPWCLDLDGRPTGAAATVIMDNATAVAVHHAA +PGVETVVTTELQINVLAPLPAFDAAAITEGRAEGPLLECWTRPLSWDAGGGVGRAWLEDA +EGRRIVEATGWFQAVPTGAPEHRAAFTAAADLPRGPETRVPMPGLLAARPETLPPAARAG +RPAVTAAVAPGARFAPKPELANPSGAVHGGAMTLRAVVAAQAAMPDRELYDVQAVRVVFT +RPGHGEMVALTRVRHAGRSLRLVDVDLVPVGEDGAPVAEKPMVQVQVTFRAAR +>MOLHKGIG_00241 +MICRVATGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA +AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA +AAVTAGDEDGPLLECWTRPLAWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA +EFVAAGRLPRGAETRVPMPGLLAARPESLPTADPDVRPAVDAAATAGARFAPKPELANPS +GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVD +VDLVPVGADGVPVADKPMVQVQVTFRAARS +>NAFOICDF_00095 +MDEITLNPDADARWRGPRRLLLGRPEQLAGLRRRETAEIQGDTLHPGDWEVGPWVRDLDG +RPTGAAACVAADNLTAVALHWAAAEAYDAMVTTQLQVNVLRPLPVFDPADPADRPRLRML +GTPLSTDALGGCARGVIVDDDGTAYVEATGWFQATPGPMSLALEAFREHAALPVAEADRA +DLPAVTAVVADSVPAPRPGERPAVSQEMTAGLRFRAEPLLDNPGGMTHGGIQCLRAVLAA +QAALPDRLEYDVQAVQVVFARPGLGEQVALTRVRHAGRSLRIVEVELVGVDPETGAPQAG +RPSILAQVSFRAAQG +>MHAAABBN_02254 +MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA +AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA +AVAAGDEDGPLLECWTRPLSWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMAE +FVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPSG +AVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVDV +DLVPVGADGVPVADKPMVQVQVTFRATRS +>LFPAFLNI_00242 +MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA +AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA +AAVTAGDEDGPLLECWTRPLAWDAGGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA +EFVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPS +GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVHVVFVRPGHGEMVALTRVRHAGRSLRLVD +VDLVPAGADGVPVADKPMVQVQVTFRAARS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000234.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000234.fa new file mode 100644 index 0000000000000000000000000000000000000000..52e8ac31fbc75345d13998570ec24a313d760083 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000234.fa @@ -0,0 +1,52 @@ +>ACLBLIBL_00131 +MARRRRRPGGRSGLGHPAGAPAAAPAPIAASASPTQSPRPAEPAAAQPRLAEQDVAAAVA +RPAAAAPVAVESDLVPLGQRRRMGGYVPLAREGEWFAELAAADAAPAGETAEPTVLEAAH +DDAAPAAEAAVTEPAAPTTTAAAAAATTAAAQAPAAPAQPAAAAAAPTAPDTRSAPPASA +AQPPRAEPAAASGRPARATKKTDAAEEAPAPSRLRKALPLVAGVVVLALVAVLAARWLRT +LDPVADFIAAYDGHPALAEGTPVGMPPWLGWQHFLNMFLMVLIIRTGLQIRNETRPPANF +TPKKDGAFSARGNTPKKFSLTIWTHQALDALWLLNGVVFVVLLFVTGQWARIVPTDPYVF +HHAFSAGIQYLSLDWPTENGWVHYNALQMLSYTLVVFVAAPLAALTGWRMSSWFPTEAKG +LNRAFPMEAARKVHFPVMLFFVLFILTHVFLVFFTGALKNLNHMYTSRGDATDAWGLVVF +LVSVAVTAAAWFLLRPSFTAPAASKFGTVGR +>MOLHKGIG_00240 +MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR +MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD +VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE +MVAQEVDAPEQATAEPTAEPAAAAPARPVVAELADVEPADAEPAVAAPVAAASAPEPAPT +APDTRSAPPASAVQPPRAATGTPARTAETDAAESAVPSRLRKALPAVAGVVVLALLAVLA +ARWLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHET +RPPANFTPTKDGLFSARGNTPKKFSLTIWMHQALDALWLLNGLIFVVLLIATGHWARIVP +TDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWF +PTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDA +WGLVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR +>NAFOICDF_00096 +MPQRMQGYTEFRGEPWPPRDRVPQAPAPTTTPAVAADERRPGRRMVGYTAFRGEPWPPVR +EAAQPAPAPAAAASPAEVTEAAAAAVPLEATAPAGIAVPGRRMAGYTAFRGEPWPPARVG +AAPQAPEPAPMATVEPAVATGPTPTVEPVAAGAPETTPKPAPSTGRRVAAAVGGVVVLGL +LAVLGARWLLTLPEVAAFVARYPGVPRHPEVTPVGIPAWLAWQHFLNLFLLVLVVRTGLQ +VRHETRPPATFTPHQPGPFAPRSATGGTYSLTVWIHQALDALWLLNGLVFVVLLFATGHW +MRLIPTDPQTPQHMVSTALQYLSLQWPEHDGWLHYNALQMVTYAGVVFVLAPLAALTGFR +MSSWWPSRNTALSRGFPMELARRLHYPTMLAFVLFVVVHVVLVLFSGVLHELNAMFLARN +AADAWGLAAFLVGCAVIAAGWVLLKPAIVAPVAERFGRVSR +>MHAAABBN_02253 +MPKQRMAGYVPLKGAPAETEPAPAPGQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR +MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD +VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMVGYVPFAREGEWFTELAAVGGPTAPE +TAAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA +APGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRGLRSLDPVADFI +ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF +SARGNTPKKFSLTIWMHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHAVSAGI +QYLSLDWPTENGWVHYNALQMLSYSLVVFVAAPLAALTGWRMSSWFPTKATGLNKAFPME +VARKVHFPVMVFFVAFILVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA +AAWFFLKPAFTAPVASRFGTVGR +>LFPAFLNI_00241 +MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR +MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD +VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE +MVAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA +VPGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRWLRSLDPVADFI +ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF +SARGNTPKKFSLTIWTHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHALSAGI +QYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWFPTEAKGLNKAFPME +VARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA +AAWFFLKPAFTAPVASRFGTVGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000235.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000235.fa new file mode 100644 index 0000000000000000000000000000000000000000..e13239421d65d2732626893fe5c9e41af9f28bf5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000235.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00132 +MSANVEESEMTMQNDAANSGQTVLVHAELGADGALRPVVAELLGAAATVGVPEAVLVTGA +ASQDAAVARLGELGAARVHVLVAEDAAGTLGDAAVQALAAVTARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVALRWADDEVIARHSVFGGDFLSESTGEGGPRIITMRPGAVSD +RAPAVASPEVVEVAAAELGAVTAGARVLETTRRVQQADRPALRGAKTVVSGGRGVGSEEG +FAIVEELADALGAAVGASRAAVDAGYTAADRQVGQTGVIVSPNLYIALGISGAIQHLAGM +KTAKTIVAIDKNEDAEIFEYADFGVVGDIFKVVPQVIEQLRARRG +>MOLHKGIG_00239 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPVVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAAAARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCTDAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITMRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM +KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG +>NAFOICDF_00097 +MTDLPVTPVLVLAELTAAGDLRPAVAEALGAAARVGVPHAVLVTDADADDALVARLGELG +AAVVHTAVAQDPAELGTAQVAALAAAVDAVLPEAVVLPNTPESRAVAGRLAVRARGAVTA +DAVGLHRADGEIVARHSVFGGDVLAESTVEGGPNIVTLRPGAVADRARPVAAPEVRPLDV +AGRTVTAGARILSSEPAAPSADRPDLRTARAVVAGGRGVGSAEGFTTLVEPLADALGAAV +GASRVAVDSGFTAPEGQIGQTGVTVAPDLYVALGISGAIQHLVGMKTSGTIVAVDSDEDA +AIFEHADLGVVGDVNEVVPQLIAALAARRG +>MHAAABBN_02252 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM +KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG +>LFPAFLNI_00240 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM +KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000236.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000236.fa new file mode 100644 index 0000000000000000000000000000000000000000..896613f63c3dcd259d341ecdea98522192293bb2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000236.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00133 +MKILVLAKQVPDTWQERELSLDTGWVVRDGAAEPVPDEISERVMEVALGWRDAGTDAEIV +ALTVGPEDSSKTLRKMLAMGADAAVQVTDDALVGSDAVETARVIAAAVEREGADLVLAGT +VSTDGGTGVVPAMVAELLDRPYLPHAEAPQLADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGAKV +SDDGTAAQQLVDFLAGRGLV +>MOLHKGIG_00238 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +VSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELIGTVATSDADVRAAVALPAVASLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKI +TDDGTAAERLVEFLAGRGLV +>NAFOICDF_00098 +MKIAVLAKQVPDTWQERTLDMETGMAVRDGAAEPVPDEIGERVMEVALAAREAGLEAEIV +AVTMGPADATKTLRKMLAMGADSAVHVVDDALDWSDAVQTARVLAAAVEHLGVDLVLAGS +ESTDGATGVVPAMVAELLDRPLLPSVEAVEITPEEVRGVLVTEDARLRASVPVPAVVALT +EKTAEPRFPNFKSIMAAKKKPLETLTLADLGLTAGPLDADRRSVMVSAAARRERAAGEKI +VDDGTAGEQVAAFLAARGLV +>MHAAABBN_02251 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV +TDDGTAAERLVEFLAGRGLV +>LFPAFLNI_00239 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV +TDDGTAAERLVEFLAGRGLV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000237.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000237.fa new file mode 100644 index 0000000000000000000000000000000000000000..1368cdd94b37ae409b2155089ab74256b7a19c51 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000237.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00134 +MSPAAPSADPADGDRPDVPAVPASSLMLVRPEQDGDTSVFALRRAGSMAFSAHATAFPGG +RVDPADDLPDALWEGTDLAAWGRRLGLPHEPVDALGTLAALDPAEGAGRVLAAAVRETFE +ETGVLLARDTATGAPVDPDRVAALPEDLRDAVERHEVDFGDLLRDEGLRPDAGALVPWSR +WITPHGGPRRYDTFFFAVHLPAGQSPERMSSEAAEHGWASPAELLRRFRAGEVNLMAPTW +WQLRTLDDAGEDVHAGRSRFEPLEGVMLVAGQGPAFSHADEYLRDLAAFRAAAHVEESKD +NIL +>MOLHKGIG_00237 +MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG +GRVDPADDLSDRLWEGTDLADWGRRLGLPHEPADAHGTLAELDPAEGAGRVLAAAVRETF +EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS +RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRVGKVNLMAPT +WWQLRTLVDAGEDVHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK +DNIL +>NAFOICDF_00099 +MDAAQTSSSETLPVEATPARAAASLLLLRDGAAGLEVFHVHRAGTMAFSAHATAFPGGRV +DPSDDALPVPGADLAAWARRLGLEDRPVETQPEDDPARVAARFLAAVVRETFEETGVLLA +RAADGGPVPPEAAAALAGRREDVEAHAADLGALLAEHGLAADVSGLRAWQRWITPLSVPR +RYDTAFFLVAVPAGQDPDRLTTEATEHGWARPADLITAFQAGDVNLMAPQWAQLRALMDL +PDVEAALRAGAAAEPVPVVQLASEASPEERTREFSHAAEYREHLRSFRTHDRVQDTPDNV +L +>MHAAABBN_02250 +MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGETSVFTVRRAGTMAFSAHATAFPG +GRVDPADDLPDRLWEGTDLADWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF +EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS +RWITPHGGPRRYDTFFFAVHLPHGQSPERMSSEAASHGWASPAELLRRFRAGEVNLMAPT +WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLMAFRAAAQVEESK +DNIL +>LFPAFLNI_00238 +MSPAAPPAEPSAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG +GRVDPADDLPDRLWEGTDLAEWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF +EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS +RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRAGKVNLMAPT +WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK +DNIL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000242.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000242.fa new file mode 100644 index 0000000000000000000000000000000000000000..d77d8486be707308bd7e6605adf901292d5fecee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000242.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00147 +MSTPSPIGLLLDVDGPVASTQTRTVPDGIVATLVRLAGRGVPVGFNTGRSADFLLHSVIG +PLRAAGLPADAPFFAVCEKGAVWFPFSAVPAGTLPEVTVDAPAPAWVRTDPAMALDPGLR +ERIWELNRERAGDLQFVDRTKLAMVSLEMRVGADQAAYEAVRDDVAAGVEEMLAERGLAD +EVRVDPTVISVDVEHRSSGKDLGVDRCRALMAEAGVPVPGRWFTAGDSRTDYAMADRLHA +IGLAVEHLDVRPADGIPATPYPVLTAADLAGRGVGNAEDVHERAGESLLRWVERDLLD +>MOLHKGIG_00232 +MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA +PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR +DAIWALNDERAGDLQFTDRTKLAMVSLEKTVGADQTEYERVRDDVAAGVEDLLAERGLAE +EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE +RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR +>NAFOICDF_00105 +MTSPSPIGLLLDVDGPVASTETRAVPEGIVTTLVRLAAARVPVGFNTGRSADFLLHSVIG +PLRAAGLPEDAPFFAICEKGAVWFPFSDVPAGDLPAVTVDAPTPGWVRTDPAMAVDADVR +DAIWEINGERAGDLQFVDRTKLLMVSLEKTVGADQDAYVQVRDDVAAGIEDLLRERGLAE +DVRVDPTVISIDVEHRTSGKDLGVDRCLGMLAEVGVAVPERWFTAGDSRTDYAMADALHA +MGAPVEHMDVRPADGIPERPYRVLTAADLAERGVGQAEDVHERAGESLLRWVERDLLA +>MHAAABBN_02245 +MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA +PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR +DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAARVEDLLAERGLAE +EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE +RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR +>LFPAFLNI_00233 +MRTPSPIGLLLDVDGPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHSVIA +PLRDAGLPDDAPFHAVCEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR +DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAAGVEGLLAERGLAE +EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE +RGLTVEHMDVRPADGVPEKPYGVVTAAILAERGIGDAEDVHERAGESLLRWVERDLLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000244.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000244.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c78ff3399a0ef8e352b8f29c0542273fc99304e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000244.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_00150 +MANVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRTHGGIEWVHTRHEEAAAFAASAES +QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF +RECSVYVEHVSSADQMPRMLRTAMRAALEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR +VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHAMRGKDRIEYD +NPYDVGLTGLLGFSSGYHALKDAETLLILGSSLPYRQFYPEDATVIQVDVRGDQIGRRVA +VDVPLVGGVKETAQALLPLLRGNASSSFLKKARRHYAKTRKDLDELAAPDRRTVHPQYVA +RVLDEAASEDAVFLPDVGSPVVWAARYLTMNGRRRIIGSMTHGSMANAVTQAIGAQAVDR +TRQVVAMAGDGGLAMMLGELLTFVQNGLPVKTLVFDNDSLNFVELEMKAAGLVPYATDLQ +NPDFAAVAEAMGLKGFRVERSKDLPAVMAEFLAHEGPALLVVKTERQELTIPPSIEFEQA +KGFALYALRTVLDGKGTQLVDLAKANLRQLF +>MOLHKGIG_00231 +MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES +QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF +RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR +VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD +NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA +VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA +RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP +TRQVVAMAGDGGLAMMLGELMSFVQNGLPVKTLVFDNDSLNFVELEMMAAGFVPYGTSLE +NPDFAAIAEAIGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA +KGFALYAMRTVLDGKGTKLLDLAKANLRQLF +>NAFOICDF_00107 +MATVAKHIVETLSASGVRRMYGVPGDSLNALTEALRQHTDMEWVHTRHEEAAAFAASAES +QLTGELAVCAGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQELF +RECSVFVEHVSDVSQMPQLLRIAMRAAVEQRGVAVLVIPGDVALQDLDAKPEVIRATRSH +VVPDEDSLREAAEALNSCKRITILAGSGAAGAHDEVVALADRLQAPVVHALRGKDHIEYD +NPFDVGLTGLLGFASGYHAMKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVS +VDIPLVGGVRETAQALMPLLKGNSSSAFLKKALKHYDKSRKGLDSLATPSRGTIHPQYVA +RLLDEAADDDAVFIPDVGSPVIWASRYLTMNGRRRIIGSMVHGSMANGITQALGAQAIDR +SRQVVVMAGDGGLAMMLGELLSFVQNRLPVKTVVFDNDSLNFVELEMKAAGFVPFGTGLQ +NPDFAQVAEAIGIKGFRVDRAKDLPDVMREFLAHDGPALLLVKTEPQELTIPPSIELEQA +KGFALYALRTVLDGKGTQLIDLAKANLRQLF +>MHAAABBN_02244 +MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES +QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF +RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR +VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD +NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA +VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA +RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP +TRQVVAMAGDGGLAMMLGELMSFVQNGLPVKTLVFDNDSLNFVELEMMAAGFVPYGTSLE +NPDFAAIAEAIGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA +KGFALYAMRTVLDGKGTKLLDLAKANLRQLF +>LFPAFLNI_00232 +MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES +QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF +RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR +VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD +NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA +VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA +RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP +TRQVVAMAGDGGLAMMLGELMSFVQNDLPVKTLVFDNDSLNFVELEMMAAGFVPYGTDLQ +NPDFAAIAEAAGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA +KGFALYAMRTVLDGKGTKLLDLAKANLRQLF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000246.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000246.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc5ecf969db079266a4dfaf2c39a6a6353833565 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000246.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00153 +MPAGRYAPSPTGALHLGNLRTAIVAWLAARATDRTFLLRVEDLDRVRSGAEAAQLSELAA +VGLDWDAEPVRQSERTGLYDDAVAALRAAHGADAVYECFCSRKDIAEATSAPHPAPADDD +GAPGPAGAAPLRPPGFYPGTCRGLTAAQRAERRRVRPAALRIDAVQVAGLPEGEIPRAEA +VDLLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSTPRQRWLAA +ALCAARGEALPQTSYLHVPLVLNAEGRRLAKRDGAVTLEDLAAADPSWTPERVRDRLLSS +LGLPPGPPADAVPAFARMLEDGSLPREPWMFDPAAFAGA +>MOLHKGIG_00228 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATNRAFLLRVEDLDRVRSGAEADQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAVHGPDAVYECFCSRKDIAEATSAPHPRPDDGA +PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGETPRATAVD +VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL +CAARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLSAQDPAWTPERVRDRLLESLG +LPAGPLAAAVPAFDPAALPRVPWVFTGL +>NAFOICDF_00110 +MPAGRYAPSPTGTLHLGNLRTALVAWLAARATGRTFLLRIEDLDRVCSGAEAGQLADLAA +VGLDWDGEPVHQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA +PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD +VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL +CVARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLGDLAAQDPAWTPARLRDRLLESLG +LPAGPLAVAVRAFDPAALPRDPWVFTGL +>MHAAABBN_02241 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRIEDLDRVRSGAEAGQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA +PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD +VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL +CDGRGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLG +LPAGPLAAAVPAFDPAALPRDPWVFTGL +>LFPAFLNI_00229 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRVEDLDRVRSGAEAGQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA +PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGEIPRATAVD +VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL +CSARGEPTPAVEYLHVPLVLNAAGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLD +LPPGPLAAAVPAFDPAALPRDPWVFTGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000247.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000247.fa new file mode 100644 index 0000000000000000000000000000000000000000..435484ea22ff02cb0273a4becec04c9467876103 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000247.fa @@ -0,0 +1,107 @@ +>ACLBLIBL_00154 +MSTALYRRYRPDRFEEVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAHLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQDGGVSYELAV +SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL +PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA +RLLLPASDDTHRGLAARLEALERRLELGGVPVASADESAGGTTTSARPGAPAAAGGGSAG +SGGAGGGEPLTGAALARAAMRRPEVQEAPTPPAQETARSEKAPAQPEPTPMPSPVGQAAP +PAQPAQSEHPRPERWAPPAAASSPEADAPAQRPDAARPEQPAQQDRPQRQTPPPAPAGQP +EQRQQQTAQAERPTTTERPAERPAAGAPEASPASTRPQAAERAAERPQAEADAAGSAVPS +SAAPAPTPSQVEKVRRAWPDILAALEDASRLMWMIVKDNASVAGYDGSLLTIGFQQDGPR +QMLLGRGGDRVLAEAVHQVLGIRPQLDLILGGDAPQGGSRHAQGQAQTPSAPRAESRADA +PTSRPDAGEAAPTRQDRPQQQGGEPDRGQQQDRGQQQGRGQASDLGPAQGGSPSGRPTGQ +AAAPTPGRGPSSPAPAQRPTAPQAASTTPPGAPPSDGWGRADEEPPAWDDAPPPEEDPWD +SLPEFDPDADMDDSDGPEGWTPPAAGQDDAPVGAAGWDGPVPAAEDWGAPPQGGAPAPDG +RRDERPAAAQGSDAPSEQPTPQGSADAGPAAETDAEPSAEEVRRAYDPGPLVREEEHTIP +VFARPEAELRAEFAQRFGATRPAGFDDGAGAGADAESTRAAAPSPGPDDLPPGQGDDPDA +TARRDTHPAASASGPSSAADHGSSGEPTADGTPDPGVPAEDHEHTSASDADDDGSPERAA +GSGHPASMFPRLMERVRAGGPLEPPVNAAPPGGATPPGGGPGGGAGPSGPGSAPGSDQGP +RPGGAPSDAQGPGAPGPDAPRGGRPSAAALGARPGGETGSPAGASAPPSLDARAAAIRAA +REAAQGRGPARPAGNGPAAPSAPAVGWEDEVASDDDVALEDSGLVGRAVVERVLGARLLE +ERANSA +>MOLHKGIG_00226 +MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV +RLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL +PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA +RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAKDGGGSAGD +ADGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQSVAEAPEGDAAAGATGSER +PQQPPQPKRPEPAEVGARSGDTRRPEAGSRAEPEGRPEGRPQAQDRTGAAPSSPAPAPAA +SQVEMIRRAWPDILTALEDASRLVWMLVKDNASVAGYDGSLLTIGFQQDGPRQSLLGRGG +DRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTDRPERPAPQQGRPDR +PTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAAPPRATQQRQTPEPSPA +WTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPEEDPWDSLPAFDPDA +EQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAPAPGGAAPDAGQDSP +VQPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELRAEFAKRFGATRPAG +FDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSSDEQRRPTGAPTADA +TPDPGVPADDADATPRTAAGPTGSDFPGSGHPASMYPRLMERLRAGGPLEPPVNAGSSGG +GGTGGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLDARAAAIHA +AREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVERVLGGRLL +EERPNDA +>NAFOICDF_00112 +MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAYLERLCQEEGVRVEPGVLPLVVRAGTGSVRDTLSVLDQLIGGAQQGQVSYDLAV +SLLGFTPEALLDDVVDAIAADDTPTVFRVADRVVQSGQDPRRFVEDLLERFRDLVIARAL +PDEASSILHGMPEDQVRRLAAQASQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA +RLMLPATDDTHRGLAARLEALERRVAGGAAFSPDDDASSGAEGPAAGGAGQGGAALSGAA +LARAAARRAEPEQAREQEPGAGSDKRAAEPATPKPATPEPVAAAPAPERPVERPAEAPAP +SSSAPAAPAAPTAHTPSQVEKVRRAWPDILAALESDSRLMWMLVKDNATVAGYDGELLTV +AFPQEGPRRTLQSRNGEQVLGEAVHRVLGIRPRLDLILGGDTPRGEERPKAEGRPAAAVS +EAPAAPSTSAPPPAPQGQPTQAQPPRAQPSPEDGRRPAASAPRPQDVAVATSWDQAPAPS +AAPWQPAPSRPAAASPAPQTGPAAPSTPDPRQDAHPGTRPGPADTTPPAAPPSDGWGHVD +EEPPAWDDAPPPPEDPWDSLPEFDPDADMEDSPGPEGWTPGAGDDAVHGSAGSAPTSAPE +AWGGAVPTPQDWGAPRPQDPVESPAPQGPEAGTQGTAPDAAAQGAPSPAAPAEAVPEDPE +TARRAYDPGPLVREEELTIPVFAKPEAQLRAEFAARFGGTRPAGFDSTAASDAAAPDAQG +PGAAARAAAHGEPVRGGQDAAEPAADREAEPEEDPQAAASAPEHPVRPSPARPTADDTPD +PGVPQEDHAEDAAPPSATAPDDRGSGHPDSHYPALMERLRASGPLEPPVNARPAGQGGAR +EEQVPAPVDAAPSPGRPSAASLGRPTGDPQAAIAPPAEDPRASGARAAAIQAAREAARGA +GPRPADGAPGGPATASGPSVDWQDEVASDDDVALEDSGLVGRPVVERLLGARLLEERPLE +PGL +>MHAAABBN_02239 +MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV +SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL +PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA +RLLLPTSDETHRGLAARLEALERRLELGGAAPVEEGAPEGTTTPARSGTPAADGGGSAEN +AEGSGTLTGAALARAAMRRPEEPAPTASTAPPERWTPPAPQSVAEAPEGDAAAGATGSER +PQQAPQPKRPEPAEVGARSGDARRPEAGSRPEPEGRPEPEGRPQAQERTGAAPAPAHGPE +ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF +QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTD +RPERPAPQQGRSDRPTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAVPP +RATQQRQTPQPSPAWTPAAPATSWGPAPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE +EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP +APGGAAPDAGQDSSVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR +AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS +DEQRRPTGAPTADATPDPGVPADDADAAPRAASGPTGSDFPGSGHPASMYPRLMERLRAG +GPLEPPVNAGSSGGSGTGGGPGAPGGPDLDATPGSPAGGRPSAASLGARPADAEPAGGAS +ALPSLDARAAAIRAAREAAQGRGPARPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLV +GRAVVERVLGGRLLEERPNDA +>LFPAFLNI_00227 +MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAYLVQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV +SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL +PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA +RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAPDGGGSAEN +AEGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQPVAEAPEGDAAAGATGSER +PQQPPQPGRPEPAEVGARSEDARRPEAGSRPEPEGRPEPEGRPQAQDRTGAAPAPAHGPE +ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF +QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDTRGQSGARPAGPARTD +RPERPAPPQGRPDRPAAQPNRPAPAPGPAPREPESSRPAPPRSAAPSTAEDDPAPPAAPP +RATQQRQTPQPSPAWTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE +EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP +APGGAAPDAGQDPPVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR +AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS +DEQRRPTGAPTADATPDPGVPADDSDATPRAAAGPTGSDFPGSGHPASMYPRLMERLRAG +GPLEPPVNAGSSGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLD +ARAAAIHAAREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVE +RVLGGRLLEERPNDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000248.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000248.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b5d96e94d30986e98b17c072fd4d276e0a90bf6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000248.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00155 +MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDKVRLCSVCF +NVSEDEVCSLCRDERRDASQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG +>MOLHKGIG_00225 +MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF +NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG +>NAFOICDF_00113 +MYEGAVQDLIDELGRLPGIGPKSAQRIAFHVLEADAADMLRLADAIRTVKDKVRLCSVCF +NVSEQEVCHLCRDARRDDSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG +>MHAAABBN_02238 +MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF +NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG +>LFPAFLNI_00226 +MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF +NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000249.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000249.fa new file mode 100644 index 0000000000000000000000000000000000000000..dfd302126f9cf25ef9824cf6f73a40b0ee2beef3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000249.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00156 +MSTVVADPTRQGPPPLRPPGGGRLSTASAVRTVVGMELRQRLRSRGWYVLLGVFFLVVGA +VTLGALGLRATTLGDLQSQGMDPAAAEVQMRSAGQWLFDGVLLFVLTLSLLVSPVLAANA +ISGDRAGGTLAITQVTLLRTGQLMAGKWIAAWIASAAFLVAALPWLAVAAVVGRVSPLFV +LVGLLMILVEFGVITGIGVAVSAIAGRTLFAVVVTYLIVAALSIGTLVAFVLSLQFLQTD +VRANMPEHDGMTMADPLEGQDVENMTQAEIDAAWAEWERQNPDAYDGIADACVGPVGVQS +VPDPRRVGWLLAANPYAVLADASPWDPTGASMQFTPETGPLNMMSAALRLTQQDPAETTE +CLDGQLRRIDTTSVPDREGTWPVWPLGLAMQAALTGGLLWWGHRRLDTPAGRLPAGTRVA +>MOLHKGIG_00224 +MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV +TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI +SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFPAAALPWLAVAAVVGRVSPWAVL +VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV +RANEADYGSTTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP +DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL +DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA +>NAFOICDF_00114 +MSAVLHTPPPAAAPAGGPTPLGSGRLGVVDALRTLVGMELRQRLRSRGWYILLGVFFLLV +GGVTLGALGLHAWTGGNSPDSTMVFGRWLYDGVLLFVLTLCLLVSPALSANAISGDRSAG +TLAITQVTLVSTWQLMLGKWLAAWIAAVAFLVAAAPWLIVAAVVGQVPPLAVLAGLAMIL +VEFAVVTGIGVAVSAITGRTLFAVVVTYLLVAMMTIGSLIAFTISLQFIETRLQTNQVTY +GYAEDAGSTKSCAGPLRDTTVPDPRRVAWLLAGNPYVVVADAVPLPELREDSAGEEFGAL +NLISLGMRVAQIDPREYTDCVDGQVNEGSVTDSPVTLVDRTWPTWPLGMLLQGGFLAALL +WWGRRRLDTPAGRLPTGTRVA +>MHAAABBN_02237 +MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV +TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI +SGDRAGGTLAITQVTLLRTGHLMTGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL +VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV +RANDAEYGSMTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP +DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL +DGELRGLDSTGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA +>LFPAFLNI_00225 +MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV +TLGALGLRSLGVTEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI +SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL +VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV +RANDAEFGSMTAEPFTEAELEKMTPEEADQAWAEWEAANPELFDGIADRCVGPVTTRTIP +DPRRSGWLLAANPYAVLADASPWEGGLVEDGTWAEPGPLNLLSVGLRWTQRDPVRDVECL +DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000250.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000250.fa new file mode 100644 index 0000000000000000000000000000000000000000..f04c0738b9d1b3582676ac2ccca5109d688c3e9b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000250.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00158 +MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGHRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMMTDTSYGRARIVKVNPHR +VQEALDAGGVAIVAGFQGVSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPSARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPIHVRSSFSDHEGTW +IMPDPNDTITLKEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAESNVNI +DMIVQNVSREGSGTTDISFTLPIVEGKDAMAALRAAQERIGFQDIVSDKEIGKLSLIGAG +MRSNPGVSATFFKALSDAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHTAFGLDAEEEA +TVYGGTGR +>MOLHKGIG_00222 +MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR +>NAFOICDF_00116 +MRLIVQKFGGSSVADAEGIQRVARRIVATQQAGNQVCVVVSAMGDTTDELLDLAAELTAD +APAREMDILLSAGERISMSLLAMAIDAQGVPARSFTGSQAGMMTDAAYGRARIIEVNPHR +VRAALDEGAVAIVAGFQGMSRESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVSSARKLPQLSSEETLELAASGAKVLHLRSVEYARRFGVPIHVRSSFSDHEGSW +IMPDPNDTIHLKEGAPMEQPIVAGVAHDRSEAKVTIVGVPDVPGKAAEIFRVIAESNVNI +DMIVQNVSRQDSGRTDISFTLPIVEGKAAIEALRAAQESIGFEEIVPNKEIGKLSLIGAG +MRSNPGISATFFKALSDAGVNVDLISTSEIRISVVTSEDKLDDAVRAVHTAFGLDTDVEA +TVYGGTGR +>MHAAABBN_02235 +MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR +>LFPAFLNI_00223 +MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000251.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000251.fa new file mode 100644 index 0000000000000000000000000000000000000000..c59d39b8cca440ee6a449c4f53dc86cd77d2af6e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000251.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_00160 +MAGTCLHTPPPSPAAPRTAPTDPTAVVVLRPEEWLARSAAHRERIEARTAPLLELHGRGE +RHPVQDFLFGYYTHSPAALARWHPGAGVVLADPDGAAAAAEAERDGAPHRGGWRHLRATE +PGEIPGAEPDGRPTVGWTVDADAFAADRATGIAFTAELLERTAARPARLGCFGLHEWAMA +YRSDLHGVRHSRLPLRLGAEGTDAVVESQRIRCTHFDAFRFFAPEARGLNEGADGVLPTR +AGMRDMEQPGCLHAGMDLYKWAYKLLPWVSSDLVADCFDLAWDIRALDMRASPYDLRGVT +DLAGGDYPPVRIETPEGRAEYVRAQRGFADRGQALRARLLAALAPLLGDDARG +>MOLHKGIG_00220 +MPEPHTAPAPSETLPPAVVALPADVWRAHARAHRERIARRTDPLVALRMRGQKHPVQDFL +FGYYTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGATPRGEWKHYRRVEAGEVAGAV +VDGRPVGGWLVDVAAVLADRASGVAFTRELLARTAERAPRLGCFGLHEWAMAYRSDVHGV +RHSQLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMRKMEQ +PGCLHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEASPYDLTGVDDLSDGRGG +YAAVRIEEPAGRAEYARRQREFAARGQSLRVRLLAVLDAAAGAAPGARPDTEWTSSARP +>NAFOICDF_00118 +MTSAAPSPVPLVLAPEDWRARARAHRERIAARTAPLMARRTRGEPHPVQDFLFGYYTLTP +GALQRWHPGAGVVLADDDGAAATAEAAELGTAPRGEWRHWRRVEPGEVVGVVLDGREVGG +WTVDVPAFLADRASGVAFTRELLERTAGRPARLGCFGLHEWAMAYRSDVHGVRHSQLPLR +LGAAGTDAVVEDQRIRCTHFDAFRFFAPEAVPLNEGAEGVQPTRAGMRDMEQPGCLHAGM +DLYKWAHKLLPLVDSDLVADCFDLAWDIRRLDMEASPYDLTGVDDLSDGLGGYTPVRIET +PEGRAEYARRQRGFAERGQALRARLLAALEAGARAAGDRRPTEDPSTPDPEEHHG +>MHAAABBN_02233 +MPEPRTDPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY +YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG +RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS +QLPLRLGAGGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC +LHAGMDP +>LFPAFLNI_00221 +MPEPRTAPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY +YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG +RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS +QLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC +LHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEAAPYDLTGVDDLSDGRGGYAA +VRIEEPAGRAEYARRQREFAERGQALRARLLAVLDAAVGAAPGTGPDAEWTSSSARP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000253.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000253.fa new file mode 100644 index 0000000000000000000000000000000000000000..57897b46bd6736f73415a3dcae3e920ae2cb7f38 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000253.fa @@ -0,0 +1,17 @@ +>ACLBLIBL_00169 +MTDPCPCGAGLPLAECCGRLHARFAADGALTAPTAEALMRSRYAAFALLGEAGADDDGTQ +GTDGASGPGGTGPGHAGPGHAGPDRARAMAAYLAATWAPEHRPAVEDLLPEAGERAPRFT +RLAVTDVRDGGPFQDRGIVEFTALGHGEEGRFRLRERSRFRREDGAWLYVDGDVA +>MOLHKGIG_00214 +MRSRYTAFARLGEAGPAEAQAMADYLAATWAPEHRPPAAELLPAAGEQAPRFTRLAVLDV +RDGGPFQDAGTVEFVAVGAGAEGRFRLHEVSRFRREDGVWRYVDGDVR +>NAFOICDF_00120 +MTEAPCPCGLGLPYPECCGRLHAAHAADGSLTAPTAEALMRSRYTAFARLGEVEGAGATG +AADVAATVAYLRATWAPEHRPSTAELTPGPGDPAPAFTRLAVLAVEGGGPFQDVGEVEFA +AVGRGPEGRFRLHERSRFRRESGVWLYVDGDVTA +>MHAAABBN_02207 +MRSRYTAFARLGEAGPAEARAMADYLAATWVPEHRPTAAELLPTEGEQAPRFTRLAVLDV +RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVDGDVR +>LFPAFLNI_00214 +MRSRYTAFARLGEAGPAEVRAMADYLAATWAPEHRPTAAELLPAAGEPAPRFTRLAVLDV +RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVNGDVR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000255.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000255.fa new file mode 100644 index 0000000000000000000000000000000000000000..6e5edcabc9071fbd420c9da5432cb2bcad9160e4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000255.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00173 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDAVLDQAR +RAAEELLSNPVIEDVVNVAVLDEAEGAR +>MOLHKGIG_00213 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR +>NAFOICDF_00122 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTEEVLAAAR +TAAEEMLSNPVIEDVVNVAVLDEDAA +>MHAAABBN_02206 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGKVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR +>LFPAFLNI_00213 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000256.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000256.fa new file mode 100644 index 0000000000000000000000000000000000000000..f89428490f3f40451d44b1a3576017934954b3cd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000256.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00174 +MTTDLPLIGDYSTPTTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHADEDPQR +TLAGVDAVVIPGGFSYGDYLRAGAISRFAPMMDAVATAAGGPEGAADGLPVLGICNGFQI +LTESHLLPGSMIKNDHLHFICRDQELTVENTDTAWTRDYERGQTITVPLKNQDGQYVADD +ATLDALEAEGRVVFRYRGWNPNGSRRDIAGIANAAGNVVGLMPHPEHAVEPGFGPDTADG +PRTGTDGLGFFTSVLTTLASRGGHA +>MOLHKGIG_00212 +MTELPLIGDYSTPATPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT +LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL +TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET +TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP +RSGVDGLGFFTSVLTTLASRGGHA +>NAFOICDF_00123 +MTEIPLIGDYSTPSTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHAEADAAAT +LATVDAVVIPGGFSYGDYLRAGAISRFAPMMGAVAQAAGGPEGSEDGLPVLGICNGFQIL +TESHLLPGSMIKNDHLHFICRDQQLAVESTDTAWTRDFEQGEVITVPLKNQDGQYVADEK +TLDALEAEGRVVFRYVGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEAGFGPDTEAGP +RSGTDGLGFFTSVLTTLATRGGAA +>MHAAABBN_02205 +MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT +LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL +TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET +TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP +RSGVDGLGFFTSVLTTLASRGGHA +>LFPAFLNI_00212 +MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT +LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL +TESHLLPGSMIKNDHLHFICRDQELVVESADTVWTRDFEQGQTITVPLKNQDGQYVADET +TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEPGFGPDTAAGP +RSGVDGLGFFTSVLTTLASRGGHA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000257.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000257.fa new file mode 100644 index 0000000000000000000000000000000000000000..5ea779bd65afed8fc0145b9c520bb82b86616842 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000257.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_00175 +MSQQFSIETVADAAANPDIEQPWAELGLKENEYAQIREILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI +GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGLGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFAGSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPDNVAAFEAVMAKWDVEYSWL +GEVTGDGRLVITWDGEVIVDVDPRTVAHDGPVYERPYARPGWQDRVQADTFRASEAGADL +PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTAMAAPDDAGVVRVDEETGMGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPENPDVMWQFAEA +VRGLADGCQVLGIPVTGGNVSLYNQTGATPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG +QAIYLLGETADELDGSEFARLRGHLGGVPPKVDLAKERLLGELLVNMSRDGMIDAAHDVS +GGGLAATLSEMVLRHGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYTVTRIGVVDADSAALEVQDAFTLPIAELREGWEATLPKHFG +>MOLHKGIG_00211 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI +GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL +GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL +PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA +VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG +QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS +GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG +>NAFOICDF_00124 +MSTQFTIETVEQAAANPDVAQPWAELGLKEDEYARIREILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGDTLTEEMKEHMMVGIGENAGVTDLGDGWAVTFKVESHNHPSFVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAVDHPDTARVVHGVVAGIGGYGNSLGLPNI +GGEVAFDPSYQGNPLVNALAVGVLRHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDDGGKPAKRPSVQAGDPFAEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEHSWL +GEVTGDGRLVITWDGETIVDVDPRTVAHDGPVYERPCHRPSFQDALQADTFRSSAAGQDL +PATGEELKAAVVELMASPNMADVSWITRQYDRYVRGNTALASPDDAGVVRVDEETGMGVA +VATDCNDRYAYLDPYAGAQLSLAEAYRNVTTTGAVPLAVTDCLNFGSPEDPEVMWQFAEA +VRGLADACQVLGVPVTGGNVSLYNQTGGVAIHPTPTVGVLGRFDDVLRRTPSGFGTDADG +QAVYLLGVTADELDGSEYANLRGHLGGVPPKVDLAQERLLGELLVNMSRDGMVDAAHDVS +KGGLAATLADMVLRFGVGARIVLDEVVRRDGVDVFTALFSETQGRTVVSVPRTEEVRFTD +MTTARGYTVTRIGVVDAQSDALEVQGQFTLPIAELREAWEATLPKHFG +>MHAAABBN_02204 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI +GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL +GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL +PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA +VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG +QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS +GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG +>LFPAFLNI_00211 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI +GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL +GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQHL +PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGMGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA +VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG +QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS +GGGLAATLSEMVLRFGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPITELREAWEATLPKHFG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000260.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000260.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf1906a28fa3efb9e0cc7ae9e327153427e0892e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000260.fa @@ -0,0 +1,27 @@ +>ACLBLIBL_00183 +MQRRRAVRAVGLGVAGVLALAGCAAEPQSAGEAWQQARTQLDEAQTVRLETAHTTGRQGP +NTVRWDIAGRLDGSNGDAKGVIQAGHESHMTMETRTVGEDSYVRVSIDGADFADDVQLAY +ADPQWRRTPAGQEQERPLKELLEQIGLPSADALEGAEVRAEEVGWAGETAHRYAVPQEVA +AAAMGQGDSTLLHSFTVDDDGGLLALTVDDGRSLRQYALSDWNEIDPAEAPEEVAE +>MOLHKGIG_00208 +MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA +ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR +VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAEVRAEEVD +WDDGTAYRYAVPEEVADAAMVEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ +IEPAEAPEEVAE +>NAFOICDF_00129 +MQRRRAVHAAGLGVVAALTLAGCGTDQQDVGEAWQHARAQIDGAESVRMTMASVNDSQGP +SVVAWDVAGPLEGADGTTTGRMQVGRDSWMTVRSVSADGKTWARVDTEGQDVPEQIASMY +RTDGWTETQQSGQNALRATLDAVGLPAADALDGVDVQPEKVDWSGGTAYRYAMPGDVASA +ARGDSQFSVRAFTVDEDGDLVGLRVEDGGVIQEFALSDWNEIEPAEAPEEAQH +>MHAAABBN_02201 +MQRRRAVRAAGLGVVGALALAGCGSEPQSVGEAWHQARTQVDEAETVRLETAYTTGRQGP +QSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVRVEVDGSDVPDDVQLMY +ADPQWRRVSAGEGQEPPLKSLLDQVGFPAADALDGAEVRAEEVDWDGGTAYRYAVPEEVA +DAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQIEPAEAPEEVAE +>LFPAFLNI_00208 +MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA +ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR +VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAQVRAEEVD +WDGGTAYRYAVPEEVADAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ +IEPAEAPEEVAE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000264.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000264.fa new file mode 100644 index 0000000000000000000000000000000000000000..a316434cf3425e5322cefa595cf58449913a575d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000264.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00202 +MARYVPAPAPEPVPAAEEAALRQGRARPWWPYLLTAAVSVALLVWTVVAYPGLPEQVPVR +WGIDGRPDRWEDTTFGTVAFGPIFGLGMTAFLALIAAMIPAMTGVHGATSAWRRVRQEGV +NRGVREGMGWIALLSLLMTAPTTAEVLSAGAWRMPWWLMPLLLTALMVGVFGALRATLGR +WTRWADGVAADLGHRPTPEELAEDKTWTPLGMKDDPEDPTVFPAKRPGYGVGTTINIGTR +AGRLLVYGFVAVFMVALPLATWIGAYLAR +>MOLHKGIG_00197 +MPHPPRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW +GVDGRPDAWEDASFGTVATGPLIGLGVTGFLALVSAMVTVLVPTDPGLSPWRRVRQAGVH +RGVQECLGWSCVLIVLVLAPTTAEVLAAGAWTMPWWILPLTLTVLMVGVFPAMRASTRRW +TRWSDRVAAELGYRPTAAERAEDEVWTPLGLKRDPDDPAVFPTKRPGYGVGVTVNLATPA +GRWLVRGFVVVVIVGLPLALWLGAFAAR +>NAFOICDF_00150 +MPHPPRPTPDDVPAAERAALRRGRWIPWLPYLLTAAVSAGLLVWAIVALPGLPDRVPVHW +GIDGRPDAWEEKSFGTVAFGPLLGLGMTALLAFCAALTPAMTATPQDASPWRRVRQEGVN +RGVREALGWLTLLIALATAPSTVEVLSNGAWRPAWWLMPLVLTLVMLGTVGVFGPALRRW +TGWADRTAQDLGYRADFAELAEDAKWTPLGLKNDPEDPSAFPAKREGYGVGATVNLATTT +GRLLVYGFVALFVIGLPAALWIGAFLNR +>MHAAABBN_02193 +MPHPSRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW +GVDGRPDAWEDTSFGTVATGPLIGLGMTGFLALVSAMVTALVPTDPGLSPWRRVRQAGVH +RGVQECLGWPCVLIVLVLAPMTAEVLAAGAWTMPWWLLPLTLTVLMVGVFPAMRVSTRRW +TRWSDRVAAELGYRPTAAELAEDEVWTPLGLKRDPDDPAVFPAKRPGYGVGVTVNLATPA +GRWLVRGFVAVFIVGLPLALWLGAFAAR +>LFPAFLNI_00197 +MTHPPHPVPADVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW +GVDGRPDAWEDASFGTVATGPLIGLGMTGFLALVSAMVTALVPMDPGLSPWRRVRQPGVH +RGVQACLGWSCVLIVLVLAPTTAEVLAAGAWTMAWWLLPLTLTVLMVGIFPAMRAGTRRW +TRWADRVAADLGHRPTAAELAEDEVWTPLGLKRDPEDPAVFPAKRPGYGVGVTVNLATPA +GRWLVRGFVAVFIVGLPLALWLGAFAAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000265.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000265.fa new file mode 100644 index 0000000000000000000000000000000000000000..63cc0060053a5d7b447a10594fc5643112d1da1e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000265.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00203 +MTTETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRLVG +VWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHSHI +PWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP +>MOLHKGIG_00196 +MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL +VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS +HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP +>NAFOICDF_00151 +MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARLVGVW +GNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHSHIPW +DTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP +>MHAAABBN_02192 +MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL +VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS +HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP +>LFPAFLNI_00196 +MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL +VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS +HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000266.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000266.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c0918ceda469070cab03cd34ccc72698276a03e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000266.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00204 +MTARAPLPPALARAAFGVDELLDAGLPWDRTRAADLHRIWRGVYTAADPAALTWDRAAAL +CRVTGGVISHTTAAAWHGIPLPRRLEASEELHLTVDRGRRQHRSARPGVVTHRLRLPPQE +IRQVGGGLRVTSPERTWLDLAVLLRPWELDWLVVAGDHLVHHPWHPDGRRPSATTPALLD +AALGRHVGRHGIRRAREALADVRVGADSAPETRLRLALIRAGLPEPALQIAVDPSDPRSP +EADLGYRDARIALQYDGAAHRTPEQQARDARREAYCLELDWLPLRCTQEDLREGFIRVIG +LVRRRLGPRGAFGATSRR +>MOLHKGIG_00195 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS +EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP +VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG +LVRRRLARTR +>NAFOICDF_00152 +MTARTPLPPALAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL +ARLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRSDLGGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMFRPHEVDWLIAAGDHLVRPPWTPTGRADPVATVPGLS +EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP +VVDLGYRAARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG +LVRRRLARTR +>MHAAABBN_02191 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS +EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP +VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG +LVRRRLARTR +>LFPAFLNI_00195 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLTRPAGLHLTFDRSARTHRTDLGGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIAAGDHLVRPPWTPTGRAHPVATVPGLS +EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP +VVDLGYRGRAWPSSTTAPATARLSSRRGTPVGTRTASSGNGRPCAAPGRTSALGSGGSWG +WSGVGSPARADPPPRPTRVELSRVPSNAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000269.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000269.fa new file mode 100644 index 0000000000000000000000000000000000000000..33bd7c4d372c7afca61a4047e84f5040bcdbc35b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000269.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_00208 +MTSELPSPSLSSAWAGRTDGDAPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST +ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG +ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGEGTRVGILNLDAH +FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRVLFDTAREHGVTWVTDE +QAQIADVTGVRRWVRSFIDAVDVLYLTVDLDVLPAAVAPGVSAPAGFGVPYEVIHACAVE +AATSGKLALADVVELNPSLDVDGRTAKAAARLIHTIVSRHRTDASLLA +>MOLHKGIG_00192 +MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTPQRDPGAGAPTSGARST +ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG +ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVAAGTRVGILNLDAH +FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE +QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE +ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA +>NAFOICDF_00155 +MSGVVRPSLRTRPSMAWNGAMTADRASELPSAALSPAWTGRTDGDAPEHLRWHQVVRSAD +GGAPAQTVDAAPARSTALVGFASDEGVRRNHGRVGAEDGPDALRGALASLAYLEGTGALV +DAGDVSVDRGDDDAPGELEAGQAELATVVSGLLNAHDLAVVLGGGHETAYASITGLTGST +RVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEEAEHQLSYAVVGISEANNTRA +LFDTARERGVTWVTDEQAQTADVTGVRRWVRSFIDAVDVLYLTIDLDVLPAAVAPGVSAP +AGFGVPYEVIHACTLEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDA +SLLA +>MHAAABBN_02188 +MTSELPSPSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST +ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG +ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH +FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE +QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE +ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTVVSRHRTDASLLA +>LFPAFLNI_00192 +MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST +ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG +ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH +FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE +QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE +ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000271.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000271.fa new file mode 100644 index 0000000000000000000000000000000000000000..da93ea90352a481e6ae467e8586e60d68b2aab86 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000271.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00214 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV +STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR +PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEA +LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR +DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER +RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ +EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH +>MOLHKGIG_00187 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV +STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR +PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA +LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR +DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER +RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ +EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH +>NAFOICDF_00159 +MTTTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTG +FGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVV +VETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEALAE +AGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDRVFV +PELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTL +AYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTD +RMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQEDH +VSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGVPGP +GPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH +>MHAAABBN_02183 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV +STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR +PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGEDGALRPAGEA +LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR +DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER +RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ +EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH +>LFPAFLNI_00184 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV +STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR +PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA +LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR +DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER +RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ +EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000272.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000272.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab7b4bd84494e838fccacf5ccf015ea8e77e1697 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000272.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00215 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPDADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLEAVREHAGWADVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDTDVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>MOLHKGIG_00186 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>NAFOICDF_00160 +MASTLITDIAELTTVDPEGRVLRDAAVVLDDEDVAWIGPAAQAPAADERVSVAGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGLTMEATRAASDERLRELVLGRVADAVR +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDVEDYLDDVV +GPMLEAVREHVGWVDVFCDTGAFDAAQTRRVLAAGVAAGLRARLHGNQIEQGPGVALAVE +FGAASVDHVNHLSDADVEALAGTWSGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>MHAAABBN_02182 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA +GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>LFPAFLNI_00183 +MRSTLITDIAELTTVDPEGRVLQDAAVVVEDERIAWIGAAADAPDADDRVSVGGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA +GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLEAVREHAGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000273.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000273.fa new file mode 100644 index 0000000000000000000000000000000000000000..ce42e5efbae5e53e539a0c000d8f60256554193c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000273.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00216 +MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD +HLVTWVRGLLGPADRWVGLAIIATGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF +GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL +GLMDIWLWYFFSALVVTFVVTAITVCIPPLSRIPDEVYPGAVHSPEQAVTRDRFRVALRA +AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGMIFYPL +FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI +LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT +>MOLHKGIG_00185 +MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD +HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF +GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL +GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPEQAVTRDRFRVARRA +AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL +FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLGARFVIGVVCVSAIIFFSAVVPAI +LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT +>NAFOICDF_00161 +MTHAHPADGELHTDTTAMAAIEADSPRPPARWRMVVYSLIGIVMFFVPVTINGASSIPLD +HLVTWVRGLLGPADRYVALALIAAGAVFPFATGRWRQSVTTTVFAFLGVVGLLTACMVVF +GFGPSWVLDKGIGPFLLDKLVIPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL +DLMDHWLWYFFGTLVVTFVVTAITVRIPPLSRIPDEPFPGAVHVPEEAVTQDRFRVARRA +AEQTLAEAPSLGRNVWLNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWVGLIFQPV +FWALGFSDPALMASASATSIAEMFIPATMLAGHEDFVARFVIGVVCVSAIIFFSALVPAI +LATDIPVKLWHLVVIWVERVVLTVLLATPLGHLVAALTS +>MHAAABBN_02181 +MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD +HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF +GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAAGFSTVSATFMVIVAKTL +GLMDIWLWYFFGTLVVTFAVTAITVRIPPLSRIPDEVYPGAVHSPELAVTRDRFRVARRA +AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL +FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI +LATDIPIPLWKLVVIWAERVALTILLAMPVAHLVAALT +>LFPAFLNI_00182 +MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD +HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF +GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL +GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPELAVTRDRFRVARRA +AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL +FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI +LATDIPIPLWKLVVIWAERVALTILLATPVAHLVAALT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000277.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000277.fa new file mode 100644 index 0000000000000000000000000000000000000000..ebec26014968e42f0247c0f2e1c289b6adc02c24 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000277.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00220 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGAELLVLPEEAMLGAREVGEEFPDAIAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRISPGDGGVAAIELDGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVVELADEREAVVTAEVTR +ERIDEVRKFLPSLANRRTDVL +>MOLHKGIG_00181 +MRISVGQFGPVGDVEENLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVATAEVTR +ERIDEVREFLPSLANRRTDVL +>NAFOICDF_00165 +MRIAVGQFGPTGRVEDNLEAMGRLAARAAAEGAGLLVLPEEAMLTFREVEDEFAHAVAGS +WEPFTEGLARLARQHGLAIVAGGYEPSATDRPYNTLVAVDADGAVAGAYRKLHLYDAFEH +RESELITPGDRGLVTVEVGGLTVGLQTCYDLRFPEVSRALALAGAQVLAIPAAWFAGEHK +VDHWRTLLRARAVENTVWVAAADTASAATVGHSAIIDPLALTLAEADDDAAPETLLCADV +TAERVEEVRRTVPVLANRRTDVLTPPVDVEPGG +>MHAAABBN_02177 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR +ERIDEVREFLPSLANRRTDVL +>LFPAFLNI_00178 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR +ERIDEVREFLPSLANRRTDVL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000280.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000280.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea070d709042478a45564f6e9fc588431385ca89 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000280.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00223 +MSTAAPHTQHSDSASPAPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM +TVIYMVFGALPHELFLMLMVGSLFLLPRVNPLDEQRGGIRLGRLLHTLLGVSWGSFALAA +ILFPDAGDHPDSAATTPVLMDLLGKSTAMDVGSVAGLALAAVSALTGLAVIVVCVVRRIR +AVR +>MOLHKGIG_00178 +MSTAAPHTQHSDFPSPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM +TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGVSWGSFALAA +IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR +AVR +>NAFOICDF_00169 +MAVPHPVMPPPGTPLPHQLRPAGPSVGTPRWLPAVLWIVAFALLPLCVIVGRFATENGGW +LLFTYIMFGWMVQGGLGVLAAASLFLLPRVNPPVERRAGVRTGVVVHLLLGASWLTGLLG +MLAFGDYGDAPGSETAPAPLVDLYGMDRAVEIGDAVGPPLVGISLLTGLAAVVLVVVRRL +AAAVRS +>MHAAABBN_02174 +MSTAAPGTQHSDFASPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM +TVIYMVFGALPHELALVLMVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGISWGSFALAA +IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGLVGGLALVAVSALTGLAVIVVCVVRRIR +AVR +>LFPAFLNI_00175 +MSTAAPGTQHSEFASPAPARKGPSVGTWRPWAVLPWALALLALPLIALALRSDFGANGWM +TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGLRLGRLLHTLLGVSWGSFALAA +IIFPDGGDHPESGATTPVLMGLLGTSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR +AVR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000281.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000281.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca717e35c9c7cc38a8c4aad3ea50f474df33adf4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000281.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00231 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEDEVVSRLGVTRTVDF +LVPAGAGVRELFRRHASGDDPDALVDHVDAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRCFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVNPATGAEHF +VFEGDQVAIDGVEVTYESLCGSCYLAESGGRLG +>MOLHKGIG_00152 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG +>NAFOICDF_00170 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPAVDTKGDAAVVSRLGVTRAVDF +LVPAGADVLALFRAHAAGDDPDALVDHVDAPPVACLLVDEAQFLEAGQVDDLLRIAVLED +VPVMAYGLRTDFRTHSFPGSARLLELAHSLEELKTICRCGRKAVLNTRKVVDAATGRSRF +VFEGDQVAIDGVEVTYESLCAACYLEESGGRLG +>MHAAABBN_02166 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG +>LFPAFLNI_00160 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000282.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000282.fa new file mode 100644 index 0000000000000000000000000000000000000000..694e3f6b62661ce057e6ff1e30af868a1b633e67 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000282.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00232 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDVVPVAPESSLVWALMAEDAWSEGR +TVDSYAYARVGYHRGLDALRKAGWRGAGPVPYDHEPNRGFLRALYSLGRAAAGIGESEEV +ERIRTFLKDSDPTAAEKIEATQGRSGS +>MOLHKGIG_00151 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEAGQGRARG +>NAFOICDF_00171 +MSESLIGKNLMEPPATLLPEEPEVLARLDAGDLPEDLVPLAPESSLVWALMAEDAWSEGR +AVDSYAYSRVGYHRGLDALRRAGWRGAGPVPWSHEPNRGFLRALYALGRAAAGIGESAEV +DRIRTFLKDSDPTAAQQIEAAQA +>MHAAABBN_02165 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNHGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEAGQGRAQG +>LFPAFLNI_00159 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEADQGRAQG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000286.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000286.fa new file mode 100644 index 0000000000000000000000000000000000000000..8bc443cd052da2ea293462c90776abf249916e80 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000286.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00236 +MMTRPLPEDSATVDAVALGRRVRHLRKQAGLTLDQLADRTGVSGSHLSLVENARREPRLS +LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL +EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAQRLLDAIGHTG +GPLGLHAVSSLAEHLGFTLSFVANLPHSTRSVTDLKHGRIHVSGGRASDHDRRTVVLQAL +AAAVLGHGEPRDYEDFLSQRVAVNYLAGALLMPQRPASALLRAAQKRRDLSVDDLKDAFG +VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGLVFPADHTGAIEGQAACRR +WGARQAFGRSDRFRAHTQYTDAPNGTYWCTSMVEHGPDGLFALSVGTAFEHARHFRGADT +RHRITSTCPDPRCCRLPDPALEAEWGGHVWPAARMHAHLLAAMPTQAFPGVDEVEVFEFL +ESQRDRTPGAPGADAPDGAGGVTP +>MOLHKGIG_00147 +MDHGNGPPLVKNVTFFPKHVISSPVPSTVPRMMTRPLPEDSATVDTVALGRRVRHLRKQA +GLTLDQLAERTGVSGSHLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELE +IEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAGLEAELRRRLEEQAATPEEARRANA +QLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDLPHST +RSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGA +LLMPQRAASSLLRAAQKRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHE +TGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQAFSRNDRFRAHAQYTDSPNGTFWC +TSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAWGGHV +WPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEEREG +>NAFOICDF_00821 +MATPTDPAHEPPRVDPLVLGRRLRHLRRVSGATLSDVAEKVGVTASHLSLVENGHREPRL +TLLTALADVHGVGVEDLLTPEAPSRRAALEVAVERAQRGPLFQRLGLPALKIGPRTPDEV +LEVIAGLQAELDRQMAERVSTPEEARRANSALREEMRACGNHYADLERRAQELREAVDVA +DGPLTHHHVSALAEHLGFAVRFVPDLPHSTRSVTDLKNRRIYLARARRPDHDPRAVLLQA +VCSSVLGHGEPADYADFLRQRVYTNYLAAAMMMPERGTVRALREAKERRDLSVDDLRDRF +GVSWESAAHRFTNLATEHLGLTCHFAKVHESGVFHKAYENDGIPFPTDHIGAIEGQTACR +HWTSRQVFSVADHLGAFPQYTDTPAGTYWSAAVVEPTSTGFYSLTVGVPFDDAKWFRGRE +TSARTRSTCPDPKCCRLPSAELEAAWGGQAWPAARANAHLLAAMPGGAFPGVEEVQVFEF +LQTQESRWPPEGSGAA +>MHAAABBN_02161 +MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS +LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL +EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG +GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL +AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG +VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK +WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT +RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL +QAQEEREG +>LFPAFLNI_00155 +MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS +LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL +EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG +GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL +AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG +VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK +WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT +RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL +QAQEEREG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000288.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000288.fa new file mode 100644 index 0000000000000000000000000000000000000000..979aebe880c4e5f2f04fb6b69e4f2606862e93a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000288.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00240 +MRAEQVTDPITYHGEGPVWAEHWGTAASGLAAGGGLRWVDMLAGDVLSLRADGAVERTHV +GDVAAVVRPRAGGGAVLAVERGFALMSPEGELTTLPELWGPEAGLRMNEGGCDPDGRFHA +GTMAYAKTPGAASLHRLSPGPDGGAGEVDVVLTGATTSNGLEWSPGGSLAYYNDTPTRQV +AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV +VEVPVQKTTACTFGGEDLGTLYITTSWENMERGEDPLAGALFAVRPGVTGLPARPFAS +>MOLHKGIG_00144 +MRAEQVTDPIAYHGEGPVWAASWGAAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV +GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC +GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTLAYYNDTPTRQV +AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV +VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG +>NAFOICDF_00174 +MRADQVTDPLCYHGEGPVWAESWGGLRWVDMLAGDVLSLGADGGVTRRNVDPKVCAVVRP +RVGGGAVFAVERGFALEDPDGTLHRLPPLWDDAAGLRMNEGGCDPDGRFYAGSMAYAKTP +GAASLHRLSPAPEGGAGEVDVVLEGVTTSNGLAWSPDGSLAYYDDTPTRQVAVFDYSREE +GLTNRRVLVDVLDGEGKPDGLCVDAEGGIWVAVISHGRIHRYTPEGVLDEVVEVPVQKTT +ACTFGGDDLGTLYITTSWEGMERGEDPLAGALFSVRPGVAGLPTLPFAG +>MHAAABBN_02158 +MRAEQVTDPITYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV +GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC +GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV +AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV +VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG +>LFPAFLNI_00152 +MRAEQVTDPIAYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRTDGTVDRTHV +GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC +GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV +AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV +VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000290.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000290.fa new file mode 100644 index 0000000000000000000000000000000000000000..851f05a02632ef134abc479d0e97f2afd719ab4b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000290.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00242 +MNSPRHAAPVVRDGRTLLPAHAVTTAPIAAFGLIGGYLTARETGIRPLGGVVLAAAGAYA +GRTWLAKRGPAVAGGLTALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDREGA +R +>MOLHKGIG_00142 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR +>NAFOICDF_00176 +MSKDTSTPVARDGKTLLPADAVTTAPIAALGLVGGYLVARETGIRWLGGVVLGAAGLYAG +RTWAAKGGPAVAGTLGALYLGGFGASHPLAKKIGAWPSVLSVAAASAGAAYAAVDRKDGR +R +>MHAAABBN_02156 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLATRGPAVTGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR +>LFPAFLNI_00150 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000291.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000291.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a25a1eb3ea78281fcd3a02df58367df502fd414 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000291.fa @@ -0,0 +1,37 @@ +>ACLBLIBL_00243 +MIDNAVYVDGRRVHAPSTLEDTWEAAEASGGMAWLGLYRPDADELRAVADELHLHPLAVE +DALEGGERAKLDRYGEDLFMVLHFQHAIRALPVIVEQLQGGARARLREEEHRREVGAPRT +GDVHEWDQDELSEEGVFEVENLRRLRDVHDHAVQINERVAAMRQMLANALELDSTLASKR +LAEQSIEQNEQVKQISSWAAIIFAPQLVGSIYGMNFDGMPELHWAFGYPFALGLMLAVAL +TLFVLFKRADWL +>MOLHKGIG_00141 +MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE +DALAGGERAKLDRYGEDSFMVLHPARYIDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA +AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR +RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL +SEQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNSALELDSTLASKRLAEQSIAQNEQ +VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW +L +>NAFOICDF_00177 +MTLIDNAVYVDGRRVFAPTSLSDTWDAIERTGGMAWLGLYRPHPDELQEVADELPLHPLA +VEDALTPGQRAKLERYGDDWFMVLHPARYIDATETVEFGELDVFTGKDYVVTVRHAEEPD +LADIRAGMEQRHTDRLAQGPSQVAFEILDHVVDAYFPVAEGLEQDIREIEDQIFSGDAAV +SRRIYELSREIIGFERATRPLPRMIEQLQEDMRARLGDAANGSHASHLEAPEPEPGEEER +AELVETLRALRDIHDHAVQVTDRVAAMRQMLENALELDSTLASKRLAEQSIAQNEQVKRI +SSWAAIIFAPQLIGSVYGMNFQHMPELEWPLGYPWALGLMLGVAVALYALFKKADWL +>MHAAABBN_02155 +MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE +DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA +AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR +RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL +SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ +VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW +L +>LFPAFLNI_00149 +MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE +DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA +AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR +RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL +SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ +VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW +L diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000294.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000294.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a45d47cf89da789e3d27badacfac440e88f0566 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000294.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_00246 +MRELQQQIIAEQGVRPQIDPAQEIERRVEFLVDYLEATGAAGFVLGISGGVDSTVGGRLA +QLAVERRRARLGAPDAVALGGPEAPRGAPAADEAPSPQRPQFTAVRLPYRQQKDEADARA +AMDFVDADREITLDIAAGVEGIASAFVEATGDEIADFDKGNVKARMRMVAQYALAGAHRQ +LVIGTDHAAEAVTGFYTKFGDGGADVLPLSGLNKRQVRALGRELGAPEHLWNKVPTADLL +DGNPGRTDEDELGMTYEHIDDYLEGGDIPEEAAEKLEGIWLRSRHKRTMPVTVHDDWWR +>MOLHKGIG_00138 +MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA +QLAVERRRAQLGVTDAVALGGPDTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD +ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA +HGQLVIGTDHAAEAVTGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA +DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW +WR +>NAFOICDF_00180 +MPEPYAGAMRELQQQIIAEMGVRPEVDPAAEVEARVRFLVDYLEATGASGFVLGISGGVD +STTAGRLAQLAVERRRAELGTEAGDDAAPSRENPRFTAVRLPYRVQADEADATAAMDFVG +ADGRVTLNIAEAVAGMASAFQEATGEPISDYNQGNVKARMRMVAQYAIAGAHGQLVIGTD +HAAESITGFFTKFGDGGADVLPLAGLDKRQVRAVAKELGAPEHLWAKVPTADLLDGSPGR +ADEDELGLSYEHIDDYLEGREIPEEAAEKLEGVWRRSRHKRTTPVTIHDDWWR +>MHAAABBN_02152 +MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA +QLAVERRRAQLGVPDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD +ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA +HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA +DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW +WR +>LFPAFLNI_00146 +MRELQQRIIAQQGVLPEIDPAAEVERRVAFLVDYLAATGASGFVLGISGGVDSTVGGRLA +QLAVERRRAQLGVTDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD +ARAALDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA +HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA +DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW +WR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000298.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000298.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed97688152c2730a57caf6c71eeffe2eee2c41b2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000298.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_00252 +MSESIPPSHPSAPPGPASAHPAAPAAGAADAREASGAVAPASSDAATGARVLLPWVFWPS +TIVVLLFVGATLLFPEPMTAAIGTVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGAIT +LGKPDEKPEFSTLSWFALLFAAGMGIGLVFFGMTEPLMHFVSPRPDLAATDPNPAQAAQA +ALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLALRWAFEPLLGERRVRGGWGHLIDN +IALIGTVFGVATSLGLGVTQMSAGLRSLGVVPEESAWVEYAMIGLVTLVVLYTVVSGVER +GMKWLSNVNLVLAAGLLLFIAIVGPTAFLFKEMVQSFGAYLQTFFGASLNVSAFQGAEGD +AWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRQFLAGVLLVPTLIGVVWFGVLGGTA +IYLETVRPDGYTSVVGADGSIDSNTALFQVVEQLPAGALLVIGAIMLSAIFFVTSADSGA +LVMGMLATGGDVNPKVPVKIFFAIATALMSAALLAAGGLSAIQTLAITIGLPFSVLMLVM +CLATFRSLGYSVARVEAVRRQAMLASIKDRFGLDTDDDEVVDGGPVAASQWWASLSRDRQ +RTIAQAASAGPDDEIRLAGSSAEEPAGSPDARR +>MOLHKGIG_00133 +MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAAGRDRVLLPWVFWPSAVIVLSF +VGATLLAPAQMTVGIGLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK +PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL +HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV +FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYVMIGAVTCVVLYTVVSGVERGMKWLSN +TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS +AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR +PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA +TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS +LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA +AGVPASEGPRRPRLRRHEH +>NAFOICDF_00188 +MTPAPAGRDADAPAANRPHRTGPDPDVKHPAPATADQADRGHAGLLPWVFWPSTLIVLLF +VVATLAFPAQMTDVIGDVQAAIIRNFSWWYAIVAFAFVVFCAYLVFSRKGSITLGKPDEK +PEFSTMSWFALLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTEAQAAQSALATTFL +HWGLQPWAIYAVVGVAVGLAIHRRGRPLSLRWAFEPLLGERRVRGGWGHLIDNIALIGTV +FGVATSLGLGVTQMAAGLRSLGIVPADSPWLEYAMIAAVTCVVMYTVVSGVERGMKWLSN +INLVLAAGLLLFIALVGPTPFLLKETVQSFGAYLQNFFADSLNVSAFYGAEGDAWQAGWT +AYYWGWWMSWTPFVGIFIARISRGRTVREFLMGVLLVPTLVCVVWFGILGGTAIWLETVR +PAGYTSVVGADGAIDSNSALFQVLEQLPAGLLLVIGAIILSGIFFVTSADSGALVMGMLA +TGGDVNPKTAVKIFFAIATAFMAAALLAAGGLSAIQTLAITIGLPFSVLMLVMCVATFRS +LGYSAARVEAVRRQAMLASIQDRLGKDTDDDEVVEGGPVAASQWWASLSRDHQRTIARLA +SPGPDDEIRLHEDATATSARPDTTRGGSTAR +>MHAAABBN_02147 +MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAADRDRVLLPWVFWPSAVIVLSF +VVATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK +PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL +HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV +FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN +TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS +AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR +PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA +TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS +LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA +AGVPASEGPRRPRLRRHEH +>LFPAFLNI_00141 +MSDPTPPLKNPLDPERADTRPSSAPTADGAVAPATSAAAARDRVLLPWVFWPSAVIVLSF +VGATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK +PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDVAAANPTQAEAAQSALATTFL +HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV +FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN +TNLILAAGLLLFIAIVGPTAFLLKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS +AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR +PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA +TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS +LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA +AGVPASEGPRRTRLRRHGH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000299.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000299.fa new file mode 100644 index 0000000000000000000000000000000000000000..78bb9a5413d0d2b92b1356d58d2dfc81a393bf17 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000299.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00254 +MPDSAPAPEPIAGERPSGGETALVVVDMQYSYFEHPDLAARQAELTEAVVELVRTAVEAG +RPVVLVRTEHERDRSTWTLNMLEDGEGFAFPGTRQAAVLDEVARAARGAVEVVKTRDSAF +HRTDLDAQLRRRGVGRLLLCGVSTHSCVFQTATDAFARDFHAATAVDAIASEDPRLSAAM +LEFLRDEMRQPLLGREDALALLRTGLVPDQG +>MOLHKGIG_00131 +MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR +TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA +ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE +MRQPLLGQDEALTLLRTGLVPDRG +>NAFOICDF_00651 +MNTLQNPALIVVDVQRGFDDVEYWGSRDNPDCETNISSLLTHWRDRSWPIVFVRHDSTNP +ESTLAVGTPGNEFKEVITGDPDLLVSKTVNSSFHGTPDLDDWLRAEGIEQVVICGITTNH +CCETTARIAGNLGYDTYFAIDATHTFDRPALDGTVLPAATVSAMTAANLHGEFATVVSTR +TLIDGNSYAPRYEQEK +>MHAAABBN_02145 +MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR +TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA +ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRAE +MRQPLLGQDEALTLLRTGLVPDRG +>LFPAFLNI_00139 +MPDSPSARATGGETALVVIDVQHSYFEHPALAAHQSELTAAVVELLRAAHEAGRPVFLVR +TEHARDRSTWTLNMLADDEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA +ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE +MRQPLLGQDEALTLLRTGLVPDRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000300.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000300.fa new file mode 100644 index 0000000000000000000000000000000000000000..55bd84fc042a73b848aa7486cb0274d6add2e317 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000300.fa @@ -0,0 +1,19 @@ +>ACLBLIBL_00258 +MSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWENPDTELFGLYEGVPLTER +AEMPWQMPDRIVVFRGPLTRHCTSRAELEHEITVTVMHEVGHFFGIDEERLHELGWG +>MOLHKGIG_00127 +MDHRPSPEQPAATWMSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWEDPAT +ELFGLYEGVPLTERAEFAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI +SEERLHELGWG +>NAFOICDF_00192 +METWMSEEEFDAAVDAALLRIPDELARLLTNVVVIVEDEYEPQRWEDPDTELFGVFEGFS +LAERAEAAWQLPDRIVIFRGPLTRHCRSRAELEHEITVTVMHEVGHFFGISEERLHELGW +G +>MHAAABBN_02141 +MDHRPSPDQPAATWMSEQEFDDAVSAALARIPDELARLLTNVVVVVEDEYEPQRWEDPAT +ELFGLYEGVPLTERAEFAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI +SEERLHELGWG +>LFPAFLNI_00135 +MDHRPSPEQPAATWMSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWEDPAT +ELFGLYEGVPLTERAELAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI +SEERLHELGWG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000302.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000302.fa new file mode 100644 index 0000000000000000000000000000000000000000..de12f6e92b0414158e23bc57a603ef8a0686759c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000302.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_00260 +MITPGVFAISSGTAEILPDPWTDGVYLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLAH +RFAPDAERLRVLHLGGAGCTFARWVTHTWPQAHQLAVELDAGLAELARTHFDLPRAPQLK +IRVGEAGQVLAGLREATREVVFRDVFAPADPLSLAPDSPHVTPAHLTGADAAAHAARVLV +PGGVYVLNIGGGPDLASVRREVAALRTAFAHVEVMADPAMLKGRRRGNVIAAASSVPLAA +EELGGRAALARALRSDALPAQLVDDVARFAGGLAPDPTPLVQASDGTSEGASTQASPGPA +Q +>MOLHKGIG_00125 +MSRRSGRSSGRSSAASSSSRGSAARRGRAAEPEGIVPGVHEISHGTAEIREDPYEPGAFV +LYVNGVESSPLDPDHPERMGFEYMRWAVAAVRAHWPEPTPLRALHLGGAGCALARWVDHA +HPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAP +DPTDLTGARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFE +HVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAE +DPRGFPAGVAPGITGLVPGPEA +>NAFOICDF_00194 +MITPGTFPISSGTAEIVPDPWTDGVFLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLTH +RFAPDARLRVLHLGGAGCTFARWVTHTYPASHQLAVELDAGLAAVAREHFDLPRAPQLKI +RVGEAGEVLAGLRDATREVVFRDVFAPDPADPTGALHVTPAHLTGLDAAAHAARVLTPGG +VYLLNIGGGPDLTSVRREVAALTETFAHVEVMADPAMLKGRRRGNVIAAASSAPLSADGL +GGRSALARALRSDALPAQLLDDVVAFTAGLTPDATPLVTPAEG +>MHAAABBN_02139 +MSRRSSARRGRAAGGSAGPAGIEPGVHAITHGTAEIREDAFEPDAFILYVNGVESSPLDP +ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA +GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP +PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG +RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI +TGLVPGPEA +>LFPAFLNI_00133 +MSRRSSARRGRAAGGAAGPAGIEPGVHAITHGTAEIRENAFEPGAFILYVNGVESSPLDP +ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA +GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP +PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG +RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI +TGLVPGPEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000303.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000303.fa new file mode 100644 index 0000000000000000000000000000000000000000..cd8cd559880ee905d0e26196c3ebe478a5ff3021 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000303.fa @@ -0,0 +1,23 @@ +>ACLBLIBL_00261 +MAVVVRPARREDAEALLRVKAQSWREAYGAHLPAEVFDRADARVPQDAPAWAALVGSDRD +LWVAEDDDGGRLVGVALAGPSRIEDEGLPPRELMVLYVLAEAHGTGVGARLLDAVVGDGP +AVLDVLAENPRARAFYAKHGFEDHGAPAPMDGAWAGLHEQRMVRRG +>MOLHKGIG_00124 +MAVTVRPATSDDVEPLLRVKAQAWREAYGGLLPAAHLDAVDAGVPEQVPGWAALVGSDRE +LWVADDGGRLLGMALAGPRRSQGGGLPDLELMALYVLAEAYGTGLGALLLDAVVGKRPAV +LRVLAENPRAVAFYAKHGFAPEGGPEPMTGPWAGLHEQLMVRRG +>NAFOICDF_00195 +MRETDGASDAVVRDVNPPSAPAPTVRPAGADDLPAVLAMKNAAWRETYAHLLEPGFLAAQ +EAELPRAVEAWTRLLGEPGMEVWLAEGAGVVVGMAAAGPADDPALGPEGRELIALYVRAR +LHGAGLGAALLRAAVGGRPARLDVLVGNERAIAFYERHGFVAVGEPAVLGGPWGDAREQR +MVRR +>MHAAABBN_02138 +MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEARIPEDVPAWTALIGPD +RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG +LGARLLDAVVGERPAMLRVLAENPRAVAFYAKHGFAAVGAPEPMTGPWAGLHEQLMVRRR +PHDGGAA +>LFPAFLNI_00132 +MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEDRIPEDVPVWTALIGSD +RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG +LGARLLDAVVGDRPAVLRVLAENPRAVAFYAKHGFASVGAPEPMTGPWAGLHEQLMVRRL +PHDGGAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000304.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000304.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd8b6d91d0a277e8e0a5aa935bb28eae79d99c2c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000304.fa @@ -0,0 +1,18 @@ +>ACLBLIBL_00262 +MIVAFSVAPSGTPADAAHQPGDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDWD +EVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS +>MOLHKGIG_00123 +MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD +EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR +>NAFOICDF_00196 +MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW +DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALTDGTPATPDRFR +A +>MHAAABBN_02137 +MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD +EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAPH +DGDAG +>LFPAFLNI_00131 +MIVAFSVAPSGQPADAEHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEWD +EVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAPR +DGDAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000305.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000305.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8ef8d36fbf03a08ca8599c512123c2d3c198b6a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000305.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00263 +MPHTADRGHPVHNPDIVGFTEAELNETPIKPRWNSLGPGIVAAATGVGAADLVATLTAGS +RYGYMLLWAVVLGVIFKIVLVEGVGRWYLSTGKTIFQGWRQLGSWTSWYFGPYILIWGFV +YGATAMSSTAIPLAALFPAVDAKVFAIAAGLIGLALVWLNKYGLIEKLMTALIGVMFVTV +LISAALTAPNVGEILSGLVPRIPSGDPQVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV +PKYMKVMKFDNATSYVLTGIFVIATMIMGVELLHSAGLAISSGDKGLLDVGNVLAERYGQ +VWSYVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPARFYL +LWLTILPMSLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNRKDVPVQHRNGWIRNIL +LGLTAAVFVAIGVNELIKALQSVLGG +>MOLHKGIG_00122 +MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS +RYGYMLLWAVILGVIFKIVLVEGVGRWYLSTGKTIFQGWRSLGSWTSWYFGPYILIWGFV +YGATAMSSAALPLAALFPGVDMKVYAIGLGLVGLGLVWLNRYGLIEKLMAVLIGVMFLTV +LLSAALTAPNVGDILAGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV +PKYMRVMKFDNATSYILTGIFVIATMIMGVELLHSAGLAISSGDRGLLDVGNVLAERYGQ +AYSVVFLVGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPGRFFL +LWLTFPPMTLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNKKEVPAQFRNGWIRNTL +LGLTAAVFVAIGVNELWKALQPLIGG +>NAFOICDF_00197 +MSHTTPPGHGLVDRHHPVHDPDIVGFTEAELNETPIKPKWNSLGPGIVAAATGVGAADLV +ATLTAGSRYGYMLLWAVVLGVVFKIVLVEGVGRYYLSTGKTIFQGWRGLGSWTSWYFGPY +ILIWGFVYGATAMSSTALPLAALFPGVDSKVFAIASGLVGLGLVWLNRYGLVEKVMTVLI +GVMFVTVLISAALTVPNLGDILGGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYGYWL +REKGWNTPKYMRVMRFDNTVSYVLTGVFVIATMIMGVELLHSAGIAISSGDKGLLDVGDV +LAQRYGDVWATVFLIGFFAASFSSVIGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS +KPGRFYLLWLTFPPMVLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNSRRVPGKFRN +GWVRNVLLALTTAVFLVIGGNELLKALKPLIGG +>MHAAABBN_02136 +MAHAVDPGRPVHNPDIVGFTDAELNETPIRPRWNSLGPGIVAAATGVGAADLVATLTAGS +RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV +YGATAMSSTALPLAALFPGVDSKVFAIASGLIGLGLVWLDRYRLIEWLMTVLIGVMFVTV +LLSAALTVPNLGAILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV +PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS +AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL +LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL +LGLTAAVFVAIGVNELIKALQPVLGG +>LFPAFLNI_00130 +MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS +RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV +YGATAMSSTALPLAALFPGVDSKVFAIAAGLIGLGLVWLDKYRLIEWLMTVLIGVMFVTV +LLSAALTAPNLGEILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV +PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS +AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL +LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL +LGLTAAVFVAIGVNELIKALQPVLGG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000308.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000308.fa new file mode 100644 index 0000000000000000000000000000000000000000..b022651639eddaa319ac2c046ca501a43091b2f2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000308.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_00272 +MPTPPTTSIETLRSGHPVVWSRPAAERPGTDLVLVLHGYGSNEVRAANRFFPMLPERCTG +LAVRGGFEIDAAATEGPGDPGAHGWFLLDLMLQSDFAQVVAAAHRVFDVLASEEVAQARF +RTVSVLGFSQGMAMATTLIRLRPEAFACGVGLSGFVVDNELLAVLDSPPEGPGPRPFFWG +RDVEDPVIHPDAVAHTRAWAEEHTLLTVRTYPGVLHGIGPEAVRDVRIFLDHSLRAATPD +T +>MOLHKGIG_00115 +MSPTPPPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPERCTG +LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF +RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG +RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG +S +>NAFOICDF_00204 +MSTGSAPESEPLASGGHAVWSRPEHERAGTDLVLVLHGYGSNEVRAARRFFPMLPERCTG +LALRGPFEIDAAAVEGPDDPGAHGWFLLDVLLQSDFAQVIAAAHRVYDALADDAVADAGF +RSVSVLGFSQGMAMATTVIRLRPEAFACGVGLSGFAVDNELLAVLDSPAEGPGPRPFFWG +RDAQDPVIRPDAVAHTAAWAEEHTLLTARTYPGILHGTGPEEARDVRIFLEHVLGGA +>MHAAABBN_02128 +MSPTPPPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPERCTG +LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF +RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG +RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG +S +>LFPAFLNI_00120 +MSPTPTPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPDRCTG +LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF +RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG +RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG +S diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000312.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000312.fa new file mode 100644 index 0000000000000000000000000000000000000000..8e80fef06710d09cb7600493f980768e0514c3c9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000312.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00280 +MSKRIQAKDVDVYYGKFKAVEGVNIDIAPRTVTAFIGPSGCGKTTFLRAINRMHEVLPGA +HVEGQLLLDGEDVYGPGVDPVTVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLSRS +RADEIVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSVAVSPDVILMDEPCSAL +DPISTLAVEDLINELKEQYTVIIVTHNMQQAARVADKTAFFNIQGIGQPGKLIEFDDTNV +IFNNPSNQQTEDYVSGRFG +>MOLHKGIG_00110 +MSKRIQAIDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA +TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS +RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL +DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTNV +IFNNPSSQQTEDYVSGRFG +>NAFOICDF_00221 +MSKRIQAKDVDVYYGKFKAVEGVSIDIAPRTVTAFIGPSGCGKTTFLRAINRMHEVLPGA +HVEGQLLLDGEDVYGPGVDPVTVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLTKS +RADEIVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSVAVEPDVILMDEPCSAL +DPISTLAVEDLINELKEDYTVIIVTHNMQQAARVADKTAFFNIQGIGQPGKLIEYAETNT +IFNNPSNQQTEDYVSGRFG +>MHAAABBN_02123 +MSKRIQAIDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA +TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS +RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL +DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTNV +IFNNPSSQQTEDYVSGRFG +>LFPAFLNI_00105 +MSKRIQAVDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA +TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS +RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL +DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTDV +IFNNPSSQQTEDYVSGRFG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000313.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000313.fa new file mode 100644 index 0000000000000000000000000000000000000000..3092bcef616adc88177d0dfbca3067cf28690c77 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000313.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00281 +MSTAIDDVSTRQDTPPSKHRQNSLTAGQKPGWVWMAIAAAAVLLGLGIEALLSGAAPFSE +DFSLARFVVLAGVLYIAGMYLVTRVMENRRRASDGLWKNLVWTAFLIALVPLVSVIWTVL +EGGGPTLLSNPQVLWNDMDGVTGATDAAYDQAGSPAGGLPGGFAHALIGTLVITIIATLI +AVPIGLLASIYLVEYGRDGWLSRAITFFVDVMTGIPSIVAGLFAYAAMTVLLELIMGPGP +AALQAVKMGFTAAVALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLP +TAISGIASGVTLAIARVTGETAPILVTAGYAMTTNWNAFDNWMTALPVYIYRQIVSPTSP +TAADPSMARAWSAALVLIFIVMALNLLARVIAKAFAPKTGR +>MOLHKGIG_00109 +MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV +IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI +ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT +SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM +GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS +GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA +RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR +>NAFOICDF_00222 +MSTALNDTPTRENTPASKHTQNSLTAGQKPRWTWMAVAAGAVVLGLGLEALLAGGFADFS +IARFIILAAILFVAGMYVATRVLENRRQATDGLWRNLVWAAFLIALVPLISVLWSVVADG +GATLFGNPQLLVNDMQGVTGVTDAQYVQAGEPMGDLPGGFAHALVGTFLITVIATVIAVP +IGLLTSIYLVEFGRDGWLSRAIIFFVDVMTGIPSIVAGLFAFAAMSVVLEMVMGSGPKAL +QSVKMGLTAAIALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLPTAI +SGIASGITLAIARVTGETAPILVTAGFASAVNWNPFDNWMTALPVYIYRQLVAPTSPTAM +DASTSRAWAAALVLIIIVMVLNLLARIVAKAFAPKTGR +>MHAAABBN_02122 +MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV +IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI +ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT +SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM +GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS +GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA +RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR +>LFPAFLNI_00104 +MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV +IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI +ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT +SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM +GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS +GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA +RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000314.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000314.fa new file mode 100644 index 0000000000000000000000000000000000000000..84c0e5a5460de3cdb236cc177ef7408c05fe0b79 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000314.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00282 +MTSPATEAPPRATTLKSSRGGAAGDKVFSGLSLAAGVLILLTLAFVAIFLVVRSLPALFP +DAYGTQLKSADTFFQYVWPLMAGTIMAAVIALLLATPVAVGVALFISHYAPPKIAQPVGY +VIDLLAAIPSVIYGIWGWLTLAPVMVPIYQWLNEYLGFIPFFGGPVTGTGRVIMTSGVVL +AVMILPIITALCREIFRQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSVMLGLGR +ALGETMAVTLVLSAGGFSLSLIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVIT +LVVNMTARWIVNKHKEFSGAN +>MOLHKGIG_00108 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID +LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM +VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG +ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV +NMIARAIVNKHKEFSGAN +>NAFOICDF_00223 +MSHTATEAAPSSSALKSSRAGAAGDKVFSGLALAAGVLILLILAFVAIFLVSEAWPALFP +AEGANLESGDSFWGYVWPLMAGTVMAAIIALLLATPVAVGVALFISHYAPPKIAQPVGYV +IDLLAAIPSVVYGIWGWLTLAPLMVPIYEWLNEYLGWLPFFGGSVTSTGRVLMTSGIVLA +VMVVPIITALCREIFSQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRA +LGETMAVTMVLSPGKFSPSVIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVITL +VVNMVARWIVNKHKEFSGAN +>MHAAABBN_02121 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID +LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM +VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG +ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV +NMIARAIVNKHKEFSGAN +>LFPAFLNI_00103 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID +LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM +VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRALG +ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV +NMIARAIVNKHKEFSGAN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000315.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000315.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5e096ccf67060c2a72d2ee959858069b301de06 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000315.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00283 +MKALRFGRSAALLSVAALALTACGGNGGGDASSSAPAGGSSSAAAEGSGAAAASGTLIGG +GASSQEAAMTAWSEGVKATSPELTVQYSPDGSGAGREGFLGGAFSFAGSDAALKEDEAEQ +AKQICGDNGAFHVPAYISPIAIAYNLEGVDEVKMDAETIAKVFSKEITTWNDPAIAEQNE +GVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWKYDEVETWPSEITAESAQGTRGVV +GQAAQTDGAITYADASAVGELGTVAVKVGEEYVPYSSDAAAKTVSASVQNEDGSIELDRA +TTEAGVYPIVLVSYHIYCNQYQNQETADQVKAFASYVVSEDGQKAAEEAAGNAPIGAETR +DAAVERIEAITAG +>MOLHKGIG_00107 +MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS +QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKEN +CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL +PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS +QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES +GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM +ERIEAISVKG +>NAFOICDF_00224 +MKALRFGRSAALLSVAALALTACGGGNDSASSSSSAASSSAAGSSSASSSAAGSSSASSS +AAESSSASGSSSAAQGGYAIDVPTASGTLMGSGASSQEAAMTAWTEGVKATSPELQVQYS +PDGSGAGRKAFLSGAATFAGSDAALKDEEKTQAQEVCGPDGAFHVPAYVSPIAVAYNLEG +VDSLNLDADTIAKIFSKKITKWNAPEIAALNEGVELPDTAITVVHRADESGTTENFTAYL +DQVAPEAWTYGKVKEWPGDITAESAQGTKGVVSQAAATNGAITYADESGVGSLKTAKVGK +DGKFAEISPEAAAKIVADGKKQDDGSIELDRANAGEGVYPIVLVSYHIFCNQYGDQETVD +QVKAFASYVISEDGQKAAQEASKSAPLDAELAKEAKTRIDAIKVG +>MHAAABBN_02120 +MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS +QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKKN +CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL +PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS +QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES +GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM +ERIEAISVKG +>LFPAFLNI_00102 +MKAHRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEHASGSAGGEQGTTSEVQG +NLVGAGASSQEAAMTAWTQGVTEIAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKE +EEAESAKENCGDEGAFHVPAYISPIAVAYNLPGVDEVKMDAETIAKVFSGEIKNWNDEAI +AAQNEGVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQG +TKGVVGLASQTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSI +ELDRATDESGVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPI +SEDTRKKAMERIEAISVKG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000318.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000318.fa new file mode 100644 index 0000000000000000000000000000000000000000..476662be7c5bc22e28bc90808ad01b2039c21fd7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000318.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00287 +MPAHETAVPPSVDVPRLHDAVLDWFAVHARDLPWRSPDCPPWGVLVSEIMLQQTPVARVL +PRWHAWLERWPTAADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHSGEVPADPA +ALRALPGIGEYTAAAVSSFAFGLPETVVDTNVRRVIARAVGGQALPGRSLTRAEMRRAHA +LMPEDPDRAQAWNAGVMELGALVCTARSPACERCPLADACAWVAAGSPPPEQAPRGQAWA +GTDRQVRGAVMAAVREHGRVAGDGLRAVVVAGGRLGAHRPGDAQWERCVAGLLADGLLAR +DDDGALAFPS +>MOLHKGIG_00103 +MPAPAPLVPPTVDVPHLHDAMLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAVVGRHDGRVPADPA +ALRALPGIGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR +DDDGGLTFPA +>NAFOICDF_00233 +MPAHDDAAPRPDLTALQDEVLDWFAAHGRDLPWRDPDCPPWGVLVSEIMLQQTPVVRVLP +RWRAWMERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHGGEVPADPAA +LRALPGIGEYTAAAVSSFAFGIPETVVDTNVRRVLARALRGEGLPGRTLTRAEMAAAHAA +LPADEHRANRWNAAVMELGALVCTARSPACDRCPIRARCAWVAAGSPAPEVARRGQAWVG +TDRQVRGAVMAAVREHGRVPRGGLREAVDGTGRLGAHTPDDAQWERAVAGLLGDGLLVAH +DDGALAFPA +>MHAAABBN_02116 +MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA +ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR +DDDGGLTFPD +>LFPAFLNI_00098 +MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA +ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPTRANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGWLGSHRPEDAQWARCVAGLVSDGLLAR +DADGGLTFPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000319.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000319.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a8dde84efa618ec587630ab694c8f497edf56ac --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000319.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00288 +MPADRQITLRSARTGDVPAIRALVEPLAQERVLLQKEAVAFYEAIQEFVVAEDADGSLAG +FGALHVMWQDIAEVRTLAVSRDHRGAGVGHLILEELLRRARVVGVERVFCLTFEVEFFRR +HGFAVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRTL +>MOLHKGIG_00102 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EADGTLAGFGALHVMWQDIAEVRTLAVSEAHRGTGVGHLIIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL +>NAFOICDF_00234 +MPAAPVVTVRPARTQDVPAIRALVSPLAERRLLLQKEAVAFYESIQEFMVAEAEDGSLAG +FGALHVMWQDIAEVRTLAVADAWLGAGVGHRILTALLERAREVGVARVFCLTFEVEFFRR +HGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRSL +>MHAAABBN_02115 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EADGTLAGFGALHVMWQDIAEVRTLAVSEAHRGAGVGHLIIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL +>LFPAFLNI_00097 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EPDGTLAGFGALHVMWQDIAEVRTLAVSEAHRGAGVGHLVIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000321.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000321.fa new file mode 100644 index 0000000000000000000000000000000000000000..c15d44e17da7fd67020e35d1028ea0bb8a326941 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000321.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_00291 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVKLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG +DVPETLKDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT +EILRGLRDRYEAHHRVSITDGALKAAATLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT +VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLEDERRQKEEAWRTGADSDV +ATVDEELIAEVLSKSTGIPVFKLTAEETDRLRTMEDELHKRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD +VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQAAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFGFSGGREALEGAELPELEPG +SGETVEAGRSA +>MOLHKGIG_00100 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG +DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT +EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT +VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV +ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD +VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELESG +AGDPVDADRSV +>NAFOICDF_00237 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLAAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGSEGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAQEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIERG +DVPETLKGKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT +QILRGLRDRYEAHHKVSITDGALSAAASLADRYISDRHLPDKAIDLIDEAGARLRIRRMT +VPPEVKAYEERIAEVKAQKEAAIDGQDFEGAARLRDQEKQLEEEREQKEQAWRAGQDAAV +ATVDEDLIAEVLSLSTGIPVFKLTEEETDRLRNMEAELHQRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHADLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSSTDTSTGYERMKGKVREELRQHFRPEFLNRVDD +VIVFPQLQKHEIVEIVDLFVSRLAKRLAEQDLSIELTPAAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFAGGRAALEGDDAAEPAAL +PAAADAPVEGREAPGADVPRGDDAGQDGPEAGGALGARLD +>MHAAABBN_02113 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG +DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT +EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT +VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV +ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD +VIVFPQLQKHEIVQIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDTTGEGEGAELTFAFSGGREALEGADLAELEPG +AGDPVDADRSA +>LFPAFLNI_00095 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG +DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT +EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT +VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV +ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD +VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELEPG +AGDPVDADRSV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000322.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000322.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea80d1d75c979c307c692eba2d25ea222bdf36be --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000322.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00293 +MATFWEYFSVLAPSIGLGLIFWLVMRSLLRSDTAERESMGRRSTGEDARAAREEADAREW +ARRRGGDDVPRRGDDSR +>MOLHKGIG_00098 +MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW +AARRRAEGGPGADPEDRAR +>NAFOICDF_00238 +MAAFWEYFSVLAPSVGIGLVFWLVMRSLLRSDTAEREARQRRGEDARAAREEAEAREWAA +RRRGDAPAGPGGAERP +>MHAAABBN_02111 +MADFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW +AARRRAEGGPGADPEDRAR +>LFPAFLNI_00093 +MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW +AARRRAEGGPGADPEDRAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000323.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000323.fa new file mode 100644 index 0000000000000000000000000000000000000000..f2dcf1188c86658f32a9dbbb55d5f90c960f1109 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000323.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00294 +MTSQNSANPQTSAVDHHDQQAVRAAKREQLLAAGREAYPVQVPRTHTLTEVREQFDGHEP +DWASGETVSVTGRVVFLRNTGKLCFATLQESGVDGEAVRLQVMVSLAAVGEDSLAQWKKA +VDLGDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIV +RDEARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLIHGGALARPFETHLNAFDQPMTL +RIATELYLKRAVVGGIDRVYEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQE +IILAAADAVGAGRRIETDRGVIDLDGEWAWVSVYPGLSEAVGREITPDTDAETLRAIAAE +HEVKVDPAWDAQKLVIELFGEIVEPTLMNPTFVHDYPPAAQPLARPHREDGRVIEAWDLI +IGGMERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGL +GIDRLVMLFTDAGIRETILFPLLKPEA +>MOLHKGIG_00097 +MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWT +SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLAEWKKVVDL +GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVREE +ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA +TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL +NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPETDAETLRAIAAEHEV +KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSDDRVIEAWDLIIGG +MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID +RLVMLFTDAGIRETILFPLLKPEA +>NAFOICDF_00239 +MTPENPAPAAVDHHDQQAVRAAKREQLLTSGRQAYPVQVPRTHSLAAVRAKFDGKHEAGW +EEGPEVSVTGRVVFLRNTGKLCFATLQESGAAGEAVRLQVMVSLAEVGEESLGEWKKSVD +LGDFLSVTGRVIVSRRGELSIQAAAWEMASKALRPLPVLHADLNEETRVRQRYTDLIVRD +EAREMVYKRAKITSAVRRTLESHGYVEVETPILQLVHGGAQARPFETHLNAFDQDMTLRI +ATELYLKRAVVGGIERVYELGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMADRIKEII +LNAADAIGAGRRIETSRGVIDLDGEWAWVSVYPGLSEAVGREVTPDTDAETLRAIAAEHD +VKVDPKWDAQKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPNRDDDRVIEAWDLIIG +GMERGTAFSELIDPVIQRERLTEQSLKAADGDDEAMQLDEDFLRALEYGAPPMGGIGLGI +DRLVMLFTDAGIRETILFPLLKPEA +>MHAAABBN_02110 +MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWT +SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLAEWKKVVDL +GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVRDE +ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA +TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL +NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPDTDAGTLRAIAAEHEV +KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSDDRVIEAWDLIIGG +MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID +RLVMLFTDAGIRETILFPLLKPEA +>LFPAFLNI_00092 +MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWA +SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLADWKKVVDL +GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVREE +ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA +TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL +NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPETDAETLRAIAAEHEV +KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSEDRVIEAWDLIIGG +MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID +RLVMLFTDAGIRETILFPLLKPEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000324.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000324.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee850e3d4304817f6aa5bdcd2ea24943956e95ed --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000324.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00295 +MSPRFLLMTEIPEPGLGMLREAGEVTLGSEVGGNDALPALAASGDYDVVVCALAQKFDAD +VLAQARLKGIANYAVGYNNVDVAAATEAGIAVGNTPDVLTDATADIALLLILGVSRRAHE +GEAMMRAGEFTGWRADLLVGKDVKGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAPEELGELAGRVEQVRWEELVERSDFLSLHVPLTADTEHLVDADVLARMKDDAVLIN +TARGPVVDEAALVEALRAGRLFGAGLDVYEDEPAMAPGLAELDNVMLLPHLGSATRDTRA +AMAELTARNAIAMATGGEVPALVNPDVRR +>MOLHKGIG_00096 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMEVVFAPRPPAH +REVAAAELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDADVIAKMKDDAVLVN +TARGPVVDEAALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEAPALVNPEVRG +>NAFOICDF_00240 +MSPRFLLMADLPEPGLGMLREAGEVVRGGDVGGNAALADLCASGEYDVVVGALDQRYDAD +LLARARVKGIANYAVGFDNVDVPAATEHGILVGNTPDVLTAATADIALLLILGVTRRAVE +GERMMREGRFEGWRADMLVGKDVVGATLGLAGFGRIGRAVAERALAFGMEVVFAPRPPAH +REVPAEELGDLAGRVRQVRWEELVETADVLSLHVPLTEDTRHLVDEDVIARMKDDAVLVN +TARGPVVDEAALVTALREGRLFGAGFDVYEDEPAMAEGLAELPNVMLLPHLGSATRDARA +AMAELTARNAIGMATDGEAPALVNPEARG +>MHAAABBN_02109 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN +TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEVPALVNPEVRG +>LFPAFLNI_00091 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN +TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEVPALVNPGVRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000326.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000326.fa new file mode 100644 index 0000000000000000000000000000000000000000..035d3545102324315c0b0792467ce5412240c488 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000326.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_00297 +MAERGHGDDRGLDGVGAERGDAGGEIDGFEAAVRGLEDAFARMVRQHRQVVTRQAAALKP +GLSAGAMKAFITLCNAGTMTPSTLAEHLLLDRAQVSRMVRDLEDEGLITREPDPVDRRSA +LLTATEEGRARLDAVRGGPAGEGLRADLAHWDRADIHTLVRLLGRLVEEQQARVDRTPDA +G +>MOLHKGIG_00094 +MADGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM +LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL +DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE +>NAFOICDF_00242 +MADPADHGSDGRGTGADAFAPEAFDAAVRELEGSFNRLVRQYRATLARQAEAVHPGLPLG +AMKAFVAICHRGPLTPSDLAEHLMLDRTQISRVLKDLEGDGLIHREPDPRDRRSALLTAT +DEARARLDAVRQGPAGGGTRARLQRWDLEDVRALSALLRRFVDEREDPAADDACRP +>MHAAABBN_02107 +MVDGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMARYAEALSPTLSVGAMKAFMM +LANEGTMTPSAVAEGMLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL +DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE +>LFPAFLNI_00089 +MADGAPDPGRGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM +LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL +DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000327.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000327.fa new file mode 100644 index 0000000000000000000000000000000000000000..0f56015ffba1fb6c200f7b1e3fd118de1695075c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000327.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_00298 +MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR +EVGAGFDPAQARVDATAAAGAEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETV +EARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLVNTGALNDAGNPDRMLLHLLQ +GGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL +HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQAL +LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAF +VNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRSIDELEWMSEETRQRALEKLS +MFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV +NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGR +LEDWWTQEDRAAFTELTSRLVAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL +EIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVTRIASDPHSPNEFRCNQVVKN +IDAFHEAFGTQEGDPMWLAPEERVTIW +>MOLHKGIG_00093 +MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR +EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV +EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ +GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL +HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL +LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF +VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA +MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV +NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR +LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL +EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN +LDAFHEAFGTREGDPMWLAPEERVTIW +>NAFOICDF_00243 +MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAAR +DAAMAAPAPEVEAPAQDEASQDPAAAERAARERIAVLWSAFMDEEAVEAAGILPLAADLE +AVDAVASPAELLALSGRLQREGVSGLIGTGALNDAGDPERMLLHLIQSGLGLPDESYYRE +EAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAHHWDVVRSRDAVAR +YNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWK +AWLTLQVLRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLY +VARHFPEGHVAAMDQLVGLLLEAYRRSIDALDWMGEQTRQSALEKLAMFRPMVGFPETWR +DYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTVNAYYTPLENAIVF +PAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAF +AERTGRLVAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTED +ESSGDREFFQAWAAVWRQLTRPETMVTRIASDPHSPNQFRCNQVVKNLDAFHTAYGTREG +DPMWLAPEERVTIW +>MHAAABBN_02106 +MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVR +EVGAGFDPAQARVQATAAAGAHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETV +EARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ +GGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL +HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL +LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF +VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA +MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV +NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR +LEDWWTEEDRAAFTERTSRLVAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRAL +EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN +IDAFHEAFGTREGDPMWLAPEERVTIW +>LFPAFLNI_00088 +MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR +EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV +EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ +GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL +HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL +LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF +VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA +MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV +NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR +LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL +EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN +IDAFHEAFGTREGDPMWLAPEERVTIW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000328.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000328.fa new file mode 100644 index 0000000000000000000000000000000000000000..483491737fee68e05955b87e48965ff46c20b874 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000328.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00299 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV +SLTYDWTAVTDPELLEKNLFPMVSEEQMEESLAKLASAVA +>MOLHKGIG_00092 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTVV +SLTYDWTAVTDPELLAKNLFPMVSEEQMEESLAKLAAEVG +>NAFOICDF_00244 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV +SLTYDWTDVTDPELLAKNLFPMVSEEQMEESLAKLASEVG +>MHAAABBN_02105 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV +SLTYDWTDVTDPELLEKNLFPMVSEEQMEKSLAKLAAEVG +>LFPAFLNI_00087 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTVV +SLTYDWTAVTDPELLAKNLFPMVSEEQMEESLAKLAAEVG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000330.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000330.fa new file mode 100644 index 0000000000000000000000000000000000000000..72901dfbdfe21e993059f01f7380336a68f36dfa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000330.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00301 +MTPLDRVPDRTPVPPRTGLTLEDQVPEAGGTRPRLTTTKADFRAAVAELVGRAAAEDPGE +EVSVGLVPTMGALHGGHAALARQARSENDVVAASIFVNPLQFGDRADLEHYPRTLEADLD +LLGAVGVDVVFAPSVDEMYPGHPDAPIVSVSAGRMGEVLEGASRPGHFDGVCTVVAKLWN +LSMPPAPAVLRSYFGQKDAQQLAVLRRLAHDLDVAVDVRAVPIVRSPEGLALSSRNTRLD +EAGLHAALVLNRALTRLEEAAVAGRVLDVQAAREEVAAEPGVTLDHLVVVDRETLEELGA +ELLCQPLRRDALALVAAHVPPVRLIDNRVLPAAGPLP +>MOLHKGIG_00090 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS +RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT +FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP +>NAFOICDF_00246 +MTPLDRTPDRRPVPAGTGLTLEDALPVADGARRPRLARTVAEARAALRELTAAAGQERGG +APVVVGMVPTMGALHGGHAALIRQARAENDVVVASIFVNPLQFGDPADLENYPRTLEADL +DLLGAAGADLVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGVSRPGHFDGVVTVVAKLW +NIVRPAVPALRSYFGQKDAQQLAILRRLAHDLDVDVEVRAVPIVRSPEGLALSSRNTRLD +ADGLEHALVLSRALRALVDAAEAGEPIDVRAARQMVSDEPGVTLDHLVVVDRETLEELGP +ELLCQPLRREALALVAAHVPPVRLIDNMVLPAAGPLP +>MHAAABBN_02103 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS +RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT +FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP +>LFPAFLNI_00085 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS +RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT +FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000331.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000331.fa new file mode 100644 index 0000000000000000000000000000000000000000..089cc064e71bd647a159f148ecfdeee3cd4fbc48 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000331.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00302 +MTTSNNPDEIRAEIERTRHQLGQDVDALAEKVSPTKAVSRQTNRMKDGLLSVKENIMGSP +EDHGRQPSMGDRAHAAADDARASMHGAADQARDAMGHASDRVSGWADDAQHAVQQAPAQL +RGRTAGNPLAAGLIAFGAGLLVSSLIPASRVEQRAAEGLKEQAAPLVDEAKQVAQQLRED +LEPVARDAAQSVKESATEAVDHVKADGADKAQDLKAESQDAARQVKGAAQDG +>MOLHKGIG_00089 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHAVVDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQAPAQL +RGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAKQAAQQLRED +LEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA +>NAFOICDF_00247 +MTTSSNPDEIRAEIERTRHALGQDVDALAEKVSPTKAVSRQTNRVKDGFITVKENIMGTP +EHHEGPGAVDRARFAAQDAAGQVQGTAHDVADQARGYAQQAGEAASQWVDDAQHAVQQAP +AQVRGRTAGNPLAAGLIALGAGWLIGSLIPASPVEKRAAERVKDQAAPLLESAKQEAAQV +AQDVREQVEPEVRDAAASLKDSAAESVQSLKSEGAEKAQDLKGSSQDAAQQVKHAAKHA +>MHAAABBN_02102 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHGVIDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQAPAQL +RGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAKQAAQQLRED +LEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA +>LFPAFLNI_00084 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHGVIDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQLALQQAPAQL +RGRTAGNPLAAGLIAFGAGLLLSSLIPASRVEQRAAEGLKEQAAPLVDEAKQAAQQLRED +LEPAAREAAGSVKESAAEAASHLKEQGTDTAQDLKAESQDAARQVKDTAKDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000332.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000332.fa new file mode 100644 index 0000000000000000000000000000000000000000..55fb50e6d834de3bc3e08755aa8b5bc52c919719 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000332.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00303 +MSTPYEPIRDATPHAGAHTPPPTQAEFRAEHESLGEMFKSLSSRLSTLVSQEIALAKAEA +TESAKKAGTGAGLLAGAAVGGFFLLMFLSLALMWALGSAMHLGWAALIVAVLWGVCAAVL +ALMGKKHLEKIKGLPQTQETLQEIPETLNPAKETR +>MOLHKGIG_00088 +MSTAHEPFRDATPHSGAHTPPPTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA +TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL +AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR +>NAFOICDF_00248 +MSHATPNGGAPRHADPAAHQSTPAAGAHTPPPTQAEFRAEHESLGEMFSSATEKVSLLMR +QEIALAKAEATDSAKKAGKGAGMFAGAAVGGFFLLMFLSLALMYALGSLMPLGWAALIVA +VLWGVVAAVLALQGKKNIEKIKGLPQTQETLQEIPETLNPAKETR +>MHAAABBN_02101 +MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA +TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL +AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR +>LFPAFLNI_00083 +MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA +TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL +AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000334.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000334.fa new file mode 100644 index 0000000000000000000000000000000000000000..d875c28ae37146b8169390c3782708f5799ef9b3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000334.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_00305 +MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER +LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ +VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKSAQRGLQVR +>MOLHKGIG_00086 +MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKTAQRGLKVR +>NAFOICDF_00250 +MTALRTTARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAERPDVVAHRGASAYRPEHT +LAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRKTTKTVDGVE +ITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREELSAKYGREI +GIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAEMNTRLGLQA +DTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQVIALNQDGS +LGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYITEVLDAGVDG +FFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPAGLAAAAAGV +LVALRRRLTAAR +>MHAAABBN_02099 +MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLQGR +>LFPAFLNI_00081 +MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLKGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000335.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000335.fa new file mode 100644 index 0000000000000000000000000000000000000000..03476ce46a5552571db10e9438a4721659050350 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000335.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00307 +MTEQPEMHPLSEPEQEWVRVRREFAAQEGVDHLDLDAVAAYYDGVLARSVSEAEALDPDE +LAVLLDVVAVLLGEHLGARHGMQWVTVSDDEGPALALRDTLSDAVVFPQPAVGQAWNEQV +TGAWLGEYVDWLGEQLQGIRAGDRPDGVAQQG +>MOLHKGIG_00084 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEADELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNDQA +TGEWMGGYVDWLGEQLQQIRADAGTLPGA +>NAFOICDF_00251 +MSEQQIRPLTAAEQEWVAVRRDFAAQEGTGHLDLDAVDAYHGRLLARSRSEDVDPDELGV +LLDVVAVLLGEHLGARHGLAWVAVTEGDATDLGLRDPLSDAVVFPQSVVAQHWNDGDAHW +IPGYVDWLGAQLAPLREERRAAEG +>MHAAABBN_02097 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEAEELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNHQA +TGEWMGEYVDWLGEQLQQIRADAGTRPGA +>LFPAFLNI_00079 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEAEELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNHQA +TGEWMGEYVDWLGEQLQQIRADAGTRPGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000336.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000336.fa new file mode 100644 index 0000000000000000000000000000000000000000..811d33dc6d237274028393aeb117a64e827ea2ba --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000336.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00311 +MTGGLDLTLDPTDPTQRPGRLGVGVVGAGRVGAVLGAALRNAGHTITGVHAVSEASRTRA +EALLPEAPVLEIPEILRRSEMVLFAVPDDVLPELVAGLAAAGHVQTGHLVVHTSGRHGVG +ALNPVRAHGAIPIALHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALAVEMGGEPV +VIKEADRGVYHAALSHGSNHLVTLTAQAAQLLRSIGVQDTERLLRPLMHASLENALADGD +GALTGPVARGDVETVRGHRETLRELVAEGMPADVLAVWETLARATADRAEARGALRPDVA +ARLREALAPDA +>MOLHKGIG_00082 +MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA +EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG +VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV +VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD +GALTGPVARGDVDTLRTHRETLGELEAGGLPPDVRAVWETLARATTDRAETRGTLRADTA +ARLREVLDDSDDPHDD +>NAFOICDF_00252 +MSRMDMSPELTGADPADRPGRLGVGVIGAGRVGAVLGAALRGAGHTITGVHAVSEASRTR +AEALLPGVPVLELPEILRRSEMVLFAVPDDALPELIAGLAAAGHIQTGHLLVHTSGRHGV +RVMDPVRAHGAIPLAVHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALVVEMGGDP +VVVKEADRAAYHLALSHGSNHLVTVTAQARQILEEIGVAEPERMLRPLMQASLENALTDG +DGALTGPVARGDVETVRGHRDTLRELVDGGMPADVLAVWESLARATAQRAARRGALRADA +AERILAVLDGADDGPDATG +>MHAAABBN_02095 +MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA +EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG +VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV +VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD +GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA +ARLREVLDDSDDPHDD +>LFPAFLNI_00076 +MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA +EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG +VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV +VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD +GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA +ARLREVLDDSDDPHDD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000337.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000337.fa new file mode 100644 index 0000000000000000000000000000000000000000..15e45f3dca4b15251c91566b3242748154ad5dd4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000337.fa @@ -0,0 +1,56 @@ +>ACLBLIBL_00312 +MSAAAPVPATRPADDDGWARVHPASPWVRGWTFLLLILFFLGRNAVEDFAAGRFGAGAGG +GSGEGEGSLLVAGGILLGVTLLVSLAFFFSWWFTRFRIGEDQIELRQGWLFRTRRQMKYD +RIQAVDLQHPLVARLLGLAVVKVEAADGGESALELSFLPKARAEQVRREILDRASGVLVG +PASAPRIAEGADAAAGVIPGVMPGVMPGAEAGPGVAPPGADADPTTPRADAPEGAAPSSS +DPGLARRADDEGELMLRVPSGRLIGSVLLSGGVAGTVAVYLVVVLGTSLFFALAPGTWLE +GEDTPLTGIVVAWGLPLAFAVVGQAWSGLNGGWGFQVRRSADGLRLRHGLTETTHQTVPP +GRVQGVTVSQPLFWRPFGWHRVKVSVAGYGEDAAGKRSTALPVGPWEDVLRVLTVVAPDP +GLDGDPREAEGLTPARLMHLGLHGSGTEGGFHHIPHRGRWWFNWFAWRRRGFTTTRALLV +VRSGRWNRVLQTLQHERVQTAALDQGPVQRRLRLATVHVRTAGGRAVLPDLDEAVALELF +AEEARHAAVSRRLADRDRWMRPEELARFEQRTREVAATEVGREELARAGVARPAAPAGGV +AGTDPEPRTSHEERP +>MOLHKGIG_00081 +MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD +GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD +LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS +APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL +LPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT +HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT +VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT +TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED +VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA +VVGEESGAHVPAVRGEEER +>NAFOICDF_00253 +MSAPAPRPEGLASGPSPEDGRIAPAPAADDAGWVRVHPASPWIRGWVMVATFLFFALRDV +VERWIGGLFGADAGGGPGVDGRGLLIGGGIALGVLLLVGLAFFFSWWFTRFRIGAEEIEL +KQGWLFRSRRQMHYDRLQAVDLQHPLPARLIGLAVVKVEAADGGGDSALELAYLPKAQAA +AVRRQILDRASGAAAARPVPSAAPEAAGGPAAAGPVRGLLVDPEEQGPVLLRVPAGRLIG +SVLLSSTVMGLLGAVVAVPAVLSLLLLLFPDANAGEEAGVWAVTLGSTFPLLFSLAGAVW +SGLNKGWGFTVRDSSDGLRLRYGFTETVSQTVPPGRVQGVEISQPLFWRPFGWHRVKVSV +AGYGGLEAEGRRRDVALPVGPWEDVLRVLQVVAPDPGLGGDARAAGELMRTAMTGSGEEG +GFRHVPRRAAWWWHWLTWRRHGYALTPTLLVVRHGRLSRSVQTVQHERLQAVALTQGPVQ +RRLRVATLRVHMAGGAARLRGLDEDVLAELFEVESRHAAVSRRLTDRNRWMLPEELERFE +RRTAEVARTEVGRAEMAAAGVVPMETGPRPGDTPPVATTEHRGEETA +>MHAAABBN_02094 +MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD +GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD +LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGVLGGAGADAS +APERAAEPGLADADPDAVDADAGELLLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLAL +VVALLPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGL +TETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVL +RVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRT +GFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRD +LDEDVAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGV +VGGAVVGEESGAHVPAVRGEEER +>LFPAFLNI_00075 +MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD +GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD +LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS +APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL +LPEAVLDEGETLTGIGAAAALPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT +HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT +VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT +TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED +VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA +VVGEESGAHVPAVRGEEER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000338.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000338.fa new file mode 100644 index 0000000000000000000000000000000000000000..7983bd17b341726ba8001184166ba46a84e941ca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000338.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00313 +MPGIDLTGVTFAPASPKLTPVKLISSSIGHLIWLVVFSVPLVLKLLGPWEGLWAWTAWGL +PAIVVVSWLVDLVLIPRRVRAMGWAEREDDVLWREGLLFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAASGSDVTLEGLPRETADELREVLMARGQARLAGL +>MOLHKGIG_00080 +MPGIDLSGVAFTPASPRLTTVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL +>NAFOICDF_00254 +MPGIDLQGVEFTPVSPALVRVEAVRELIALVIWLAVVSVPLVLKLTGVWPDMWSWTAWGL +PALVLAWSLVELVLIPRRVVAKGWAEREDDVLWREGILFRRVVAVPYGRLQYVDVTDGPL +LRWAGLQKLTLKTAGGADVELVGLPRETCDRLREVLMARGQARLAGL +>MHAAABBN_02093 +MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL +>LFPAFLNI_00074 +MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000339.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000339.fa new file mode 100644 index 0000000000000000000000000000000000000000..c1687bc3ef83c82273a4299eb5bdf676d0dc2099 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000339.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00314 +MIALRSWWTVVAVAVAVLLGWLAGLAAPSLGWGAPVVGRSGLITVTAVSVLCLVLGWRVR +RDREKPPAARMDPIAAARTLVLGQAAGFAGAALAGWHAGVALQVAARAGAGAPTVREAAL +QAAGGLVLLAVGLVVERWCRIPPEGDAAEGGRGEDGTAGRGRAPRPETEGGYARARD +>MOLHKGIG_00079 +MIALRSGWTLLVVLAAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCIGLGWRVR +RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVGAPTVREAAL +QAAGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRGRPVRPETEGGYARARH +>NAFOICDF_00255 +MISLVSGRTALLAFAAAVLGWLAALTAPSLGLAAPVMHLAALVTVVAVGVLCLVLGWRVR +RDRDRPLAQRMDPLAAARTLVLGQASGLTGAGLAGWHAGVGLEVASRAGIEAPAVLTAGL +LALGGAALLTVGVVVERWCRIPPEGDGAEPGAGQDGGGSGGHGARRPEAEGGFARARD +>MHAAABBN_02092 +MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR +RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL +QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH +>LFPAFLNI_00073 +MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR +RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL +QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000342.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000342.fa new file mode 100644 index 0000000000000000000000000000000000000000..7179fc7d7c8d02a8acdfb73a9a5361be9cdfd352 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000342.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00318 +MTEQTHHDDAARGPVPAADGSAAAPTASTPAAAGVPGTFDPDSTAIDRPRIEAAVREILL +AIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLVKDIPFYSTC +EHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVVEALMEHLAP +RGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG +>MOLHKGIG_00075 +MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF +FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG +LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK +TVTSAVRGQLRDPSTRSEAMSLIMHG +>NAFOICDF_00259 +MTEQHRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRIEA +AVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLVKD +IPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVVEA +LMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG +>MHAAABBN_02088 +MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF +FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG +LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK +TVTSAVRGQLRDPSTRSEAMSLIMHG +>LFPAFLNI_00069 +MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF +FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTG +LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK +TVTSAVRGQLRDPSTRSEAMSLIMHG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000343.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000343.fa new file mode 100644 index 0000000000000000000000000000000000000000..4013196a129f701032006a19c382419ff8188383 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000343.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_00319 +MKKLFNKPYIWILLGLLVLAVAIPLATSQTGRTMVDTNVGMAMLQDDKAAQARVVDGDQR +VDLTLREPYSQDGRDLGKEVYFHFATARASDVVTAVDDSALDGYTDEPVRSNWLLSLLGF +MIPFLLIALLFWFLLSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE +IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLEGRAKILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYALGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGNSEPFVG +GGGGGSSREYSEELAYLVDAEVRGLLDGAHAEAHWVLTENRDVLDRLAYELLEKETLTQE +AIAEIFRDVRKRPERDVWLASDERLPQDIPPVLSPSERRSRHEGGEQTPVGVEGTTVPVH +PEGAPPSSLGGDAPTPGLPPHGGPSSSPGAGEGPTY +>MOLHKGIG_00074 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR +VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF +MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE +IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG +GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE +AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR +PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF +>NAFOICDF_00260 +MKKQFNKPYIWILLGLLVLGLVIPLTTAQSGRGMVDTNVGMALLRDDKVAQARVVDGEQR +VDLTLREPLSQDGRDLGRDVYFQFSAARAQDVVRTVQDSSVDGYQDEPVRDSWLLSLLGL +MIPFLLISLLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELHE +IKEFLTEPERFHAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKANAPAIIFVDEIDAVGRSRGVGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLDGRAKILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSRNNVIDNAALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPENDKYSVTRNELLDQL +AYAMGGRVAEEVVFKDPSSGAANDIQKATETARKMVTDYGMSSKVGAVKLGSANTDPFLG +GGGAASREYSEELAYLVDAEVRALLDGAHAEAHWVLTENRDVLDRLAAELLEKETLTQEQ +IAEIFKDVRKRPERPLWLAADDRPPHDVPPVLTARERASRLEGEQPEAVGVEGTTVPDAP +EGAPPTALGGAGGSAGGPGDLPGQHSPTPGPTY +>MHAAABBN_02087 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR +VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF +MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE +IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG +GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE +AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGQQTPVGVEGTTVPVR +PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF +>LFPAFLNI_00068 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR +VDLTLREPYKQDDRDLGKEVYFYFASARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF +MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE +IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRARILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG +GAPGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE +AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR +PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000345.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000345.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a662797cb66c3be785e54818eb0ba378a51b364 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000345.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00321 +MPSGSAAPPALESWPPRGRWPEPLHRAVAALRPVLAAHDGGALIGLSGGADSCALAVAAA +ALRGTRAGAALGPVGAVVVDHGLQAGSADVAEAAARVARTLGLEPVLVRRVAVREAGDGP +EAAARRARRGAFADAAREAGAGLVLTAHTADDQAEQVLLGLARGSGTRSLAGIPAGGALP +GGTALARPLLGLTRADAEAICRWAGVRWWEDPHNADPALLRSRVRTRVLPALEDLADGLG +PGVREGLVRTAAIAAEDAAALEQWAACALAECRVRGEAGPGPGAEPGDDPGAGTGRSEAP +GRGDVVVRLDLAAFAALPPAVRHRVLGLAVVEAGGPRPTRERTLAVDALAVPADPGAGGP +RGPWSCPAGWK +>MOLHKGIG_00071 +MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG +RAGSRPRGLVALSGGADSLALAVACAVLVGTREGARLGPIGAAVVDHGLQSGSDAVAAAA +ADVARILGLTPVTVTRVEVARTGDGPEADARRARRVALAAAAREAGQGGAAPGAGTAVVL +TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAG +LTWFEDPHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWA +GDEFTRLRVDPPGRDPRVVSLDLDTLAALPAAVRHRVIARAARAAGGQAPPRERILAVDT +LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP +>NAFOICDF_00263 +MSSPFVRDVVAVPGAPTLPALAGPWPPRSRWPEPLHRAVESVRAVRAEHPGPVLVALSGG +ADSLALAVACAVLAGTRAGERLGPAGAVVVDHGLQDGSAAVAAAAARTARALGLAPVTVE +AVTVTPAGDGPEASARSARRTALARAAEGVGEGTPALVLTAHTADDQAEQVLLGLARGSG +TRSLAGIPAHGALPGGVALARPLLGLSRADTEAICRWAGLTWFTDPHNADPALLRSRVRT +RILPALEDPDTGLGPGLRAALVRTAAIAAEDAAALDAWADDALARLRLPAPETDRPAPVL +LDLDALAALPAAVRHRVHARAARAAGAGTPSRERILAADALVAAAHAGGGSAGPVELGHG +VTVRRVAAGEGGVGGRKEGGPSGCARLAYIPRPADR +>MHAAABBN_02084 +MPRPEARDPGPTPAGGAGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGSCRADAGPG +RAGNRPRGLVALSGGADSLALAVACAVLVGTRDGARLGPIGAAVVDHGLQSGSDAVAAAA +ADVARILGLTPVTVTRVEVARTGDGPEADARRARREALAAAARDAGQGRAAVVLTAHTAD +DQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAGLTWFED +PHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWAGAEVTR +LRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAVDALVTGAR +AGCTSAGPVELPGGVAAHRACARLDLIPCLPGP +>LFPAFLNI_00065 +MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG +RAGSRPRGLVALSGGADSLALAVACAVLVGTREGRRFGPIGAAVVDHGLQSGSDAVAAAA +ADVARILGLAPVTVTRVEVARTGDGPEADARRARRKALAAAAREAGQGDAVPGAGAAVVL +TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVVRPLLGLTRADTETICRWAG +LTWFEDPHNRDPALLRSRVRTRVLPALEDPDVGLGPGVRAGLVRTAAIAAEDAAALDAWA +GDEVARLRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAADA +LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000346.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000346.fa new file mode 100644 index 0000000000000000000000000000000000000000..8778ed0945048e859b79c45fa3ed3f1b1a9043be --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000346.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00322 +MDTAPADRVPQPVDWAFAARTAAALAPAGPRFTAREAAREAAGLRAAAEASVPHVHRLTG +LAAAEDLRDSQVLVVDRPTWSASATQSFATMLEPTFAHLQATRPQEYQAALTPVARHATA +LEMGGILAWLSGKVLGQYDPFAGPSGGRLLLNAPSVAQVRTEINVDPEDFRLWVCLHEQT +HRVQFAAAPWLRGHLQEQITALASGLFDKAESLPERLRSALAAANPLGRGSGAGAASTGP +ASGPDDGRPGPAQAGGDVVPARGAGLLGALQDEEDRARLSHVTAVMSLLEGHANVVMDGV +DADVVSSVKTIRRRFEDRADRRSPLDRMLRRLLGMDAKMAQYRDGQRFVSAAVAELGMDG +FNVVWDAPELLPTEDELHRPERWTARVRAQA +>MOLHKGIG_00070 +MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREHAATTRVTRHATALEMGGILAWMSGKILGQYDPFIALPGPGGTAAGPAGGRLLLV +APNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRGEITALTVGLFDKAES +LPERLRTALAAANPLGREADAGRTGTRDGHDAQDAVAARPAPGLLGAIQDEEDRERLSRL +TAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRLLGMDAKMAQY +RDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQA +>NAFOICDF_00264 +MTADQPVPSPAHPVDWDAAARAAGSLAAAGPRIGTREARREAEGLRAAAAASVAHVHRLT +GLAAAEDLRDSQVLVVDRPTWSLANTQSFAGLLEPSFAHLRATRPQEYALTTAPLTRRAA +ALEMGGILAWLSSKVLGQYDPFSALPGPDGVPAGPAGGRLLLVAPNVAQVRREIHVDPAD +FRLWVCLHEQTHRVQFAAAPWLRGHLQGEITALTGGLFDKAESLPERLRSALAAANPLGA +STSPGAGRAGQDDGAAGPGGRPALGLLGAIQDEEDRARLSRLTAVMSLLEGHANVVMDAV +DSSVVSSVKTIRRRFDARGDRRSGLDRLLRRLLGMDAKMAQYRDGQRFVDAAVAELGRDG +FNVVWDAPELLPSEEEIHAPDRWVARIRAQA +>MHAAABBN_02083 +MSDDHATDRPRAAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAGGPAGGRLLL +VAPNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE +SLPERLRTALAAANPLGREADAGRTGARDGHDAQDAAPARPTPGLLGAIQDEEDRERLSR +LTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRVLGMDAKMAQ +YRDGQRFVAAAVAQLGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQA +>LFPAFLNI_00064 +MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAAGPAGGRLLL +VAPNVAQVRAEINVEPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE +SLPERLRTALAAANPLGREADAGRIGTRDGHDAQDAAAARPAPGLLGAIQDEEDRERLSR +LTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRLLGMDAKMAQ +YRDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWGARIRAQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000347.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000347.fa new file mode 100644 index 0000000000000000000000000000000000000000..5ad24fcd58d34eec16284279a2269d8607eb29a0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000347.fa @@ -0,0 +1,46 @@ +>ACLBLIBL_00323 +MTPGSPFASLLAALAAALLSAAPVLTPLAGPAALAPGNPVTAEAVAAPSPDARALASAVD +AALDASPGRVAAQVRDAATGEVLHARDADFLAAPASSLKVLTAAAALRTLGPERTLRTRV +VAVPAADDGATELVLVGGGDVLLGDGASDPDAVAGRAGLRTLAERTVAGLAEAGVSGDVV +VSVDLRLFDGAAVNPAWTPDLLEDGHVSAVQPLATWGGREVPGVDEERIEDPAGHAALVF +QRLLDEEIERTGADLDLGLRDSIPATTAVRDDVVAAEPTAQVESAPVAEVAAYMLAHSEN +QVAEALGHLSAYAVGRPATHEGAADLLEDVAADLGADTAGMAVLDASGLAEGSLVSPAQL +AAVVSAASRVPWLAPVLDGLPRPGEDSTLDERFRGTAAEGAVAAKTGTLDHTVSLTGTVT +TQDGRVLAFSIVASDLDWRLDEAREAVDAAVTAMAGL +>MOLHKGIG_00069 +MGQVDTGRTGRRDRRTERPRSRSLHAVLLAALAAVLVACGPVTAPPAPSSAPASSTTAAP +TSSSPSAGPTAAEVAAAVEPGLETSPGTASAEFRDLATGEVLYARDADEPVAPASSLKVL +AAAAIVSALGPETTLQTTVVAQPTADDAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT +LAQRTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE +APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA +AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATVEDLGVDTAG +MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ +AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL +>NAFOICDF_00265 +MTPSNRAARVAAVTRVLLALAICALLGLLAHDVLLPRLPTPAAPAASAPSAPVPAASPSG +GATAPSSTALASVAPVDPADVAAAVAPALAQAPGTASAEVRDAATGEVLYARSADQAVAP +ASALKILTAVTAVDVLGADRALTTSVVALPGGGATELVLVGGGDALLGAGASDPGRVDGR +AGLRTLARRTVAGLRERGVTGPVAVSTDLRLFTDASPLNPAWSAGLVESGNITAVQPLAT +YGGRTAPGTGEDRIADPAAFAALAFQRELTAAVADSGADLSVRARDVVPATSAPRGDVLA +TEPVARVESAPVGQQVAYLLAHSENQVAEVLARVAAAADGRPATHAAVPGLLRDRAAAHG +VDTAGMRLVDASGLSPQNRVTAHQLAGLVEAVQADPALAPVRDGLPRPGEDSTLAERFPG +SPAREAVAAKTGTLDQTVSLTGTVTTGSGRVLAFSIVCSGVDWRIAPARAAIDEAVSALA +AL +>MHAAABBN_02082 +MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPTAPSSASASTSTAAP +TSSSPSAGPTAAEVAAAVEPGLETSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL +AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSKAVSGRAGLRT +LAERTVAGLVEDGVTGRVVVSTDLRLFADRTALNPRWTSDIPESGNIAPVQPLATYGGRE +APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTFPATEVPRATVLAAAPVA +AVESAPVGQQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATQLLTATAEDLGVDTAG +MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALGTVLEGLPRPGEDSTLGDRFPDAPARQ +AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL +>LFPAFLNI_00063 +MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPPAPSSAPAASTTAAP +TSTSPSAGPTAAEVAAAVEPGLATSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL +AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT +LAERTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE +APGTGEDRIEAPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA +AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATAEDLGVDTAG +MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ +AVAAKTGTLDQTVSLTGTVTATSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000348.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000348.fa new file mode 100644 index 0000000000000000000000000000000000000000..82f11f154a0e8ecb8fa29c80bcea5f584a9cb60b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000348.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00327 +MLVLTINQRDTLDAGDRVDAFLRSLGDAPGLAGAVALPFQRAVGDELIGAVTDPAAAVEV +ALRALRERRWNVGIGVGALRGADGTEGAPSSGSLDDAAGPALAHARRAVEAAAVSTARIP +LAVRGADAQASAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAADALGITAQA +VSQAVQRAYWNEEHACRPAASRLLALAEEG +>MOLHKGIG_00067 +MFVLTINQRDTLDAGDRVDTFLRALQDVPGLDDAVVLPFQRAVGDELIGAVEDPRVAVDV +ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP +LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA +VSQAVQRSYWNEEHACRPAAARLLTLAGG +>NAFOICDF_00267 +MFVLTLNQRDTPDAGDRVDALLRELTDAAAAVPGLRSPALPFQRSVGDELVGVLEDPHAA +VDVALRALRQRRWNVGIGVGTVCHADGSAGIPASGDLHHAGGPGLAAARRAVEAAALSTA +RIPLAVRGRDAEAAAEAEAVLKLIGQLVWTRTAAEWSVLDLLVPGVRGQQKPAAQALGIT +TQAVSQAVQRSFWNEEHACRPAAARLLALAAG +>MHAAABBN_02080 +MFVLTINQRDTLDAGDRVDTFLRALQDVPGLDDAVVLPFQRAVGDELIGAVEDPRVAVDV +ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP +LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA +VSQAVQRSYWNEEHACRPAAARLLTLAGG +>LFPAFLNI_00061 +MFVLTINQRDTLDAGDRVDTFLRALQDVPGLGDAVVLPFQRAVGDELIGAVEDPRVAVDV +ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP +LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA +VSQAVQRSYWNEEHACRPAAARLLTLAGG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000350.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000350.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c4d09d37ca16bd23227c47f1d5a5ab7bbc2be59 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000350.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00330 +MVPISGAQLTYRLRPAARLKPVIDVKDLIEQPEKYRASQEARGEDASLVDRMVEADASRR +ASITAFEELRAEQKAFGKKVAKAQGEEKQALLAEVKDLAARVKEAEAAAGAAEGRVAELQ +RAFPNLVLDGVPTGGEDDFVVLREVGAPRDFAAEGFEPRDHLELGELLGAIDMERGAKVS +GARFSFLKGVGARLELAIMQMGMDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYR +LERDDLYLVGTSEVALAGYHADEIIDVDAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQF +NKLEMFVYATQEDAEAEHARLLEWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWV +PTQGTYRELTSTSNCTTFQARRLNIRERVRQEDGDGGARRGGTRMVATLNGTLATTRWIV +AILENHQNADGSVTVPVALRPYLGGMERFELV +>MOLHKGIG_00065 +MIDVKDLIEQPEKYRASQEARGEDASLVDRLVEADASRRSSIAGFEQLRAEQKAFGKRVA +QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV +LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL +GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGFHA +GEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEEAEAEHERL +LAWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR +RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG +MERFELV +>NAFOICDF_00272 +MIDVKDLIDQPEKYRVSQEARGADVSLVDQVVAADAARRAAISRFEELRAEQKAFGKRVA +QAKGEEKQALLAEVKDLAASVKEAEAASNEAEAELLRLQRLFPNLVIEGVPQGGEDDFVV +VKEVGTPRDFAAEGFEPRDHLELGELIGGIDMERGAKVSGARFSFLKGAAARLELALMQM +GLDLAVENGFVPVIPPTLVRPETMQGTGFDVAHDDEIYRLERDDLYLVGTSEVALAGYHA +DEIIDVADAPIRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFVYTTVERAEEEHAR +LLAWEEQMLARIEVPYRVIDTAAGDLGMSAARKFDCEAWVPTQGTYRELTSTSNCTTFQA +RRLNIRERQVKEDGTGSNAKKGGTRTVATLNGTLATTRWIVAILENHQNADGSVTVPEAL +RPYLGGLERFELV +>MHAAABBN_02078 +MIDVKDLIEQPEKYRASQEARGEDASLVDRVVEADASRRSSIAGFEQLRAEQKAFGKRVA +QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV +LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLTGVGARLELALMQL +GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA +DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHARL +LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR +RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNVDGSVTVPAALRPYLGG +MERFELV +>LFPAFLNI_00059 +MIDVKDLIEQPEKYRVSQEARGEDASLVDRVVEADAARRSSIAGFEQLRAEQKAFGKRVA +QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV +LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL +GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA +DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHERL +LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR +RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG +MERFELV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000351.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000351.fa new file mode 100644 index 0000000000000000000000000000000000000000..53af795f74d51aebb4da48b71db6b148699f1ffe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000351.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00333 +MTRDDAAPLGRCTFLGPAGTFTEAALRAVPGAEQAELIPATSVPAALAAVRAGEADHAMV +PIENSVEGGVSATLDDIASGDDLQILREELVQISFVLVGRPGVELADVRRVSTHTHAWAQ +VRGWVEANLPGVEYTPSGSTAAAARALADAEPGSEPFDAAVCAPLVAEQTGLPVLARAIE +DVTGAVTRFVLVGRPGPLPAHTGSDKTTLTVPLPDDHPGALREILDQFATRGINLSRIES +RPTGEGMGKYFFSIDLEGHLAEERVAAAMGALHRIFPGVRFLGSYPRAEHRPVAVRRHTS +DDAYRAGRAWVDGLLAR +>MOLHKGIG_00062 +MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVPAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVAISFVLVGRPGVAIEDVRRVTTHPH +AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED +VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR +PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD +AAYRSGRAWVESLRSR +>NAFOICDF_00274 +MSPAPRYAFLGPAGTFTEAALRQVASPEDVDLLPASSVLAALAAVRVGEAERAVVPIENS +VEGGVTATLDDIGADEPLQILAEVLVPISFVLVGRPGVALEDVRRVTTHTHAWAQVRGWM +EAHLPGVEFTPAGSTAAGARALLPSAGGDGAVASFDAAVCAPLVAEQTGLPVLAEAIEDV +TGAVTRFVLVSRPGPVPEPTGADKTTLTVPLPDDHPGALREILDQFATRGINLSRIESRP +TGEGMGRYFFSIDLEGHVAEERVGAALAALHRTFPGVRFLGSYPRAEGRPPTVPEHVTDA +AYRRGTAWVRGLRSR +>MHAAABBN_02075 +MTGTGSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVSAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAMEDVRRVTTHPH +AWAQVRGWAETALPGVDFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED +VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR +PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD +AAYRSGRAWVESLRSR +>LFPAFLNI_00057 +MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAKAEFVSAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAIEDVRRVTTHPH +AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED +VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR +PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD +AAYRSGRAWVESLRSR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000352.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000352.fa new file mode 100644 index 0000000000000000000000000000000000000000..5c0b46f940350a872dae5fdb2c1c883b988555bb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000352.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00334 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHLPLGQLPDRLEELDPDTDYYVIC +RTGGRSARAAEFMVGRGYTAINVAGGSGAWLEAGKPMEADGGAEPTVK +>MOLHKGIG_00061 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>NAFOICDF_00275 +MSHFETVTVDQIPADAAILDVREDDEWALGRAAGAQHLPLGQLPERIEELDPDTDYYVIC +RTGGRSARAAEYMVGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>MHAAABBN_02074 +MSAFETVDVNEIPADATILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>LFPAFLNI_00056 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000355.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000355.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d7ddbf2aa9a763ed0db360756110d9435eb32c2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000355.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00338 +MAQPEPVRLAPPGRTAEPDAARPAERALLAAASACDGDVAPMLALLGAGRAPDTEASAPD +AAAPLELPLTGEGRTRQQWELLASVAAQDLSAARVLEPHLDALSILSQASVPAPAGLLGV +YASESGGRTPRLTPAPHDDDAGSASDGRPDAGPDAWLLDGEKPWCSLADECAAAVITGRE +ADGTRRAVLVDLDHPGVAETSSAWPALGLAPIRTVGLGFDAVPGTAVGGPEWYLRRPGFA +WGGIGVAAVWFGGAVGIARTLRDATRSRAAAEAEGRGPGPDQVAQAALGRVDRLLHAMAA +LLARAAEDVDAGRLDHGRGMVEADRIRGTVAQLCTEVVDVVGQATGPGPLTGSAAHARAV +ADLQVYLRQHHAHRDDARLGRALLDGDADGGWTW +>MOLHKGIG_00057 +MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAPSGEDAAPLDLPL +TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT +PALRPAPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS +AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR +NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE +ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA +LLTGETDGGWTW +>NAFOICDF_00278 +MSETPWVHLPGAEGDGRPAAPTEAEAALLAAARDGEDGEAGIEPILALLSGDDAAASLDL +PLTGAGRTRRQWELLASVGAVSLPAARVLEPHLDALSILDQAGVPAPRGVLGVYASESGG +VSPSARPAPGAAVGDEDAVWRLDGDKPWCSLADRCTAAVVTARQEDGLRRAFLVDLGEPG +MEVADPRWPSLGLAPITTVGLRFADVPAVPVGGPEWYLRRPGFAWGGIGVAAVWFGGAVH +VARTLRTSLERRTAAASDGSGPGPDQVGLAALGRVDRHLHAMASLLGRAADDVDAGRLDH +AHGLVEADRIRGTVAQLCTEVLDVVGQATGPGPLTGDAAHARAVADLQVYLRQHHGPRDD +ARLAESLLAADPAERAELQPW +>MHAAABBN_02070 +MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL +TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT +PALRPAPDGPDTAWLLDGEKPWCSLAGRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS +AWPALGLAPIRTVGLAFDAVPGIAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR +NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE +ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA +LLTGETDGGWTW +>LFPAFLNI_00052 +MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL +TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT +PALRPVPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS +AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR +NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE +ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA +LLTGETDGGWTW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000358.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000358.fa new file mode 100644 index 0000000000000000000000000000000000000000..a80e1663f4cf7c0b61560a024cb3da59db75bc59 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000358.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00344 +MSTQHPGIATDSPVSSDDDLRPGLDAAPVGPAGEDGDDPVREPLPTEALPLAPAGPRPED +PRAAVVRLRAAARSRAAHPRAVRVRQLKGLKRLLTEGQDRLVAALGQDLGKPATEALMTE +VVSVRSEVDHALLHLTDWMEPRPAKLPLALRPASAEVRPRPKGLVLIIGAWNYPVQLTLA +PLVGALAAGNAVVVSPSEKAPATAAALRELVAEHLDSALVSVVEGGKDCNTALLAEPWDH +ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQT +CVAPDYVLAVGDVAHRQVVEELPGALREFYGADPRASKDYGRLVSAEHAERLRDLLREDL +DAGAVVLVGGDVDVAGRYMAPTVVTGVRPDGALMREEIFGPILPVLRVDTFQEALDFIAE +RPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGVGASGIGAYHGVH +GFETFSHLRASITKSDQVDTLKTAYPPYGWVKRTMIPKML +>MOLHKGIG_00054 +MSTQPPGLTTDAPDTPDDDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP +RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM +EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK +APATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDHILYTGGERVGRIVYEAAAK +TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT +AELPAALREFYGDDPRASKDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYM +APTVVTGVKPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA +FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSITKSDQVD +TLKTAYPPYGRMKRALLPKML +>NAFOICDF_00282 +MSTQPPGLTTDSPDSPADDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP +RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPSTEALITEIVSVRSEVDHALLHLTDWM +EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK +APATAAALRELVPQYLDSALVSVVAGGKDCNTELLAEPWDHILYTGGERVGRIVYEAAAK +TLSPVTLELGGKSPAVVTPSRNTGAMARRITWAKFTNAGQTCVAPDYVLAVGEAALRQMT +AELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELFVGGDVDVAGRYM +APTVVTGVKPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA +FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSIAKSDQVD +TLKTAYPPYGRMKRALLPKML +>MHAAABBN_02067 +MSTQPPGLTTDSSDTPDDDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP +RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM +EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK +APATAAALRELVPQYLDSALVSVVAGGKECNTELLAEPWDHILYTGGERVGRIVYEAAAK +TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT +AELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYM +APTVVTGVTPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA +FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSITKSDQVD +TLKTAYPPYGRMKRALLPKML +>LFPAFLNI_00049 +MSTQPPGLTTDSPDSPADDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP +RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM +EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK +APATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDHILYTGGERVGRIVYEAAAK +TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT +AEIPAALREFYGDDPRASKDYGRLISAEHAERLREMLQTDLDAGAELLVGGDVDVAGRYM +APTVVTGVRPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA +FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGVYHGIHGFETFSHLRPSITKSDQVD +TLKTAYPPYGRMKRALLPKML diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000360.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000360.fa new file mode 100644 index 0000000000000000000000000000000000000000..dbf1c26cb7330601451fad5bad5c08cfc7f5259a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000360.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00349 +MGRRADAPAGPGRAVVVPTTTSSPAPASAPVHTPAPAPATSSAPAGSLGQVSESTTYLLV +DGENIDATLGTSILQRRPQPDERPRWNRLLSFMGEHWDQPVKGLFFLAIDGDIPVPFVQA +LTAIGYKPIMLRGAGKVVDIGIQKTMEALQEREDDVVLVSHDADFAPQLTDLAATPDRRT +AIIGFEEFLSHELRRIPDVEFFDLEYGVGAFDTPLRRLRVIDIDEFDPLEFL +>MOLHKGIG_00046 +MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID +GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT +DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE +FL +>NAFOICDF_00294 +MSRRADLPTGPATAVPAAPAAPVSPTAEDRSAATPADTLDTMSARTTYLLVDGENLDATL +GMSVLNRRPNPEERPRWNRVLRHVERAWGQEVRPLFFLAVDEDGDIPFGFVQALTTMGYQ +PILLRGAGKVVDIGIQRMAEALIGRDADVVLASHDADFAPQMLDLAAHGHKIAVMGFDEF +MSAELRAVNGMEVWDLEHDVAAFDVPLPRLRVIDIDDFDPRDFL +>MHAAABBN_02059 +MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID +GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT +DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE +FL +>LFPAFLNI_00041 +MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID +GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVILVSHDADFAPQLT +DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPNE +FL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000363.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000363.fa new file mode 100644 index 0000000000000000000000000000000000000000..23c9619b0b7e2ecccf59046657200fb3d8f71248 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000363.fa @@ -0,0 +1,39 @@ +>ACLBLIBL_00356 +MRARRRAGLFSAGVRGYDGRVSTVSAPSRAPRTVTVTGAAGNIGYALLFRIAAGGMLGPD +TPVRLRLLEIPAALRAAEGTAMELADAAFPLLADVEVTDDPAVAFDGVQHAMLVGARPRT +KGMERGDLLEANGGIFGPQGRAINDHAADDVRVVVVGNPANTNALIAAAHAPDVPAERFT +ALTRLDHNRAVAQLAARAGVAVTDVDGVTIWGNHSATQFPDLTHARVRVAGAWRPALEVV +DPAWAAEEFVPRVAKRGAEIIEVRGASSAASAASAAVDHMRDWTLGTGAGAGGAGTDAGP +RWTSAAVVSDGSYGVPEGLVSSFPVTSDGGAAWRIVPGLAPDESLLPGTGGRLAATVAEL +EAERDAVHGLGLL +>MOLHKGIG_00044 +MGGVDTAQQTTAQDTAQDPASTTPRTVTVTGAAGNIGYALLFRIAAGGMLGPDTSVRLRL +LEIPAALGAAEGTAMELADAAFPLLADVEVTDEPARAFDGVQHALLVGARPRTKGMERSD +LLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPDVPAERFTALTRLDH +NRAVAQLAARAGVAVTDVAGVTIWGNHSATQFPDLTHARVRVDGTWRPALEVVDPVWAGE +EFVPRVARRGAEIIEVRGASSAASAASAAIDHMCDWTLGTGVDADGASRRTSAAVVSDGS +YGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVAELEAERDAVRGLGL +L +>NAFOICDF_00298 +MTQDTLRTPATVTVTGAAGNIGYALLFRIASGQLLGPDTPVRLRLLEIPAAVRAAEGVAM +ELADSAFPLLASVDVTDSADAAFDGTTHALLVGARPRTAGMERADLLRANGGIFGPQGAA +INASADASVRVVVVGNPANTNALIASAHAPDVPAERFTALTRLDHNRAVSQLAARAGVGV +ADVDGITIWGNHSATQFPDLTHARVRMSGDDGAPVWRPALEVVDPAWAAEEYIPRVAKRG +AEIIEVRGASSQGSAASAAIDHMRDWSLGTGVDADGAPRRTSAAVVSDGSYGVPEGLISS +FPVTSDGSGAWTIVPGLEPDESLLPGDGGRLAATVAELEAERDAVRALGLI +>MHAAABBN_02057 +MRRAGVSSAGERGHDGGVDTALQTTAQDTAPDPVSTTPRTVTVTGAAGNIGYALLFRIAA +GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL +VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD +VPAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW +RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG +APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA +ELEAERDAVRGLGLL +>LFPAFLNI_00039 +MRRAGVSSAGERGHDGGVDTAQQTTAQDTAPDPASTTPRTVTVTGAAGNIGYALLFRIAA +GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL +VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD +VQAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW +RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG +APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA +ELEAERDAVRGLGLL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000364.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000364.fa new file mode 100644 index 0000000000000000000000000000000000000000..2250bd8b06e4cb97f75b37e97789e1a1bf3460a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000364.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_00357 +MDVVVSDTATPRAHVGGSPLNVAVGLSRLGRPVLFAGRFGRDEHGDMIASHLRDNGVHCL +LEQDAAPTSQATARLDPTGAASYEFELDWTLPPAEELAEEFAAAAGGRLRHMHAGSIATM +LAPGDAEVMSLLERISADTTISYDPNVRPSIVPDRAFARARAEESVRLADVVHASDEDVA +WLYPARPLVETLQAWQRMGPALVVMTRGAEDIVAVTRDGVVERPIVPVDVADTVGAGDSF +TAALLAALDDRSLLGAENRERLNAMDPADVESVLIYASRASAITASRPGADPPTRDELAD +>MOLHKGIG_00043 +MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG +DMVASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA +GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES +VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI +VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA +SRPGADPPTRAELAD +>NAFOICDF_00299 +MGLVAEYFGVVGEALVDVVLSDTATPRAHPGGSPLNVAVGLSRLGRPVRFAGRYGTDEYG +DMVAAHLADNGVHCVLGADDAPTSVATARLDPTGAASYEFELDWTLPEAAELERLLTGAA +GGRLLHVHAGSIATMLAPGDASVMGLLEAVQPTATISYDPNVRPSIVPDREFARARAEES +VRLSDVVHASDEDVAWLYPDRPLMDSLRAWQQAGPALVVMTRGAEDIVAVTAEHVLEQPI +VPVDVADTVGAGDSFTAALLGALDDRSLLGAENRGRLHAMDLADIRSVLIYAARASAITS +SRPGADPPMRDELAD +>MHAAABBN_02056 +MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG +DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA +GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES +VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI +VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA +SRPGADPPTRAELAD +>LFPAFLNI_00038 +MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG +DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA +GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES +VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI +VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA +SRPGADPPTRAELAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000366.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000366.fa new file mode 100644 index 0000000000000000000000000000000000000000..a2e874a1272b38177cf7b5d75ded0eba716b9a60 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000366.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_00360 +MGPRRGLPEGEGPLSGARGGRGAGRQRASRGGPARSTRTGGRAGAKGGGPQRAGSGSRAG +GEGRRRAPSAPADLAAPPETLFLATIPGATPSTWVDRFTTRQRVVQLVNHDEASQLAHLA +HDDAGMPRHPLPQLGYVRRRRDVEAEEMLRAAGVDPRRVHLVGVYAELPVVCVGRDHLLA +AWDAEADGPVPLAELDSHEELDPARFAAAPVEDPLDSAELPGAGERMALEIAASGAGHVV +LPMSVARMFGRKDVVVLPLASALDDTVGMSRADREAAATRAEVEADAGDAGTAAAGPGEA +DDDAARHPGWDVALAWLKEADSELVQSFVGVARGRRGNSSR +>MOLHKGIG_00040 +MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL +VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDVDPRHVHLVGVYSE +LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERM +ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ +ARAEAEAGAAVVDGADPAGHGDDDARHPVWDVALAWLKAADSELVQAFVGVARGRRGASS +R +>NAFOICDF_00301 +MPAAPADLPTPPETLFLATIPGATPSTWVQRFSSRARTVQLVNHEEAQQAAHLAHDAAGA +PLHPLPQLGYVRWLRDAGVESVLRESGVDPRFVHVVGVYSELPVVCVGKEHLLAAWDLEA +DGPVPLAELDPAEHMDPARFAPEPGAASNPLDSAELPGAGERMALEIVASGVGHVVLPQS +VARVFGRKDVVVLPVACELDDVVGLSRADREAAATRAEVAEEGDGVVPDGADAPATTAPR +HPGWDVGLAWLKEQDSELVQSFVGVARGRRGGTSR +>MHAAABBN_02053 +MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL +VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGGVDPRHVHLVGVYSE +LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSAEPMDAAELPGAGERM +ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ +ARAQAEAGAAVVDGADPAGQGDDDARHPGWDVALAWLKAADSELVQAFVGVARGRRGASS +R +>LFPAFLNI_00035 +MKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHD +DAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDIDPRHVHLVGVYSELPVV +CVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERMALEI +AASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAE +AEAGAAVVDGADPAGQGDDEARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000369.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000369.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f0d13306fe39bfe128543f33926bcfd6c95f41c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000369.fa @@ -0,0 +1,44 @@ +>ACLBLIBL_00365 +MTRIPAPDEAAAAPSSPLDNALAQLAAAVRTLGYDEGLHQTLAAPRRELSVSIPLRRDDG +AVEVLRGYRVQHNISRGPAKGGVRFSPDVDLDEVRALAMWMSWKCALVGVPYGGAKGGVS +IDPRRYSKAELERVTRRYTSEIQPIIGPEVDIPAPDMGTDEQTMAWMMDTYSVNVGHTTL +GAVTGKPVSLGGSLGRASATSEGVVHVALAALRDRGIDPQGATAAVQGFGKVGAGTVELL +AAAGVRVVAVSDQYGAVRCEDGVDFATLSAHVAETGKVVDCPGTEAMDADELLLSDVDLV +VPAAVQGVLTAQNADRVRARVVVEGANGPTTGEADRILNENGVLVAPDILANAGGVIVSY +FEWVQANQAYWWTREEVAERLERRMVLAWEAVQAAAREHDLTLREAATVLAVKRVAEAHR +TRGLYP +>MOLHKGIG_00033 +MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG +STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVA +IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL +GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL +EAAGVKVVAVSDQYGAVRDDEGLHYDALQRQLWDTGSVKDTPGTASMDADELLEMDVDLV +VPAAVQSVLTEDNAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY +FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR +TRGLYP +>NAFOICDF_00463 +MTSASSPLANALAQLERAVETLGYDEGTHQLLANPRRELSVSIPLRRDSGEVEVFHGYRV +QHNFSRGPAKGGVRFSPSVDLDEVRALAMWMTWKCALVDVPYGGAKGGVAIDPRTYSQAE +LERVTRRYTTEILPIIGPEKDIPAPDVGTDEKTMAWMMDTFSVAMGYTVQGVVTGKPVSL +GGSLGRAEATSRGVVHIALAALKHKGIEPAQATASVQGFGKVGAGTVEFLADAGVTVLAV +SDQYGAVRREEGIDYAALAAHVAETGSVVDCPGTEPMDPAELLTMEVDVLVPAAVEGVLT +KDNAGDVKAKIVVEGANGPTTGEADAILNENGVLVAPDILANAGGVIVSYFEWAQANQAY +RWTLQEVNDRLAARMRTAWDGVLAASQKHGVSLREAATVTAVKRVKEAHEIRGLYP +>MHAAABBN_02050 +MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG +STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVT +IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL +GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL +EAAGVKVVAVSDQYGAVRDDEGLHYDALQRQLWDTGSVKDTPGTASMDADELLEMDVDLV +VPAAVQSVLTEENAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY +FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR +TRGLYP +>LFPAFLNI_00032 +MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG +STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVT +IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL +GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL +EAAGVKVVAVSDQYGAVRDDEGLHYDALQKQLWDTGSVKDTPGTAPMDADELLEMDVDLV +VPAAVQSVLTEENAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY +FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR +TRGLYP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000370.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000370.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7d33165f282934d54ee090cf2a9bd5b9617de9e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000370.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00366 +MTMTLPAAITPSPAFQAVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA +VAPKDKDRARADALAWLTSGHTGWVRLNGYGSKWWEDDVAALAEALPAHLGGPVAEGGLA +GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD +TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL +APEQCAAVNEGLSPSQEELAWAHEFLADFEADGSEIRNGSDLPRKARAEKILGLAAAFGV +HSTRYPDQDNAITAPSDTYHY +>MOLHKGIG_00032 +MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA +VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA +GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD +TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL +APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLAAAFGV +HSTRYPDQDNAITAPSDTYHY +>NAFOICDF_00304 +MTVTLSPSPTQPFQPTPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDVEDSVA +PADKAKALADTVEWLTSGHTAWVRLNGYGSKWWEDDVDALASALPAHLGGPVAEGGLAGV +MLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRDTG +LGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGAKLAEATAVTTEFGMTGKLCLAP +EQCAAVNEGLSPSPEELAWAQEFLEEFAAAGGQIRNGSDLPRKARAEKIQALAAAFGVQL +AHIPDQENRAAAPSDTYHY +>MHAAABBN_02049 +MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA +VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA +GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD +TGLGESPQALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL +APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV +HSTRYPDQDNAITAPSDTYHY +>LFPAFLNI_00031 +MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA +VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVAEGGLA +GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD +TGLGESPMALAYTRSQFTIAARATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL +APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV +HSTRYPDQDNAITAPSDTYHY diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000372.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000372.fa new file mode 100644 index 0000000000000000000000000000000000000000..3dcaffd246c55f17dfe1d26d4ca5ec02f27ad10f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000372.fa @@ -0,0 +1,54 @@ +>ACLBLIBL_00373 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV +GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLHMAHIGDSRAYRL +ADGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLFCSDGLTDVVSSEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEEMAPVPDVHLTEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV +VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDRDAAPRPDASAPPAAPSGTAAAAG +SSSAAAPTATVADHPSDEAAEVSTRAATPAPATAGPAGGSQDGAARRRRGKDDRPVQYRR +GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ +TDLPVDALPVYARDRVNAGMAARDVDHAEQIVAELRDSLHPDAPAPAGEPSERAQPSTTP +SSSSARPSDASGSAAPTSPTASPSATGGEAP +>MOLHKGIG_00023 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV +GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAALLAGTTLHIAHIGDSRAYRL +ANGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLFCSDGLTDVVSPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVRTDRIPV +VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDPDVAARPDPSAPPAAPRGTAAAVG +SSSAATPAATAADQPSDEAAEASATAPTPAPATSGPAGGPEDGAARRRRGKDDRPVQYRR +GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ +TDLPVDALPAYARDRVNAGMPARDVDHAEQIVAELRDSLHPNAPAPAGEPSERARPSTTP +SSSSARPSDASGSTAPTSPASSPSATGGEAP +>NAFOICDF_00355 +MTLVLHHAARTDVGRVRSKNDDSAYAGRHLAVLADGMGGHVGGDVASASTVLDLAHLDDV +GYEDPATVLPDEIQNANLVLTSLVHANPKLAGMGTTCTAGLLAGEVLHMAHIGDSRAYRL +KDGEFTQVTRDHTFVQKLVDEGRLEAAEAQFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLLCSDGLTDVLSVERIRELIEPPATLAEAADALVAHTLRGGAPDNVTVVVFDVAEG +SPEELEPAGEVHLSDEALAAAHPADRGPVSGRLLAEELDARPHELVGAADAAVHSDRIPV +VTRSATRRRAGVLLGESPVPENRPRRTAAHLTAPNASDVDDAPAAPLTAAASPIETPAPA +DAATETPAVDAPAPAPGPEVDPADADAAPAPAADPAPAHAVETGRTSRRRRRDRPVEYRR +GWFIPVFTALLALILVVVAVWSYLWTQTQYYVGEDAGSVAVFQGVPQQLGPLELSHLDHT +TDIPLDRLPAYAQERVGRGMAATDRAHADQIVEELRTVSDTAAKGGGTP +>MHAAABBN_02041 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV +GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLHIAHIGDSRAYRL +ADGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLFCSDGLTDVVPPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV +VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDPAAAPRPDASVPPAAPSGTAAAAG +SSSAATPAATAADHPSDEAAEPMTTAPTPAPATAGPAGGPEDGAARRRRGKDDRPVQYRR +GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ +TDLPVDALPAYARDRVNAGMPARDVDHAEQIVAELRDSLHPNAPAPAGEPSERARPSTTP +SSSSARPSDASGSTAPTSPASSPSATGGEAP +>LFPAFLNI_00023 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLAVLADGMGGHVGGDVASASTVLDLAPLDAV +GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLYMAHIGDSRAYRL +VDGEFCQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLFCSDGLTDVVSPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +SAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV +VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPGPAADAAPRPDASAPPAAPSGTAAA +AGSSAAATPAATAADRPSDEAAEASTTAATPSPVTSGPAGGSEDGAARRRRGKDDRPVQY +RRGWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVD +RQTDLPVDALPAYARDRVNAGMAARDVDHAEQIVGELRDSLHPDAPAPAGEPSERARPST +TPSSSSARPSDASGSAAPTSPASSPSATGGEAP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000373.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000373.fa new file mode 100644 index 0000000000000000000000000000000000000000..4aa6bded0137eda7980f0329af8f4041d960360b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000373.fa @@ -0,0 +1,46 @@ +>ACLBLIBL_00374 +MTEVISPARPRRNIELVLLLAALAIALGADLLGTIGTDAALDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAIVVASALLF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRNFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYFLLV +TRMMRAALGVRDGFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPMRGGEAR +>MOLHKGIG_00022 +MTEVISPARPRRNIELVLLLAALTIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER +>NAFOICDF_00356 +MTEVISPPRPRRATELMLLLGAVALTLGADLLGTYTTTGALESTAWVPLTVFGCASLVLH +AVLRLRARYADPFILPIATLLNGLGIAMIHRLSADTAAARPTSQLAWSVLAVLVAAALVF +LVRDHRMLRRWPYVFLAVSGVLLLLPLVPGLGLSANGARIWINVGVGTFQPGEIAKITLA +IFFAGYLSTNRDLILLAGRRVGPMTFPRMRDLGPLLVAWAVAMGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWVLLGLSLVAVGAAVAFLFLPHVTARFEIWLNAFDPEIYRRDFGGS +YQVVQGLFAMASGGLLGTGLGGGNPTQVPLSFSDMILAAIGEELGLVGLSAVLVLYLLLV +TRMARAALGVRDAFGKVLAAGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIILGLVLRISHAARRPAVVDGMVNASGPGAGHLDPGAALPEPAQRPGPWRAAAPAGGE +AR +>MHAAABBN_02040 +MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGVFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER +>LFPAFLNI_00022 +MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLAWSVLAIVVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000376.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000376.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c55b7cedbb624d256a5a6953bc4a16e7e3c50f1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000376.fa @@ -0,0 +1,66 @@ +>ACLBLIBL_00377 +MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEA +RSVASLNHPSIVSVYDTGEVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAV +AWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKVMDFGIAHALADTSATTSQTQAV +VGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPPAP +SEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRA +GAAGAGGAAVAAGREVRRDGARDSADVPTAAVPLTPAPAPAAPAEPAEPPGGEPRRGRGR +AARRRLRRPAGGRRLRGRPAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPPDGAAAGG +AACRSPGCCWPASSC +>MOLHKGIG_00019 +MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA +RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAV +AWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV +VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP +SDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHP +ALVGAGGAVLGATPAEHGADVADVPTAAVPLTRPAPSVPAEPDTAQPQAVNHAVAGAGLP +GAASAAQLAAAAAMDGPRPVTGGQPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRR +RTLLAAGVVLVALALVLAPWLAAALRTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYM +ADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLR +VSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQL +ALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAP +PSSEAPEPTPSASTSPSPPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSP +TQSPSPPSAAPSTSSEPTEQSPSTSPTATPVDPLPTLTPDPEPSIDPPPST +>NAFOICDF_00359 +MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEA +RHAAALNHPNIVSVYDTGDALLDDGPQSVECPYLVMEHVDGRTLRELLDAGEVAWRDAVE +WTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKVMDFGIARALSDTSAHTGQTQAVV +GTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPPAPS +AVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASG +AAPLATGSGALAAAVAGSTAAGPTASGSTALGAGGAPEARPATGPPATTPLGAAAGPTEP +LIAGHAVAGAAVPGAPSASQLAAAEAVETAPAAASTTGGSAGAGATSGAERAGRRHRLSW +AVLAAVAAVAAVAAILALGAALLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISP +DYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVLPTSLRGASEARVRQELARL +GLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADAR +TTLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVT +VAPPDPALPSATTTTAPAEPSPGVPAPTTPAAPAVDTPAPAPATTPAPAPESSSTPGAGT +DPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVGTPAPSPSGEPVPQPSPSVEPLPEPT +APTEAPTADPAG +>MHAAABBN_02037 +MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRK +EARSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDR +AVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKVMDFGIAHALADTSATTSQTQ +AVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP +APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAF +PPALVGAVLGAAAAEHGADVPTAAVPLTRPTPSVPAEPDAAQPQAANHAVAGAGLPGAAS +AAQLAAAAAMDGPRPVTVGQPVMPGAAATPWPEPQGDTPAPATATPRRVRRRLRRRTLPA +AGVVLVALALVLTPWLAAALRTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPD +GTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIALSDSLHGLSEDAARRELERLGLRVSSVQ +YQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAP +ELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEA +PEPTPSASASPSPPPSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAP +SEPTEQPPSTSPTATPVDPLPTLTPDPEPSIDPPPST +>LFPAFLNI_00019 +MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA +RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAV +AWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV +VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP +SDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHP +ALVGAVLGATPAGHGADVPTAAVPLTRPTPSVPAEPDTTQPQAANHAVAGAGLPGAASAA +QLAAAAAMDGPRPVTAGQPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRRTLLAA +GMVLVALALVLAPWLAAALRNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDG +AVTQSDPQTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLRVSSVQY +QDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAPE +LRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAP +EPTPSASAPPSPPPSESPEPSESAEPSPSPSASATPSPDPTSATPSPTQSPSPPSAAPST +SPEPTAQSPSTSPTGTPVDPLPTLTPDPEPSIDPPPST diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000378.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000378.fa new file mode 100644 index 0000000000000000000000000000000000000000..97236eb55c46fc830884129ff17a7f5b35c9396c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000378.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00380 +MAAPSGKRKDSARRKHEELEDARRGARRGSSAVTTDLGDVDPGPKPLSPVYKAVMFGLMI +VGLLWIVVYYLTQGLFPIVAIGGWNILVGFGIALVGFLMMSRWSE +>MOLHKGIG_00017 +MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL +WIIVYYLTQGLLPIVQIGGWNILVGFGIALVGFLMMSRWSE +>NAFOICDF_00361 +MATTSGKRKDSARRKRRELEQARSRRGRTASVSTDLGDVDATPAPLPRWYKAVMFGLLIL +GLLWIVVYYLSQGLFPIPDAGGWNILIGFGIALVGFLMMSRWSE +>MHAAABBN_02035 +MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL +WIIVYYLTQGLFPIVQIGGWNILVGFGLALVGFLMMSRWSE +>LFPAFLNI_00017 +MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL +WIIVYYLTQGLFPIVQIGGWNILVGFGIALVGFLMMSRWSE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000379.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000379.fa new file mode 100644 index 0000000000000000000000000000000000000000..80d48d5496bef7b151599e656547f66d9867524f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000379.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_00381 +MDCAAQGGAPAGTTTSPAAVGSPGPGGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTV +AAYVAQWATRDTVPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALW +VIGRVLEPALGWWRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRV +RGGQVRSIAVLIGLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGRASAPSA +GAQAAGLVLVAAVLAVLTVLGADRIGLDAVLR +>MOLHKGIG_00016 +MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAGPAPTVAPAGAAASVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQASGVTEA +LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY +VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS +FLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQVAGLVVVAAALAALTV +LGAARVTVAGLLG +>NAFOICDF_00362 +MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA +RLAAGVPGPASGTTTSPAPASAGAGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGSR +TGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGWW +RFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLIG +LNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGGPPGRSAAADGTARRSSAGVHVAGL +VLLAAVLAVLTLVGAARLSPAALLG +>MHAAABBN_02034 +MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAGPAPTSPPAAGAAATVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQASGVTE +ALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLAL +YVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVF +SFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARLPSVGAQVAGLVVVAAALAALT +VLGAARVTVAGLLG +>LFPAFLNI_00016 +MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAGPAPTVAPAGAAASVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQASGVTEA +LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY +VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS +FLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQAAGLVVVAAALAALTV +LGAARVTVAGLLG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000380.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000380.fa new file mode 100644 index 0000000000000000000000000000000000000000..c27a16fd3f053f672c7068ac8de28bd35f219389 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000380.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00382 +MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA +>MOLHKGIG_00015 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA +>NAFOICDF_00363 +MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA +>MHAAABBN_02033 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA +>LFPAFLNI_00015 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000381.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000381.fa new file mode 100644 index 0000000000000000000000000000000000000000..c31a1b314f081ffba7a56a3b352e7b98b27ff231 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000381.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00383 +MARTTLNDEIQHDGGADTFVTRQTENLRHWAAPKLEAARTWGEYGAAFTGVGASVAAEEG +RRAAHDAKQEYGPRVEKQAKRAGDAVADRYAKLAPAVATGAGVLQDVLHRLQEQAQEAGH +EAQKQFADARKDAEKAAEKGRKRGAKKAKQVRRAGRGARKDVTKAARGARKDARQAGSFL +ADRAGQAGSAAAAGGLTLAGALAAAVNALQEQGEKLAPQVQARLSDAGDYAQRRKEEVVP +LAAARLADGAAHARKTAHDVQVPDAVEQALIALTGDKAIVRKLRKGAEQYAGSAEKDLNR +AAGRKARSGGRGWILGGMALAAAGAGYALWRLTKPVQDPWTAPVPGPITANIPVVEANNP +YAQQQKVVAESGSAAAGEGVRVDTAAPVTTAVPAQDPVAEANAKVLGTDR +>MOLHKGIG_00014 +MARKTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG +RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH +EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS +AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE +EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVQRLRQGAEQYAGAAEK +DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV +EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR +>NAFOICDF_00364 +MARTTLSNEIEHNGSADTFFARQAENLRHWAAPQLENARAWAEVTTGFGQVGGKVAAAEG +RRLAEEEVAPRVKDSAERVNAAAKGRYEKAAPVVATGLGAAGTVLQQLLEAAQDKAQQAG +QQVQDLAEQAQKDAKKSAKRTRKDAKKAGKRVSKKADKAQSLFASKAGDAKGAAAAGGLN +VAGLLAAAVAAAQDRGQELAPQVKGRVEQAAQYAQDRRAEYAPKAAASLAGVAGRAEKAA +GDVTVPASVEQLLVKLTGDKNAVKHLRQDVQSRARETQKGLKKQARQESRRGGATGWIIA +GMAAAAAGAGLAVWKLTKPVQDPWAAPVPGPITANIPVVQADGTVNPYAKQEQAVAEARA +AQGGMVNVRPQVG +>MHAAABBN_02032 +MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG +RRKAQDAKQEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH +EVQQQFAAARKDAEKAAKKGRHRGGRKAKQLRRDGRQAAKGARKDAQRSAALFSDRAGQA +KDAAAAGGLTLAGLLATGLSALQEQGGKVGPQVQARLADAGDYAQRRKEEVLPVAAARLA +DGAAHARKTAHDVEVPDALEQALIRLTGDKAIVQRLRKGAEQYAGAAEKDLNRAAGRRTS +RSGGRAWIVAGMAAAAAGAGYALWRLTKPVQDPWTAPVPGPIAANIPVVEANNPYAQQQK +VVAEAGSAAAGEGVRVDTAAPDPVAAANAKVLGVQPGQQR +>LFPAFLNI_00014 +MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG +RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH +EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS +AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE +EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVKRLRQGAEQYAGAAEK +DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV +EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000382.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000382.fa new file mode 100644 index 0000000000000000000000000000000000000000..040d3f6fb420b23a42a95b2266afb9e1205d07e0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000382.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00385 +MGARILADMDTGIDDACALLQLVGAGAELAAVTTTGGNATARECALNTAALLDLMGRTDV +EVAVGAEAPLQRPPETTPETHGDGGLGYARLAHRPERLSARSAVDVWVEELRARPGRTTI +LCTAPLTNLALALRAEPALPELAAGVVIMGGAFYYPGNTTPTAEWNTWCDPDAAKEVFAA +FEGLPEDRLPLLCPLETTERIEYTPALLDALLTGVGHAPTGWSVDRARHAGPQADTGSPV +LDVLADALRFYFEFHHDYDQGYVAHLHDLFAAQVALGTAQIRTQATVVDVEADSDLLRGT +TVHDDRHIWGRRPNARRVVDADPAGVFAAFAQAASAAARAGDDAGR +>MOLHKGIG_00643 +MTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVLDLA +GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSPRPAVDVWLDELRAHP +GETAILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK +EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGAHPVGWSADRPRVAGPDAA +TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE +LLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR +>NAFOICDF_02182 +MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVL +DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIDRRPERLSPRPAVDVWLDELR +AHPGETTILCTAPLTNLALALRAEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD +SAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPARWDVARPRVSGP +AADTGHPVTDVLADALRFYFEFHHDYDQGYIAHLHDLVAAQVAAGQADVTLQATVVDVEA +DSELLRGTTVHDDRRIWGRRPNARRVTGCDPRRVFEDFAQAVGALTGAGVG +>MHAAABBN_00380 +MTARLLADVDTGIDDACALLHLVGAHRLGVGPELAAVTTTGGNATARDCALNTAAVLDLA +GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSSRPAVDVWLDELRAHP +GETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK +EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGPDAA +TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE +LLRGTTVHDTRDIWGMRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR +>LFPAFLNI_00613 +MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELVAVTTTGGNASARDCALNTAAVL +DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRHPERLSPRPAVDVWLDELR +AHPGETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD +AAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGP +DAATGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVIDVEA +DSELLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTPDGGAPAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000383.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000383.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a6576b074f67d8092a90a369f90d6c39771d7ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000383.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00386 +MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG +PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL +TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF +RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV +KASEPTYRPASSPARAAADAA +>MOLHKGIG_00011 +MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI +SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS +WTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAFRLILST +VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT +YRAPGFEIHRDDDPALAPAASR +>NAFOICDF_02181 +MNTTPASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYGPTVPGVSD +VFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAALTYRLVALT +TPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAWRLIASTLV +GEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWLKRHEPTYR +AQPTPAPVSAPTA +>MHAAABBN_02029 +MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI +SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS +WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAFRLILST +VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT +YRAPGFEIHRDDDPALAPAASR +>LFPAFLNI_00011 +MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI +SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS +WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAFRLILST +VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT +YRAPGFEIHRDDDPALAPAASR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000388.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000388.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b3730bf31aec5dedf995800165c98af95dea0a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000388.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00417 +MSTSASSRPGKAAGAGRTAERSGRPVRKASGSSQENLVRAVPKAKVRRARLMLNRVDPWS +VLKLAFLLSVALGILTVVAAVALYSLSDALGLFQRINDALGTVLGAESGRYTVQSLAPLS +TVVSLATVLAVLNVILLTALATVAALLYNVCAALVGGVGVTLTDD +>MOLHKGIG_00007 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW +SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL +STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGIGVTLTDD +>NAFOICDF_00369 +MSTSASSRPAGAKGASASRPARRSSSRDSQEDLVRAVPKAKVRRARLQLTKVDPWSVLKL +AFLLSVALGIILVVATVGFYTLAELTGVFGKINDVLGTVLGTESGTYTVENLAPLSTVVS +LATVVAVLNVILLTALGVVGALLYNVCASLVGGVGVTLADD +>MHAAABBN_02012 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW +SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL +STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD +>LFPAFLNI_00007 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW +SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL +STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000391.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000391.fa new file mode 100644 index 0000000000000000000000000000000000000000..30fe6ed32c3b95c400f1974c0c6354112764de7c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000391.fa @@ -0,0 +1,23 @@ +>ACLBLIBL_00420 +MSSVFGRLIRDRGWSTPVAVGSVLTRWDELVGPEIALHCRPESFEDSVVRVRTSSTAWAT +QLRLMTPVLLQRFDDALGPGVVTRLEVAGPQAPSWRKGPRTVRGGRGPRDTYG +>MOLHKGIG_00004 +MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD +RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED +SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR +GPRDTYG +>NAFOICDF_00373 +MRERSPEPDALAELPPDRPDLALVQLRRVRDAARQRGEAPLNRRGTAAGLAQSMAGSEAA +AAAGGAVARSGHRRPGAPADRDPAVVSSVFGRLIRDRGWSTPVAVGSVLTRWADLVGPEI +ALHCRPESFEDSVVRVRTSSTAWATQLRLMSPMLLSRFDEALGPGVVTRIDVAGPAAPSW +RHGPRTVRGGRGPRDTYG +>MHAAABBN_02009 +MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD +RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED +SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR +GPRDTYG +>LFPAFLNI_00004 +MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTTSAGRERQD +RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED +SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR +GPRDTYG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000392.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000392.fa new file mode 100644 index 0000000000000000000000000000000000000000..f11e45a487237b8007b3e15799d4a5a7dd65f5fb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000392.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_00421 +MHLSHLTVADFRSYRWADLELGPGSTVLLGANGVGKTNLVEAVGYLGSHQSHRVSSDAQL +VRFGQDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLNLVTGEPGGRRRLLDQLMVQLRPALGEAAADFERVLRQRNALLKSARKARRWGPEEEA +TLEVWDEHLCAAGARLLHGRLHVLRLLAHPLREMYGALTNGSKAATYAYESTVPLARGTH +AEVPPVAELAADMRRALVAQRDEEQARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRLAAYDVLVADDPDPDGRPVLILDDVFAELDAARRRRLAALVGRAEQVIVTAAALE +DVPAELAGPRVLIRQDAEGSEAVPAAAPVEGDIRAPRGAGGTEGEAPGARRGRRRRRRHA +PADPAEDDPDG +>MOLHKGIG_00003 +MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL +VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA +TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH +AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE +DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG +>NAFOICDF_00374 +MHLSHLTVQDFRSYRWADLELSPGSTVLLGANGVGKTNLVEAIGYLGSHQSHRVSQDAQL +VRFGQDRARIAGRVHRGARSVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLGLVTQDPGGRRRFLDQLMVQLRPALGQAAADYERVLRQRNALLKSARKARRWGAEEDA +TLAVWDEHLCAAGARLLHGRLHVLRLLAHPLQEDYAALTNGSKTATYSYESTVPAARGTH +VQAPPVAELAASMHAALVEQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRLAAYDVLVADDSDPEGRPVLILDDVFAELDAARRERLAGLVGRAEQVIVTAAALA +DIPASLAGHRVLIRQDAEGSEAVAAAEPVEGDIRAPRPGAAPGAAASEAEEPEDGDARA +>MHAAABBN_02008 +MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL +VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLGLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKAGRGSRRWGPEEDA +TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH +AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE +DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG +>LFPAFLNI_00003 +MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL +VRFGRDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA +TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH +AEVPAVADLAADMHRTLEAQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE +DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000393.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000393.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ee09d7be9ccb2631d6d8387252d306793b7e3e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000393.fa @@ -0,0 +1,39 @@ +>ACLBLIBL_00422 +MPVLSGLLITAEAGVVSIASFDYETSARLEIEADVETDGQVLVSGRLLNDIVRALPHAQV +TVELDGGKVVVTCRSSRFALATMPVGDYPALPELPTPAGTVDGAAFAHAVAQVTVAASKD +DTLPILTAVKVEIEGDTMTFLATDRYRLAMKEIRWTPADPSISTSLLVKARTLTEVAKSL +GAGGDLEILLGEGTDLVGFSSGGRRTTSVLVDGEYPKIRSLFPETSPIQAVVDTAALVEA +SRRVALVAERNTALRMVFTDGQVTLDAGTGDDASANESVPCTLEGEDITVAFNPSYLSEG +LAVVDQPQVRFAFTSAPKPALLTGVNQEDGVVSDYRYLVMPVRIA +>MOLHKGIG_00002 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA +>NAFOICDF_00375 +MKFTVARDILSDAVSWAARSLSPRPPVPVLSGLLVTAEAGLVSIASFDYETSARLQIEAD +VEDEGQVLVSGRLLNDIVRALPNAPVTLELDGGKVLVTCRSSRFQLATMPVADYPALPEL +PEPAGTVDGAAFAHAVNQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMTEIR +WNPADPAISTSLLIKARTLTEVAKSLGGGGRLEIMFGSSHDLVGFSSGGRRTTSVLVDGE +YPKIRSLFPETSPIQAAVDTEELIAASRRVALVAERNTALRMVFTDGQVTLDAGTGDDAT +ANESVPCTLEGEEITVAFNPAYLSEGLAVVDQPQVRFSFTAAPKPALLTGVHEEDGTVSD +HRYLVMPVRLT +>MHAAABBN_02007 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA +>LFPAFLNI_00002 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000394.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000394.fa new file mode 100644 index 0000000000000000000000000000000000000000..287add17d0c7c65d43e7358a52df9004140b09e2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000394.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00423 +MVADQAVLSSWRSVVGALEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +AQVAEALTDALTAEFREEILLAISIDANLQPPRAPEPEARRSALAGEPVTPAAPAAPGPE +QSAGTGEPSRRAVAEELPGFRTEPPADVVPPEAAGAQAGKPTPAPPSTSAETSRLNDRYH +FETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLR +VRYVNSEEFTNDFINSIRHDEGASFKQLYRNVDILLIDDIQFLADKEATVEEFFHTFNTL +YNNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVA +PPEALEYIASRISTNIRELEGALIRVTAFASLNRQSVDIELAEHVLKDLITDETAHEITP +ELILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTT +VIHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA +>MOLHKGIG_00001 +MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +TQVADALTDALTQEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPSGAAAPDVELPP +AATAATSRRAVAEELPGFRIEPPADVVPAANAAPNGNGKPTPAPPSTSAETSRLNDRYHF +ETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRV +RYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLY +NNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAP +PEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEITPE +LILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTTV +IHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA +>NAFOICDF_00376 +MAADQELLDRWREVVTALDDDPRVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +AQVADALTDALTAVFREEILLAISIDSSLQPPRTPSADDRRAEELPDLAAARAETSPAPA +PAAGMHRGVAEELPGMPAPREEPAPSRAAAPAAGAPTPAPPSTSSETSRLNDRYHFDTFV +IGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRVRYVN +SEEFTNDFINSIRHDEGASFKAVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLYNNNK +QVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAPPEAL +EYIASRISTNIRELEGALIRVTAFASLNRQPVDIELAEQVLKDLITDDATQEITPELIVH +TTAEYFNLTIDELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQELGGRDHTTVMHAD +RKIRELMAERRTIFNQVTELTNEIKRKQRGA +>MHAAABBN_02006 +MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +TQVADALTDALTKEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPSGAAAPDVELPP +AATAATSRRAVAEELPGFRIEPPADVAPAATAAPNGNGNGKPTPAPPSTSAETSRLNDRY +HFETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGL +RVRYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNT +LYNNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLV +APPEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEIT +PELILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHT +TVIHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA +>LFPAFLNI_00001 +MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +TQVADALTDALTKEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPAAAAVPDVELPP +AATAATSRRAVAEELPGFRIEPPADVAPAATAAPSGNGKPTPAPPSTSAETSRLNDRYHF +ETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRV +RYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLY +NNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAP +PEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEITPE +LILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTTV +IHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000395.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000395.fa new file mode 100644 index 0000000000000000000000000000000000000000..4d785a1c2fe7adc0ef4def2084621daafbb74619 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000395.fa @@ -0,0 +1,12 @@ +>ACLBLIBL_00424 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILAARRGKGRAELSA +>MOLHKGIG_02312 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA + +>NAFOICDF_00377 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSTRRGKGRAELSA +>MHAAABBN_02005 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA +>LFPAFLNI_02253 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000396.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000396.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b627767c67af0e76a6877f56963e26d3b454c0e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000396.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00425 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDHTRSTSPSVPRPRAGFVVSKAV +GNAVTRNRVKRRLRAVVAEQMRAAPLRELPVLVQVRALPPAAEADHALLRRETVGALAKA +LRPHLPAVPRDEA +>MOLHKGIG_02311 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTPPSAPRPRAGFVVSKAV +GNAVTRNRVRRRLRAVVADQMRTAPLRELPVLVQVRALPAAAEADFALLRRETVGALGKA +LKPHLPAASEHA +>NAFOICDF_00378 +MLPRDRRVRTPEEFRRIRRTGSRAGRSTVVVSVAADTDPARPGATSQPRRPRAGFVVSKA +VGNSVVRHRVTRRLRALLRAELDSPALRDRALLIQVKALPAAVDADHATLRRDVHGALGA +AVRKLDQADRSR +>MHAAABBN_02004 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV +GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA +LKPHLPAASEHA +>LFPAFLNI_02252 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV +GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA +LKPHLPAASEHA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000398.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000398.fa new file mode 100644 index 0000000000000000000000000000000000000000..e8764d256c7cd7013aca7bccfb9d3f6d542ba43d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000398.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00427 +MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI +KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF +FFALYQVLIGARGASERGESMDALSADQIRSFEGSMIFGARMSDTFLNSFGDPGSAPLII +TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEQELNERRAAKGLPPVGQKVTDSKAEPSSAH +TQAAGGGTATLNGEPVRDSGQRVQPQRKNRRRK +>MOLHKGIG_02309 +MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI +KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF +FFALYQVLIGARGASERGESMDALSADQIRSFEGSTIFGARMSDTFLNSFGDPGSAPVII +TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVTDSKAEPSSAH +TQAAGGGAVLNGEVVRQSGQRVQPQRKNRRRK +>NAFOICDF_00380 +MFDAILAPFRWIMSWLLGAFHTVLDTIGLPADSGWTWALAILLLVILIRTLLIPLFVKQI +NAQRAMQTMQPELQKLQAKYKGKKDQLSRQAMALEQQALMREHKANPFAACLPLLIQMPF +FFALYQVLVGARGAAERGESMDALSAETIRSFESSQIFGARMSDTLMGSIGQPGGAAVVV +VAIVLILLMTGSMFFMQKMLMTKNMTQTALEGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRHNPTPGSLAEQELNERRAAKGLPPVGKKVASSEAKPGSAH +TEAAQGAVVNGEVLREGGQRVQPQRKNRRKK +>MHAAABBN_02002 +MFEAILSPFRWLMSWLLGAFHSILEFAGLPADSGWTWALSILLLVVLIRTLLIPLFVKQI +KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF +FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSGPVIV +TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH +TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK +>LFPAFLNI_02250 +MFEAILSPFRWLMSWLLGAFHSILEFAGLPVDSGWTWALSILLLVVLIRTLLIPLFVKQI +KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF +FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSTPVIV +TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH +TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000399.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000399.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb2af1034fc2567a6876ab6332f9877f8a5e58da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000399.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00428 +MSAENVNPAAEAEDAVVETTPAPDAPQAPAAEERTGSDAAVAAGEGAESSAAESASDGVR +RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVVSEDHDERLNALVGRDGKTLE +ALQELVRLAVLAATGHRSRLILDICGHRERRDADLRETAQDAVERVRAGEGPVHLSPMGA +YERKIVHDVVADAGLASASEGEGARRHVVISADA +>MOLHKGIG_02308 +MSAENVTPAPEAEDAVVETPAGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA +DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL +ILDVCGHRERRNVALRTAAQAAVERVRVGEGPVHLEPMGAYERKIVHDVVADAGLTSESE +GEGARRHVVISADD +>NAFOICDF_00381 +MTAEHEGPLADAAEDSPAVEAPVEATAPDAAVDEQAEAVRRLEEEGDVAADYVEELLDIA +DLDGDIDIEVRDGRTYVSVVPGEDDEDDRLADLVGPDGKALEALQELVRLAVLTATGHRS +RLILDIAGHRRRRDAELRTLAGEAVERVRSGAGEVHLDPMGAYERKIVHDVVAEAGLASE +SEGEGPRRHVVISG +>MHAAABBN_02001 +MSAENVTPASEAEDAVVETPVGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA +DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL +ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE +GEGARRHVVISADD +>LFPAFLNI_02249 +MSAENVTPAPEAEDAVVETPAGQGSRVAEQDDAAVSEAVRRLEQEGDVAADYVEELLDIA +DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL +ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE +GEGARRHVVISADD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000400.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000400.fa new file mode 100644 index 0000000000000000000000000000000000000000..4dd94def1b319a1cdb492ae5b52f3b470d73b9ff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000400.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_00429 +MPEQASPYERRPGLDPKERGDRPAPVGQPAPPLIDALRPAAVELFGEDLPRAERYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELIPEGALVADVGSGAGLPGLCLALARPDCR +FLLIEPLERRVEWLDMVVEDLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGDGQLLAIKGRAAADEIAAARKVLRKYGGDEPEILTVGEGLLPETTTVVRVSARA +R +>MOLHKGIG_02307 +MTERGSAYERRPGLDPQDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVAARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP +R +>NAFOICDF_00382 +MSAPQLTAELRPAAEDLFGEALPLAERYVDHLATTGIEWGLLGPREVPRLWGRHVLNCAV +VARLLPEGSLVADVGSGAGLPGLCLALARPDCRFTLIEPLERRVAWLEMVIADLGLTNVE +VVRGRSEQVADEIQVDIVTARAVSALKTLLPLTMPLLRSSGHLLAIKGRSAAEEITAAQK +PLRKYGGGDPEIVTVGEGLLPEPTTVVRVPARRAR +>MHAAABBN_02000 +MTEQGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP +R +>LFPAFLNI_02248 +MTERGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP +R diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000401.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000401.fa new file mode 100644 index 0000000000000000000000000000000000000000..30275ba811db2e0817be73c17f61f0274f99d1ad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000401.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00430 +MAQEQESRGGAWRALRQKWSGRSAEQGAGEAEESSRLKARRLARPERTRVFTTSNQKGGV +GKTTTTVNLAAALARAGMRVMVIDIDPQGNASTALNIPHTGDVASVYDVLLGEMEMHDVV +QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREENGQERLDYVFID +CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTM +FDARTNLAVQVAEEVRAHFPEQLLGTAIPRNVRISEAPSYQQTVLTYDPTSAGAVAYREA +AAEIAGRGAPAAKG +>MOLHKGIG_02306 +MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV +GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV +QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWRAEDGQERLDYVFID +CPPSLGLLTVNAFVAAQEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM +FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA +AAEIAGRGAPSVKG +>NAFOICDF_00383 +MAKDQDSRGGTWKALKQRWSGRASDKASPEEAARLKARRLPVPDRTRVFTTSNQKGGVGK +TTTTVNLAAALARAGMRVLVIDIDPQGNASTALNVPHAGDVASVYDVLLDEMEIHEAVQD +APDVDGLQVVPATIDLAGAEIELVSMVAREQRLARALDRYMAWRADQGQERLDYVFIDCP +PSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTMFD +ARMNLAVQVAEEVKAHFPEQLLETAIPRNVRISEAPSYQQTVVTYDPASAGAVAYREAAA +EIARRGAPQAR +>MHAAABBN_01999 +MAQEQESRGGAWRALRQKWTGRTAEKGGADVEEPARLQRRRLTRPDRTRVFTTSNQKGGV +GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV +QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID +CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM +FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA +AAEIAGRGAPTALKS +>LFPAFLNI_02247 +MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV +GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV +QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID +CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM +FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA +AAEIAGRGAPAVKG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000403.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000403.fa new file mode 100644 index 0000000000000000000000000000000000000000..c50f426741cc180ca7ddf56aee9c281645a4f364 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000403.fa @@ -0,0 +1,61 @@ +>ACLBLIBL_00435 +MAPGAAETDTVETRADEPAAAEPESTATAPAEDVDPEPTAPAPVVPASTAPDSAPDTEAI +PVRRQRPVPRRAMVVEPTTPDADRSPDAQRSRGAGAPLAAAGAGAVAAAGATAASAAAAG +AAPSATSAPSTASAAPEATAAGTSPADGDGGAPVDPDQGGSRRGGWPLALLLLAVLVGAL +VLGGVLLAQNLRGAPHRAGRPARLPHRDRRGARTRRQPPPTQSDEASPTEASPTESSPAA +STSASPTESETAAAAPQPARALRMVPDLPAHESEHDGELPNLIDGDPSTAWRTFAYARPN +FGGYVESMNLVVELEDRAEVNEVTLQSTGATGGAWFAYIADSPEGENAREIGNGTFDQDS +VTVPVPFDGAEAEAEYVIVSLTSLPRLDGTTPDLPFGLRLGEIGVR +>MOLHKGIG_02302 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR +ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF +GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA +AAGASALAAADAATRKQQEERERAEREAAERAERERKEAAERAERERKEAAERAERERKE +AEEKARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEERA +AREREAEQARLAAEREEAERRELERRAEARRRAEEERAREAAEREAEKRAAQEREAAERE +AQAGTAALPAVAAGAAAAQAPDADADGATPPTEPVESVAAEKTDPPEPVAPDTEAIPVRR +QRPVPRRAIVAESAPTAHEESRGTAAPVAAGAGVATAAGAAAAGSTAAAAAPDAQAAPAT +TGGGDGATVADPGDGHGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAASSE +SESASSESASDTPSPSESTSPSPTPSSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNL +IDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADS +PEGANAKEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGE +IAVR +>NAFOICDF_00387 +MPQPLAVGSVLGGRYRITDHVVTSADQNMVFQGADQVLNRRVTVLVASPENATQVAASAR +ELATGERQDDVQVLDLGLSEGRTYLIAGGNPDPDVLLGLAYAQELYVEPFQTDSLGSEIF +GESRTEQAHEYDDDDAYYADLDRRLRADQKQSQRRPGFLNRISEKLNERVRPADGTAAKA +AAGASALAAADAATKAQLAEQERAEREAREAQERAEREEAQEAERREREAQERAERERLE +RAAAAQAEKDRAAREAAEAEAAARREREAQRHAEAETRRREEEAAAAAALAAAAPAADAD +PADAPTQAVPVTEPASTPEAVPAPVRRPRPAPRRALPAVASAAAVAASVSAEEGASAAEA +APAESVAPEAVPTATATSSAAIAVAEAEPAVTEHREEAHAAPVAGGAGAGAPAAGATAAP +ARSTSGKGWLMVLGLLALLALAGLAGLFLLGQNTRSVEPAPSASASSAAPSTAQASSAPP +AASSSAAPTASSSAAPSTEPAPSTSAAAPAPTAAPQAVAVTRQVPEMPELEAPNDATLAN +LIDGDPNTAWQSYTYARPNFGGYVGSMNLVVQLQERTTISEVQLENRGATGGKWIAYVAN +TAQGGEGDARVIGQGTFDEDSITIPVDIAENQGQYVILSITGLPQLEGAGQRPYGLQLTE +IGVR +>MHAAABBN_01995 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR +ELATGERNDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF +GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA +AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEEKARAEREAAERAERERKEA +AERAERERREAEERAEEERRAEAERARRQAEQEAEERAAREREAEQARLAAEREEAERRE +LERRAEARRRAEEERAREAERREAEKREAQEREAAEREAQEREAAEREAQAGTAALPAVA +AGAAAAQATDADADGATPPTEPVEPVESVAAEKTDPPEPVAPDTEAIPVRRQRPVPRRAI +VAESAPPVHEESRSTAAPVAAGTATGATAAAAGSTSAAAAPDALAAPATTGGDDGATVAD +PGDGNGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESASSESASD +TPSPSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRT +FAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAKEIGN +GTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR +>LFPAFLNI_02243 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR +ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF +GESRTQDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA +AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEERARAEREAAERAERERKEA +AERAERERREAEERAEEERRAEAERARRQAEQEAEDRAAREREAEQARLAAEREEAERRE +LERRTEARRRAEEERAREAERREAEKRAAQEREAAEREAEKREAQAGTAALPAVAAGAAA +AQTTDADADGATPPVEPVEPVEPVAAEKTDAPEPVAPDTEAIPVRRQRPVPRRAIVAESA +PPVHEESRSTAAPVAAGAATGATAAAAGSTSAAAAPDALAAPATTEGDDGATVADPGDGN +GRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESESASSESASDTPS +PSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAY +ARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAQEIGNGTF +DQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000405.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000405.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4489aec9850e54815306be5eb54bb428aa41880 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000405.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00437 +MDLTTATLALPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRVSGDLDFT +TDAGPDAAEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEEDLLRRDFTVNAMALRLPGLELVDPYGGVQDLAAGVLRTPGAPEDSFSDDPLRMLR +AARFASQLGFTVADEVEAAMTAMAERIGIISAERVREELVKLVCGAHPRRGLDLLVRTGL +AEHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEAEYSPSAPDPVLRLAALLHDV +GKPATRRFEKGGAVSFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGEA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNKRKAERLAHAYDDLERRIAEIAEQEEL +AAVRPDLDGEQIMALLGIRPGPVVGRAYRHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +AEG +>MOLHKGIG_02299 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEITEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +QQD +>NAFOICDF_00390 +MEPRTDTRPLPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLLLGRPVVDLDFT +TDADPDATERIGAGWAEAAWDVGRHFGTIGFQKGGWQLEVTTYRAEQYDPTSRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPAMELVDPHGGVRDLAAGVLRTPGAPEDSFSDDPLRMMR +AARFASQLGFGVADEVEAAMTDMAERIGIISAERVRDELVKLVRGDRPRAGLDLLVRTGL +AQIVLPELPALQLETDEHHRHKDVYAHSLQVLEQAMGEEERYSPERPDVVLRLAALLHDV +GKPATRRFEPSGAVSFRHHENVGAKLVRRRLKALRFDNDTIKAVARLVELHMRFYGYGEA +GWTDSAVRRYVHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIEEISAAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYAHLLEWRLDEGPHEQAAAEAELRRWWAEQPEA +AGASSGGGARD +>MHAAABBN_01992 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRTSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEEAMAAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYNHLLEWRLDEGPHEQAEAEAELRRWWAEQPEA +QQD +>LFPAFLNI_02240 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +QQD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000406.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000406.fa new file mode 100644 index 0000000000000000000000000000000000000000..0dad90c5969043cd1179d5f54b3946cee281c37e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000406.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00440 +MATTPIRVAIAGVGNCATSLIQGVEYYRDAKATDTVPGLMHVQFGDYHVSDLQFVAAFDV +DAKKVGLDLSEAILASENNTIKLADVPHADVTVQRGPTLDGLGKYYAETIEESDAEPVDV +AQALRDAQVDVLVCYLPVGSQLATEHYAQTAIDAGVAFVNALPVFIAGTPEWADKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAKLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGTGGPILSASSYFMKSPPVQHNDDEARELVEAFIRGDIE +R +>MOLHKGIG_02296 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESDVEPVDV +AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFQDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R +>NAFOICDF_00393 +MAENPIRVAIAGVGNCATSLIQGVEYYKDAQASDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAILASENNTIKISDVPATGVTVQRGPTLDGLGKYYRETIEESSAEPVDV +VQALKDAKVDVLVSYLPVGSEEADKFYAQCAIDAKVAFVNALPVFIAGTQEWADKFTEAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAELAEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHADDEAHELVEAFIRGDIE +R +>MHAAABBN_01989 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGVYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV +AQALRDAEVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R +>LFPAFLNI_02237 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV +AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000409.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000409.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e82e511cc771d710dd98c105734bc76524b6f9a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000409.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00443 +MTAVTRDTAPAPEMSAHVQDLAAFVTASPSSYHAAAEVARRLVAVGFTCLDEAADFPAAP +GGYVVVRDGAALAWVVPTGAGSDVSDGAGAAGGSGAGAAVPVFRVLGAHTDSPGFKLKPN +PATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQLAIH +LDREVNDGLKLQRQRHTNPVVGALAPRGEGAGEAVADVSEGVDGRSAPLEQAAGAGAGVG +AGAGEGAGAREGDGAGLEARAPGDVLSALAAAAGVDPAAVRGHDVMVADAQAPGLFGLAG +EFFASGRLDNLSSVHAGLVALEELARANGGASGAIAYAGTVAEGVAGEAAGAPVIPVLAA +FDHEELGSASRSGAAGPLLEEVMGRVLEALGVAGQGRARAIAGSWLLSADAGHLVHPNYA +ERHDPVNHPRVNHGPLLKINANQRYATDAGGEAAFARWCGVAGVPFQEFVSNNDMPCGST +IGPISATRLGIRTVDVGLGLLSMHSAREMCGVRDVEHLTAAVREFFRGV +>MOLHKGIG_02293 +MTPVTRDTVAELHAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG +YVVVRDGAAVAWIVPMGARALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK +LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ +LAIHLDREVNEGLTLKRQRHTNPVVGALVPRGEGAGEAEADGLAARVPGDVLTALAAAAG +VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA +IAYEGTVAGGVAGVAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG +QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA +FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD +VEHLTAAVREFFRGV +>NAFOICDF_00396 +MSTVTSESTVTAAVPGAPALSAHLQDLAAFVQASPSSFHAAAEVARRLEAVGFTRVDPAQ +DLPAAPGGYVSVTDGAVLAWILPEALAERAADAVPVFRLLGAHTDSPGFKLKPQHLTVTA +DGWVQAGVEVYGGPLLNSWLDRELRFAGRLALADGRQVLAATGPVGRIPQLAIHLDRSAN +DDLTLGRQRHTQPIVAAVAGAPDAAGTDAADGASADPVVRLTGDILELLAAQAGVDPAEV +RGADVVVADAQQGGAFGANGEFFACGRLDNLSSVHAGLRALESLAADADRAGRGVVVAEG +VAGEAAGAPVIPVLAAFDHEEVGSATRTGAGGPLLEELMGRLLSACGVTGQGAARSRAGS +WLLSADAGHLVHPNYTERHDPVNHPRVNHGPLLKINANQRYSTDAAGEAAFARWCAAAGV +PFQRFVSNNDVPCGSTIGPISATRLGVRTVDVGIGLLSMHSAREMCGADDPARLAAVARA +FFAGV +>MHAAABBN_01986 +MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG +YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGPSAGVVPVFRVLGAHTDSPGFK +LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ +LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG +VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLAALEELAREHGGAEGA +IAYEGTVAGGVAGEAADAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG +QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA +FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD +VEHLAAAVREFFRGV +>LFPAFLNI_02234 +MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG +YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK +LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ +LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG +VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA +IAYEGTVAGGVAGEAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG +QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA +FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD +VEHLAAAVREFFRGV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000410.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000410.fa new file mode 100644 index 0000000000000000000000000000000000000000..08304483fbccc18be9b0038e07782eea39c6b0d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000410.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00444 +MWLPAEAEQRVHLSRVRPGAQPRIAGVAGHRIRIDPVTGLTVLGVGDKAYTVTTPERTWT +DLASMGLTREDLIVAGDALLHRRDGPGGEVAAGRQHPLSSLADLGVAVAEARGVTGWRLL +GEALPHLRERSDSPQETRLRVRLVGAGFPEPQVNPEVPLVWDAWGRILRSTPVDLYFAAA +KVALQFEGEHHFSRARQYRRDMRRDEELRDVGVETVRVDSAVFGAGEWARFMARLQRLLT +TRGGA +>MOLHKGIG_00269 +MVAPPPHHDAAPSPVFPVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL +QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL +VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA +EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALADAGVPEPEVNPLLMLSDGSTVR +PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL +RDLAAHLRLPLPA +>NAFOICDF_00397 +MDGPRDLVWREARVAIEYEGAHHFEDADQYRRDMRRDEELRALGWVVLRVDRDVWTPQGW +EVFLGRLGAALARWSC +>MHAAABBN_02282 +MVAPPPHHDAAPSPVFSVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL +QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL +VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA +EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALTDAGVPGPEVNPLLLLSDGSTVR +PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL +RDLAAHLRLPLPA +>LFPAFLNI_00267 +MVAPPPHHDAAPSPVFPVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL +QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL +VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA +EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALADAGVPEPEVNPLLMLSDGSTVR +PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL +RDLAAHLRLPLPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000411.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000411.fa new file mode 100644 index 0000000000000000000000000000000000000000..67d583a48caa5f768ad732e44473feef5720d7df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000411.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00445 +MSEHPASPTHVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTPDTGDH +VDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLLAPGETLDSVDPKTVHLV +LLDTVPHPEAGEALAAVDAGDDRAVVVGRGVWVRYAGPSHSSHLGLPRIERAASGDAPPA +QRRVGTARNLATVRVLAGR +>MOLHKGIG_01260 +MSPAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD +AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD +PAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTPARLDRALGVRGTA +RNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGRDVTVRSHPCDGVTPSSASLP +>NAFOICDF_01525 +MSRAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLPDA +DDDAGPAFLRAFRDAALADDGPDVPLILTTPAELRGALAMHDRLPWSGGEAKLTQLTVLA +ESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTPARLEKALGVTG +TARNLATVRVLAGMA +>MHAAABBN_00979 +MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD +AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD +PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA +RNLTTVRVLAGLPSED +>LFPAFLNI_01218 +MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD +AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD +PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA +RNLTTVRVLAGLPSED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000412.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000412.fa new file mode 100644 index 0000000000000000000000000000000000000000..8751882e8479f878869f0cb1fcada33518b3bd15 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000412.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00446 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDKVDVWGRRKTAYEIQKKSEAIY +VVVDFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>MOLHKGIG_02292 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>NAFOICDF_00398 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVEKIDVWGRRKTAYEIQKKSEAIY +VVVDFTAEPAATQELDRVLNLNETILRTKIIRPEEQKISAE +>MHAAABBN_01984 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>LFPAFLNI_02232 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000414.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000414.fa new file mode 100644 index 0000000000000000000000000000000000000000..541ff6d4715e60c2e08e8f8435442890b76a7e3d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000414.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00448 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>MOLHKGIG_02290 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>NAFOICDF_00400 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AIKNAREVALLPYAGAGRG +>MHAAABBN_01982 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>LFPAFLNI_02230 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000415.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000415.fa new file mode 100644 index 0000000000000000000000000000000000000000..f07df3015d02ff8b0ed3fdcbacd94d5282b26dac --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000415.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00449 +MAKLILTQEVTGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV +ANLEDAQAQAEKLQSATVKLERTAGAEGRLFGAVQAADVAEAIEAAGLGSVDKRAVTLPA +HIKSVGNHQAQVRLHEDVVAVVDLQVVAAKAKK +>MOLHKGIG_02289 +MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV +ANLEDAQAQAAQLQSATVQLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA +HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK +>NAFOICDF_00401 +MAKLILTQEVPGLGIDGDVVEVKNGYARNYLLPRGFATVWTQGGEKQVESLKAARAARAT +ANLEEAQALAAKLQSATVRIDRKAGAEGRLFGAVQAADVAEAIEAAGLGSVSKRSVTLPN +HIKTVGNHEAQVRLHDEVTATVALQVVAAKGSKK +>MHAAABBN_01981 +MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV +ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA +HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK +>LFPAFLNI_02229 +MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV +ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA +HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000416.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000416.fa new file mode 100644 index 0000000000000000000000000000000000000000..3177d636833f2b1d6f065fd9af5c3545440c1d26 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000416.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_00450 +MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI +HGNEVAGIEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR +GSLASRIAHLMMTEVIGRCSVGVDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF +HARLRDGSLRAAAREAGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALGMVDPAEVGL +TEPGPAAVVDAPGPLPGEVPGDATTDVPEATDATGEDTEAVHADVVDGGQDAPHLVWHSS +WVRARADGLVHLDVSLGERVAAGDRIGALYNSFGRRVAHVKAELTGVVIGRTEAPLVHRG +DALVHIGGWDA +>MOLHKGIG_02287 +MSRRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI +HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR +GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF +HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL +TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST +WVRARADGLVHLHVALGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG +DALVHIGGWDA +>NAFOICDF_00403 +MSAPQKDPDRGGRTGDEAAAEKATGRRRASRAPFELAGVEVRPGRRHEVSLPVSRLVTGA +EVTLPVHVLHGREDGPTVWVSAAVHGDEVAGIEIVRRVLERLKPSRMRGTLLALPIVNVL +GVMTGDRYLPDRRDLNRSFPGAARGSLAARIAHLMMSEVVRRCEVGIDLHTGADRRSNLP +QIRCDLEDPRTRALAESFGAPVLFHARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAI +SPGVEGVLRVLAALGMVAAEDVGLATPVDAPAPLPGEVPEDRTTEVPEALDATGRDTGGV +HADVVDGDLAAPHRVWHSRWVRARADGLVHLDVALGEQVTAGDRIGALYDSFGRRRSDVK +AELTGVVLGRTEAPLVHRGDALVHIGELDGRPAGTFPAPSPGRRTAPSVAEGDPEAEAPP +AATP +>MHAAABBN_01978 +MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI +HGDEVAGVEIVRRVLERLQPTQLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR +GSLASRIAHLMMTEVIGRCTVGIDLHTGADRRSNLPQIRCDLEDSQTRALAEAFGAPVLF +HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADIGL +TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST +WVRARADGLVHLDVALGERVNAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG +DALVHIGGWDA +>LFPAFLNI_02226 +MSPRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGRDDGPTVWVSAAI +HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR +GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF +HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL +TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST +WVRARADGLVHLDVSLGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG +DALVHIGGWDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000417.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000417.fa new file mode 100644 index 0000000000000000000000000000000000000000..245e935a981430c4b10ea5090aeca878bd6342e5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000417.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_00451 +MSESKHTATAPHGVPPIDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG +IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGKAQERVVVVMPLTLAG +RTFEAEVTLTHRDEMGFRMLVGRTALAAGGFHVDPAASYVGGQPPRGVRRRNRGRA +>MOLHKGIG_02286 +MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG +IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVIVMPLTLAG +RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA +>NAFOICDF_00404 +MGHVTESNHTPGRAAARPPHGDAHDAAPRPAQADADARPVREAATGVVVGWREWVGLPEA +MTPWIKAKIDTGARTSALHAFGIERYTGADGAARVWFEVHPWQASAADARTVDLPVADLR +AVRSSNGEVQERVVVMMPLRLAGRTVDAEVTLTHRDEMGFRMLVGRTALAKGFLVDPGAS +YLGGQPPRGVRRRNRGHA +>MHAAABBN_01977 +MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG +IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG +RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA +>LFPAFLNI_02225 +MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG +IERFARDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG +RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000418.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000418.fa new file mode 100644 index 0000000000000000000000000000000000000000..34e8f0f0f51943927205aadc9d9cb0976822c503 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000418.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00452 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +ILPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGKDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA +>MOLHKGIG_02285 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTCVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRRLPATPILASVAEEAPAPEAPADDA +>NAFOICDF_00405 +MKLAILSRSLRAYSTQRLKSAALDRGHDVKVLDTLRFGIDLAGDEPDMMFRGKPLSSYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRASQILSRHGIAQPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGKDVRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVEQVELSEEYAETAVRAAHIM +GLRVAGVDMLEGEDGPLVMEVNSSPGLEGIERATTLDVAGAIVDYIADQAGFPEVDVRQR +LAVSTGYGVAEIAVLAGSDMAGQSIEDSGLLEKDLQVLTLHRGASVFPNPADSKVLEEGD +RLLCFGKTENMRALIPARSQRPKRVKKLPKNPIIEAPPAEPAVRPDAESGES +>MHAAABBN_01976 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA +>LFPAFLNI_02224 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000420.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000420.fa new file mode 100644 index 0000000000000000000000000000000000000000..150fe9862fc2089912cf573d76fef3a926fbd50a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000420.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00461 +MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV +IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVHNAIVWQDTRTDRLCERLAGDV +GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGAG +GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET +PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEKPVHSDNGLLTTVAYRIGDQ +KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAASVEDNGGVYFVPAFSGLFAPHW +DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE +LLMQFQADLLRVPVVRPKVTETTALGAAYAAGLAVGFWSSQDELVANWEEDKRWEPTMDE +EEAERALRLWKKAVERSRDWVDEDVESAQG +>MOLHKGIG_02270 +MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV +IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDRLCERLAGDV +GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG +GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET +PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ +KPVYALEGSIAVTGSLIQWLRDNLGMIASAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW +DAAARGVMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE +LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTTDE +EEVERTLRLWKKAVERSRDWVDEDVESAQG +>NAFOICDF_00494 +MSAPRYVMAIDQGTTSTRAILFDHAGDAVATGQLEHAQHFPRAGWVEHDPLEIWRNTREA +IGQALSRADATRDDVAAIGVTNQRETAVVWDRTTGRPVHPAIVWQDTRTQHLCERLGGDA +GPDRWRERTGLPLATYFAGPKVAWILEHVDGAREAAERGDLLFGTTDSWTVWNLTGGVLG +GQHVTDVTNASRTLLMDLETLEWDAEIAAEMGIPGGMLPRIVSSSAEVGHAAPTSLLGGV +PIAGILGDQQAALFGQACFEAGQAKNTYGTGNFLLVNTGARPVRSRHGLLTTVAHRIGDE +PPAYALEGSVAVTGSLVQWLRDNLGLIRDAAEVEELAAGAPDNGGVFVVPAFSGLFAPHW +DPTARGTIVGLTRYADRRHLARAVLEATAFQSREVLDAVLADVAEAEEGAGVVGGLTELK +VDGGMVANDLLMQFQADVLGVPVVRPEVTETTALGAAYAAGLAVGFWASTAELAAHWSED +RRWEPAMDPERAARLLRLWARAVARSRGWIDDDVEALAAETRTAPDATPAGRTP +>MHAAABBN_01963 +MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV +IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV +GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG +GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET +PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ +KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW +DAAARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE +LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE +EEVERALRLWKKAVERSRDWVDEDVESAQG +>LFPAFLNI_02202 +MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV +IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV +GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG +GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET +PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ +KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW +DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE +LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE +EEVERTLRLWKKAVERSRDWVDEDVESAQG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000425.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000425.fa new file mode 100644 index 0000000000000000000000000000000000000000..f57eb6be95c05721c41e06614bb3869780fb53b4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000425.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00476 +MNGAELADSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPIAVGVTVGSLTAM +VSAVLIVRLMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVFAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>MOLHKGIG_02255 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMNGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>NAFOICDF_00431 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTAGSLTAM +VSAVLIVRVMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>MHAAABBN_01955 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>LFPAFLNI_02186 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000426.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000426.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e043c45be700d513200502da8da06cebeb3ffcf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000426.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_00477 +MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHAL +PPLTEWMSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAAF +LAAVAAKALRLLPNRGWRAAWALGILVAGAATVLSDGLWWIPASVAVGVSVHILGDALTN +NGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWAFVSVVTAFTVVRAVRLVPL +AARGVAGLLGAGAPS +>MOLHKGIG_02254 +MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA +LPPLTEWLSRGIRHVAGGHRRGTHSLVGVAAFTAIATAAASIQVPIAGHVYTPGQGVIAA +FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT +NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVP +LAARGVAALF +>NAFOICDF_00432 +MSTPPAALALFLPRGPPAGPRGCGDAAWLALTHGQSPVGVRHLPAELQLLGAVTTAGAAM +ISDWDYPRATAIATAAASIHVPIAGHVYTPGQGVIAAFVAAVAAKALRLLPNRGWRAAWP +LGILVAVSATVFSDGLRWIPVSVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQS +SGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVPLAARGAALF +>MHAAABBN_01954 +MMGPSHAATGAAAWLALTHWQSPIAALHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA +LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAVATAAASIQVPIAGHVYTPGQGVIAA +FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT +NNGVALLWPLSPEPPTRLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLIP +LAARGVAALF +>LFPAFLNI_02185 +MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA +LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAA +FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT +NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLLP +LAARGVAALF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000427.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000427.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a2a17d46aa4da8d5310aadedcf0e39c5229a209 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000427.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00496 +MPSRLHLRPLTVADAEEMSAVLADPALYAHTGGEPPSEELLTQQFRIQTRGESADGSERW +QNLIVVLEETGEAVGYVQATTPKDGGPTEVAWVIGVPWQGRGLGGEAAAQLVEHLAGQGV +RELIADIAPGHAASEAVARHIGLEPSDVVVDGEVRWTGTVADRER +>MOLHKGIG_02201 +MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW +ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV +RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG +>NAFOICDF_01297 +MTPPIHLRPLRPDDADEMVAVLADPALYTFTGGEPPTRGALSGQYAVQARGHSEDRSETW +LNHLVVLDDTGEAVGYVQATIPVAGGAAEIAWVIGVPWQGRGHATAAARLLLDELARRGV +SEVVADIHPGHAASAAVARRLGLRPTGHIVDGEQRWEGPVAVVDGAASAPGG +>MHAAABBN_01914 +MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW +ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV +RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG +>LFPAFLNI_02145 +MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW +ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV +RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000428.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000428.fa new file mode 100644 index 0000000000000000000000000000000000000000..d295209e47a1a7b8f35f4155bfa4284da3f9321e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000428.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00499 +MEQFLAGANAIMWSLPMVFGLLALGLYFTIRMGAPQLRRIPDMIGQLVRGGSSSAGISSF +QAFAMALGGRIGVGNIAGVATAISLGGPGALFWMWVTALLGAPVALAESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVITGPQIQANAVTAATTQAWGWDPLW +VGLAMAVLFCVIVFGGMHRLGRTVGLVVPFMAAAYIIVGVVVVALMWQQVPAMFGLIFTS +AFAADSLYAGMLGAAISWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAFVD +TLFVCTVTGLMILSTNSFNVLGPDEETVLVEHVPGIEAGPAWVQTAIDSVIPAFGPAFVA +VAVFLFSFTTLLSFAFYAETNLAYLIPNKSVQRACIAVARLGLAASMVFGAVQTSTLVWS +FADFGVGLYTWVNILALVLLSPVAIRLMKDYDRQRRAGQDPVLDPRAIGVRNATLWEQIH +DEYERTGDVTAALDHVADTAPDTRAISVVRSHGERGQG +>MOLHKGIG_02247 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF +QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW +VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD +TLFVCTMTGLMILATNSFNVLGPDGESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA +IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS +LADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG +>NAFOICDF_00437 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLKDMVGQLVRGGSSSAGISSF +QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW +VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD +TLFVCTMTGLMILATNSFNVLGPDGESLLAENVPGVEEGPAWVQIAIDAALPAFGPSFVA +IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQSSALVWA +FADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVRGGPERGEG +>MHAAABBN_01949 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLRDMVGQLVRGGSSSAGISSF +QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW +VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD +TLFVCTMTGLMILATNSFNVLGTGEGPPIVEHLPGVEEGPAWVQIGIDVVLPSFGPSFVA +VAVFLFAFTTLLSFAFYAETNLAYLIPNKKAQRICIAAARLLLAASMVIGSVQTSAFVWS +LADFGVGLYTWVNILALVLLSPVAIRLLKDYDRQRRAGQDPVLDPAAIGVRNAHLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG +>LFPAFLNI_02179 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF +QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW +VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQIPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD +TLFVCTMTGLMILATNSFNVLGPDEESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA +IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS +LADFGVGLYTWVNIVALILLSPVAIRLLKDYDRQRRAGQEPVLDPHAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000429.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000429.fa new file mode 100644 index 0000000000000000000000000000000000000000..9835543a801d5f2e7fdc30aa7466cff22403b5bf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000429.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_00500 +MTPRSLAGLALAVAALAAAFALMAPTAPGLFVGVLTAGTLGFGPFYGEPTRHLVDRPWRR +DRRWHELARRVRTDWLSRQLGAAGWNAAIRRRITGRADLRRIRTAAVGSLVSHAASVGLH +GIAALALAVVGHPGWGLLAVLLGLVVHAWPALLQVAVLGRIDGLQAQLRGDRLLW +>MOLHKGIG_02245 +MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR +DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH +AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW +>NAFOICDF_00511 +MRIPAVCAAVAVVTLLAWGFRQVVPASPGAYVAVLTAATVGFGPFYGVPTRAVVDLPWRR +LRRLRALAARAHTWWLARQLRVAGSDARIRRRIRSRADVLAFRREAVGRLLNHGLSAVLH +AAAGVALAAAGHPLWGVVAVVAGLLVHGWPGLLQVGVLGRVDELQATVQARRGVGGAASA +GR +>MHAAABBN_01947 +MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR +DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH +AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW +>LFPAFLNI_02177 +MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR +DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH +AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000431.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000431.fa new file mode 100644 index 0000000000000000000000000000000000000000..6997b13bc70c2785957f0c31894f4a97f29cdd8c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000431.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00505 +MPDSAARHSAARHDVPAPPPFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPA +EPAAQGGFQYARWGTPTWAALEAALGVLEDADVAVVPSGMAAIASVLLSHLRPGDRALLP +SDGYGATRALAAEHLSPIGVHVDLVPTPALASADLSAYDLVFVETPSNPGLRVADLADVA +ARAHANGRRGGAGALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHSDALGGHVASR +DADVLARVRGWRTLTGAILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHSAVRA +VAYPGLPDHPDAEVVARQTTAAGSVVGLEFADAAAAERFLAAARLVVPQTSFGGTHTSAE +RRARWGDDVPAGFVRLSVGVEPTAELLADVERALEAAG +>MOLHKGIG_02240 +MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA +RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA +AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG +AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW +RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD +AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD +GFVRLSVGVEPTAELLADLERAMTAAGGGPTA +>NAFOICDF_00441 +MASPQPPAFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPVAPGADVAFQYAR +WGTPTWAALEAALGVLEDADVAVVPSGMAAIAAALLPVLRPGGRALLPSDGYGATRALAA +EHLVPAGVHVDFVSTPGLADAGFSAYDLVFVETPSNPGLRVADLADVAARAHANGRRDGK +GALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHTDALGGHVASRDPELMTRVRGWR +TLAGGILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHPAVRAVAYPGLPDHPDA +AIVARQMTAAGGVVGLEFADAAAAERFIGAAAYVVAQTSFGGTHTAAERRARWGDDVPAG +FVRLSVGVEPTAELLTDLARALDAAAGPA +>MHAAABBN_01942 +MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA +RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGATRALA +AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG +AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW +RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD +AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD +GFVRLSVGVEPTAELLADLERAMTAAGGGPTA +>LFPAFLNI_02172 +MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA +RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA +AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG +AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW +RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD +AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD +GFVRLSVGVEPTAELLADLERAMTAAGGGPTA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000432.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000432.fa new file mode 100644 index 0000000000000000000000000000000000000000..af54e485e08050bddfc29b27511b81d105b9f637 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000432.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_00506 +MQLDLIVENAHLLTGDPARPEATRLGVWRGAVVGVDEELDGLGARERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGAHTAQEVYDRIRARAAELTPGAWVTCTGFDPGHLTGPQPD +RDGLDAAAAGRPVLIRHNTGHAFTVSGAVLFLAGVGEQVMQQPEGGRIITDAADRPTGLL +EETAMNLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGIAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQAMVTLDALRPVDGHADDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTADYCGHGHGRGYLQQDAGEMRRECLGAAAAGWSLALHAIGDAALDFALDV +IAEARARFGRPVMPHRVEHGGVVRDDQVARLAELEVVMATQPNFISAFGGSVRERIGPER +AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLDVIQDFVLRRTETGEQYGPDLERLTVAQA +LQAYTVGSAEATGWGGRKGRLVAGQLADFTVLSADPRAVPSEEIAAIDVVATAVGGEFVH +GGL +>MOLHKGIG_02239 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAARERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD +RDGLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAEGRPTGLL +EETAMSLVTRLLQSESHEHIGACLARASQGYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALHSVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV +IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER +AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRVVPSDQIAAIDVVATAVGGEFVH +GGL +>NAFOICDF_00442 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAAGERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD +RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL +EETAMSLATRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV +IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER +AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLAAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH +GGL +>MHAAABBN_01941 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLTARERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELGPGAWVTCTGFDPGHLTGPQPD +RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL +EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV +IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER +AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH +GGL +>LFPAFLNI_02171 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEQLDGLATRERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD +RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL +EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALHPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV +IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER +AVLSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH +GGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000436.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000436.fa new file mode 100644 index 0000000000000000000000000000000000000000..725ddadc36a691aa8cda78dd19b6fb44ea77beb7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000436.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00525 +MRAHPSPTGRTVHLSATGEDARILADELGGSVLEIGGAVQSHVDPADPTALRYEYLRRMA +NVLDGVAPAGAPLRVLHLGAGALTLPRYVQATRPGSEQTAVDLDRELVSFVLAELPLPAG +TDLVSVVADARLAAVDLLMDGERFDAVVLDIGTGEDGAAHLTGAEFYGELLGLLTAAGVL +LVNIGDDDGLRFLGAQLRHMEAACAEAGVPGPWTLASAAMLERLELGNAVLAAGPALRGD +GAAAGGDAGPEEDGGPLTPAALLARGPHPGAVLDEAASADLARRVAGR +>MOLHKGIG_02216 +MPAQPSPSGHTVHLSTSGVDARITPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA +HVLDAASPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG +TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL +LVNIGDDAGLRFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA +GCTERLAAAGPHPAAVLDPAESAALADRIRRA +>NAFOICDF_00467 +MPTQPQDDASSPAPSPTARTVHLAASGVDARILPDPHAGGWMLEVGGAVQSHVDLADPTQ +VRYEYLRRIANVLDALAPAGEPLRVLHLGGGALTLPRYVAATRPGSVQTVVDLDRELMGL +VLEELPLPADADVYVVVADARAVVDDLLDPLEGESQAGAWDAVVLDIDTDAGAVAHLTGA +AFHAELLELLAPGGVLCVNIGDDDGLAYLATQLTALEAACADAAEGAGVPGPWTLGPNSV +LERRELGNAVLVAGPGLAGMDAAALHAAGPHPAVVLDAHESAALAERITAAP +>MHAAABBN_01929 +MPAQPSPSGHTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA +HVLDAASPTGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG +TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL +LVNIGDDAGLHFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA +GCTERLAAAGPHPAAVLDPAESAALAARIRRA +>LFPAFLNI_02155 +MPAQPSPSGRTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA +HVLDGVAPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG +TDLVSVVADARLAAVDLAMDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL +LVNIGDDAGLRFLGAELGALEKAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLREA +GCTERLAAAGPHPAAVLDPAESAALAARIRRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000437.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000437.fa new file mode 100644 index 0000000000000000000000000000000000000000..87fd1bfcb964f67c6f4d8768993194772d7bdae1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000437.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00527 +MSARAARAARAGEGRQGSDAPAGADARPGAAGSALLFAMAIVAGSTIPVQARLNSALAER +SGDPTLAAVASFAAGLVLVAAVTVLTPAGRRGLRAVRPALAAGRVRWWYLLAGTIGGAMV +FSQATTVGLIGVAVFTVAVVTGQLIGGMVVDRLGLTPAGVRRMTPRRLAGAALALACVVL +VVAPQLGARGDGGPPLWLLVALAPLAVGLATSIQQTLNARQAAAYGSVLPVTTVNFVAGT +GILALVHLGGRLGGGVGGTLPGDWWLYLGGPMGVVFIAFSAYLVPRVGAFLTMLGLVSGK +LLGSLAVDALAPVGEVAASPWTVVGTLGALAAVVLASGAARPARKG +>MOLHKGIG_02219 +MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH +LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL +VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA +LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL +FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN +LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR +>NAFOICDF_00465 +MPASSPALTPAPRSGATTALLFLLALVAGLAMPVQGRVNSALSLAVGSPALAACASFATG +LAVLVLATLLLPSGRRGAARIPAAVRNGDVRWWQLLAGTIGAAFVLTQAWTIPLIGVAVF +TVAVVTGQMLGGMLWDRLGWTPAGVQRISRRRLFGALLAFCAVTAVVWPRLQESGSPGAW +LALAVLPLAAGVATSGQQAMNGHQTAHFGTPLPPTLVNFAAGTAVLAAATAVAAGTGAGM +GPLPAAWWMYLGGPLGTVFVGLGAFLIPRVGAFLTTLGMVAGQLVGSLLLDVVAPAPGAQ +VTWLTVVGTLGALAAMVVASSPQVPAGLRASRRRARRG +>MHAAABBN_01932 +MPPESSVPSAERGPSRPRPAAVAARPEAPSPRATALLFALAVAAGSVMPLQGRINSRLAH +LTGDPVLAALCSFAAGLAVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGMIGGLL +VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA +LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL +FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN +LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR +>LFPAFLNI_02158 +MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH +LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL +VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA +LVVWPSLGEVGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL +FLGIVWGGIALASGHGMPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN +LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVTLASWPARRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000439.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000439.fa new file mode 100644 index 0000000000000000000000000000000000000000..649fe00b27d366df15a55652672b21eccbb9a1fd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000439.fa @@ -0,0 +1,37 @@ +>ACLBLIBL_00539 +MTSPRPESDWRPPWQDLPADLPGRLAHALPGIMERIIQTVPDQIPAYAAARDGRYGKNLT +LGVTTALEQLMSLPGTSRPALSAQSRELMARLGAGEFREGRSMDALLGAYRTSARIVFRD +LSAECARLGMDMSVVIELGESIWAYIDELSAVSAQAYAEAQSAQAGVRELHRTALAAALV +RGGAEEKEVERLAALADWRVPARLAVVALPPDAGQAVRARLGRGGLVVERDSEVVAVVGA +DAPARRRRLLRILAGTAAVVGPAVEWPLAPHSYRVARTLAGQEAARRAAEQRAAARPEGD +GSAADGPGAEEAVGFEPVGGADPAPGTPILAEEHLARVVLGAEPRVVAELAERVLAPLAE +LTDAKRAVLEQTLLSWLVHWGQRAPIAAELSVHPQTVGYRVARLRELFGDALEDPDARFD +LELVLRARAGGMAA +>MOLHKGIG_02206 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD +DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ +RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG +>NAFOICDF_00469 +MVLSAPPRSPVVTRRLLAALQGTGAVVGPEVDALEVARSLHVARAVLARRDALSGVAPGA +AVLAEEHLADVVLGAEPEALRRLSERVLAPLDGLSDAKRATLEATLAAWLAHRGARGPMA +AELNVHPQTVGYRVGRLRELFGGALDDADARFDLELALRSRRGQG +>MHAAABBN_01919 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD +DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ +RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG +>LFPAFLNI_02150 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD +DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ +RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000440.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000440.fa new file mode 100644 index 0000000000000000000000000000000000000000..83805285c09d84d8b0aab7386fba64fce5873e64 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000440.fa @@ -0,0 +1,27 @@ +>ACLBLIBL_00541 +MLPAPTARLRFREMTEADLDAMAALLGDPAVMRFYPAPRTREQAAEWIAGNRRRYAQDGH +GLWVIETLPEHSDDGEPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACR +DHARDALGHHELVAIIHPENSVSRRVAEKIGLREAEQDFTGAAEARETMGLASRTVMAMR +F +>MOLHKGIG_02202 +MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH +GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR +DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG +A +>NAFOICDF_00472 +MTQPIPRHPDPGNTGTDALDDVVREHMLLLRRAVHGLGAYRRPEALDRSAVLLLARLEAQ +GPMTMAELAAAFGLDVSTLQRQIGAAQRAGFVERFRDPAGGQARLHRATDAGRAALEGEL +AARRAAVAEVTRSWPAPDVAALARLLRRFNEGSEELREQPWPRERPEAPGAAAVPAGTAR +LRFREMTEADLDVLVGLLGDPEVMEFYPAPKTRAEVADWIAWNRRSYAEHGHGLWIVETH +AGAFVGECGLTWQRVNGERRLEVGYHVAPVLQGRGYATEAAAACRDHARDVLGAPELVAI +VHPENTASRRVAEKIGMEVLEEDRTGVDASYLEAIGAEARTVLGMRLA +>MHAAABBN_01915 +MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH +GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR +DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG +A +>LFPAFLNI_02146 +MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH +GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR +DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG +A diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000441.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000441.fa new file mode 100644 index 0000000000000000000000000000000000000000..9e569528c050b7b14913ca86f3f56fb4faebbc5c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000441.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00542 +MLAAVLAFALIGAVLWAALALGPDGVPGQQGSRRPAASTPAPPTVSAEGFAEPVRGRVTS +RFGPRPNPFGEGSAPPSTDTDALTDHTGVDLGGVPEGTPFHSVSDGRVLFVEAGEDAGGN +LLAVDSGDGHVWRYLHAAPDSTVVNAGQRVSAGDALAGVGQTGTATGVHLHLELRVDGTP +VDPEPYLRERGVELGSSWERPRRR +>MOLHKGIG_02200 +MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF +TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT +PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG +VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR +>NAFOICDF_01787 +MKKLAVIAAVLVLFSPALLLLGVGMIFSPGANASCTTSTTGPSVVGPVPDSLDVTTADGQ +TFTLNTTQLTHAATIIQTGSQIEGVTRDGLQIALMAALTESNLRMLANTSVYPDSGNHPN +DGDASDHDSLGLFQMRPQAGWGTVPDLMDPGYQARAFFGGPTGPNHPSPRGLLDIPGWQT +LSKGEAAQAVEVSAYPDRYANYEPVAEQILTTLTTPTADSPQLPETGRVVFPLPEGTWVA +TSPFGMRVHPITGENKLHTGADYSAPDGTPVLAAADGIVTHASMSGGYGGLIIIEHTTGG +QKIATAYAHLWETGIHVNVGDQVTAGQHIGDVGSAGYSTGAHLHFELRQGGSDGEFTDPQ +PWLDQHTSGNLPAPTTPVEQEGCNPVATQPAPPQGPDAGDPDRKVDDPTTDGQITARMLH +VYTQALTAYPDSSWACYSPRPGTKSEHPLGRACDVTFGNAIGSRPTPQQLEAGWALTNWL +QDNAETLGVEYLIWQGQIWSLARDAEGWRPYNGGGMHDPTDVTGGHYDHVHITVKEGS +>MHAAABBN_01913 +MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF +TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT +PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG +VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR +>LFPAFLNI_02144 +MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF +TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT +PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG +VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000442.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000442.fa new file mode 100644 index 0000000000000000000000000000000000000000..5c23d54c75fb1562672c0838a30f54a9b28435cb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000442.fa @@ -0,0 +1,28 @@ +>ACLBLIBL_00543 +MSFTAPRRVLRRHRLTQVGALGAGLALLLTACGGGSEPAESSSPAPTGSSSSPAEATTAS +PSAESSPTTSPSGSVGSTAAAGSSGSGGAYVPASAEGPARNVPKPEMPAVTKEETQEGAE +AAVEYFWEAAYYLQQTGDSEYQESVSSPTCKFCDLQRTSMEGHYRDGGWMKVEAVNIASM +VTRPSANGYMSTLLLDMPKEEAFASQGGKAESIGTQPALEESPWIAETSFSEEAGHWVIE +AMIAGGS +>MOLHKGIG_01043 +MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS +TSETAGVSSSPTATESGSGEYVPASADGPARSVPKPEMPADMKEETKEGAEAAIRYFWDV +HYYAEQTGDTELLDSLYSEYCEFCQFSSNDLQMIYKDGGWYTGTEVQIDSILTHRSETGY +VSTLLVTTGTGTGYTKGGVVPENGDVEAASKQPWIAEVSFNPESSHWIVDEMSYEGSIGS +N +>NAFOICDF_01734 +MTLPAPRRTLRRRRLARTGALSGALLLALTACAGGGADSGASSASTTTTAPAASSTSAAA +SSSTGGASASESDATTSGAAGEYVPASSKGPAQNVPKPVMPAAVKENTPEGAEAAVKYWW +EAVNYLQQTNDPEPLKSISMEECNLCSAHIKTIKRIYGDGGWATGENFAVNSVSMEKKKD +FTLATVAISTDDSATFNADGVKVDQAPADAGTDAPWGVLLKFDSNKGQWVVREAEYDFQE +G +>MHAAABBN_00756 +MSLTAPGRALRRHRFAQAGTLSVALALTLTACGGQSEPAESSTTSPSSAKPAVETSAPAS +TSATAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA +IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY +TATLVRDASAVDVFDSQGVRDDSASGAETHDETWLADVVYEPSKGHWVIDEMQNQQDAQ +>LFPAFLNI_00984 +MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS +TSETAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA +IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY +TATLVRDASAVEVFDSQGVRDDSASGVETHDETWLADVVYEPSKGHWVIDEMQNHQDAQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000443.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000443.fa new file mode 100644 index 0000000000000000000000000000000000000000..82490a76a240f65b1032df2fb76f543b15e4ab18 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000443.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00545 +MSVVVLTGADGGARLGHTAPMDMSLVMLVPALVALAALMVGGALQRVSGMGVGMIAGPTL +SLLLGPVAGVSLANVAAVVSAVLLFALLRRHVDWGRFLRLAPLLIVGSFAGAWAVRSLDV +HALEVLLGGSVLVAIAASLGLQRRFTASGSAPAALAGTAAGFMNTTAAVAGPALAVYAVA +SRWEQRSWAATLQPIFLLANLTSLATKSLFGTAVPASVDVHWTVWTAVVVGGPIGVLIGS +RIAPRVNPSRARLLAICVAGVGASVALLRGIVGLLA +>MOLHKGIG_02198 +MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA +VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL +QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL +TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLLGSVVARRVDPAKARVLAICLAGV +GGTVALVRGVAGTLG +>NAFOICDF_00481 +MAATAAAAVRTAERARSGGGVTVPVWHAPAVASRRRGARAHTAGVSISLAAVVFLCVAVG +GVLQRISGMGVGMVAAPTLSLLVGPVAGVTMSNAAASVSALILFWMLRRHVDWPRFLRLA +PLLVVGALAGAWTVRVMDHAWLEVVLGACVLVAIAAVLGLQDRLTLRGSAAVFGSGAVAG +FMNTTAGVAGPALAVYAVASKWEQRSWAATLQPIFLTANVTSIVLKASLGATAGAAAVPW +WAWAAAVAGAPAGIAVGSRLARRVDPGRARRVAVTLAGVGAAVTLVRGLASL +>MHAAABBN_01911 +MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA +VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL +QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL +TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLPGSVVARRVDPAKARVLAICLAGV +GGTLALVRGVAGTLG +>LFPAFLNI_02142 +MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA +VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL +QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL +TSLVTKSLFGAAVPAGLHVPWPVWVAVVAGGPLGVLLGSVVARRVDPEKARVLAICLAGV +GGTVALVRGVAGTLG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000446.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000446.fa new file mode 100644 index 0000000000000000000000000000000000000000..c2ae77de97ecb6d7d234c1a9f62b832e00befd20 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000446.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00548 +MSSTPTDADHHGPGPVSVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLRGVRGELVLTGGPVDVALDGPERPAARAYRPLIDATRHPYA +LRARTAIAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLTVAPEAV +VGELSAPDRALLAAVVACLRPARLVTFDDVDATLTLDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>MOLHKGIG_02196 +MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV +VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>NAFOICDF_00479 +MTEDQTPAPIETDDVVAERAPEPAPGGSHQVGRALTARGLTLRSIRGTVFGPVDVDLPPG +VPGAVLGTQGSGRSALLLALVGRLQGVGGELTLGDMDGIRHPHRLRRATTVARITDYVEL +EPLLTIRECIDEHCLAEGISRRTGRKRFARLEAAVGFHPDHGDQVSSLPVEDRTILTCML +ACLRPADVIVYDDIDSSLTRPQLEHVYRVLETLGRLGHRFVVSALTSAPVPRGAVVVELP +TPGHDDLPAALPTRPSLED +>MHAAABBN_01909 +MSSTPTDADHHGPGPAPDPAHLDDLPPATLVARGLTLRGSRGPVFGSLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLTDGVRRRAGRARFALLADAVRLTVAPEAV +VRELSAPDRALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>LFPAFLNI_02140 +MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV +VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000447.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000447.fa new file mode 100644 index 0000000000000000000000000000000000000000..b6c81aed0372ec7b88e76b6bf9042d7ab838362f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000447.fa @@ -0,0 +1,75 @@ +>ACLBLIBL_00549 +MLFRYELRRFRRGLPLLALLFILLVPAIYGALYLSANWDPYGAMNRLPVAIVNEDEPVQR +GDTTLRTGADMTARLKEDHAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG +GTPQQAQITLRRDDANGFVIGSVTASSQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD +AADGAAQLADGSASAVDGASQLEDGIVQAHDGSGRLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGATSAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL +QTGSAELTDGATQVADGTQQLYDTVVPGLDRVIERQDAVAADVAAVDEDVQRVAEVAGTA +GDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA +AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA +GQLESGATELDDGLAQLQDGAGELHTGLRTLDDGAHELASGLSDGVDRVPALTEDQRDEA +ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGHRNPV +AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLILQLASTGGTYPAEVLPGFFRALHPFMPMSYSIEAFRNAISGGLDQHF +WVPVVVLMGVGAAALALDVLVVRRRRRFRMKDLHPALQA +>MOLHKGIG_02195 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR +GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG +GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD +AADGAAQLADGTASAEDGASRLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL +QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA +EDGAGARIADAQTALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA +AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA +GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGADRVPALTEDERDEA +ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV +AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF +WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA +>NAFOICDF_00478 +MLFRYELRRFRGVLPTIALLFIVLVPTIYGALYLSANWDPYGNLSSLPVAIVNEDRPVES +DGKTLTTGADITEELVDQHTFDWHETTRDDAEAGLRDGRYYLVMEIPEGLSADLVSANTS +DPQQAHITLRRNDANGFVIGSVTSSSQSKIENAVDKAAVEAYFKAVFENLATIRQGMADA +RDGAGRLADGAGQADDGAAQLADGIVQAHDGSGQLAQGASDAQDGAGQLADGAGQLKDGA +DQLAAGATSAKDGAVQLQTGIGQAREGSQKLADGAGQIAAKVPDLRDGATALSNGLTQLD +TGSADLADGAHQVADGTQQLYDTVIPGLDAVIERQDKVASDVATVNQDVQTLNDAVATAG +SGAGGDIDTASEQLQALAESNPDIAVAPEYAALQQSLTDAKEKAGSATSTAQDVADRSAA +VNSRVQGFVSEDVAGNAKADITKLNDGAHAVAEGADTLHAGIGQANTGAQALADGVGRFA +DALDQLAAGATALDDGLAQLEDGSGRLVDGLGKLETGAGDLADGAGRLDQGAGELQTGLG +KLSDGATSLDSGLAQLETGSGDLKTGLDSLSDGATQLHDGLASGTDKIPALSEDAADEAA +LVMSRPVQVDMDVLNPAGVYGRGVAPLFFSIALWVFGIAAFNVMRPVNGRLLAGRRNPLL +LALSAWLPVGLLSVVGSLVMLAATVPLGIDPVHPWHLVGLVVFTALAFSLFAHLVMTALG +TPGSAVLLVTLILQLGSAGGTYPADVLPPFFRWVSPLMPMTHSINAIRYALSGGQPAQFW +GAVAFLAVFGAACLFLDMAVVRRRQRFRMKDLHPALEK +>MHAAABBN_01908 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR +GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG +GTPRQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD +AADGAAQLADGTASAEDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL +QTGSAELTDGATQVADGTQQLYDTVIPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA +EDGAGARIADAQAALAELAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA +AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA +GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA +ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV +AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF +WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA +>LFPAFLNI_02139 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR +GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG +GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD +AADGAAQLADGTASAKDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL +QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA +EDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA +AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA +GQLESGATELDDGLAQLQDGAGELHTGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA +ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV +AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLILQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGLDQRF +WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000449.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000449.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ac65c644a0a8a3708bcf21c80d6a581bc2d5b81 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000449.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00557 +MSIPATEVEARWNEASEPFTAVVRAVRDWDAATPCEGWDALDLLDHVVGAERDFAARQGR +EVPLFDGSRQQTANQWTKHSAALSALAGDEEFIMKPMHTALGEMTVGEAMIRFHAFDLIV +HRWDLARSQGVDERFTDAEMDCIEESLDLFGDAAYTPGILAQPVPVADDADRQARLLGRL +GRRA +>MOLHKGIG_02189 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG +>NAFOICDF_00484 +MSTQTDVEQYWMDCVEPFTDVVRAVEDWDASTPCKGWSAQDLLDHVVVAERDFAARQGRE +IPVFDGSRNELWTQWVKHASAVTALAGDETFIMQSLHTATGDMTVGEALLHFHGFDLLVH +RWDLARSQGRDEQWTDEEMDRIERALDSFGEQAYQPGILADPVPVADDAPRQVRLLGRLG +RRA +>MHAAABBN_01903 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG +>LFPAFLNI_02134 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAALSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000451.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000451.fa new file mode 100644 index 0000000000000000000000000000000000000000..1561a7c305052ffad7456142fb9b031c1fdf37c4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000451.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00563 +MEQDRDPEESSQSTAIETLRGTPVSELTHLPPAMAGALDRLRRDVERFDLEYRSALLQVE +ARLEVLRDEFTHLHDYNPIEHIVTRVKTPESILRKAASRGLSMDLDALRSNVTDIAGARV +IVSFARDVYEVFRLFTRQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPVHLSTGSIPVTV +EMQFRTSAMDFWATLEHKINYKFDGAVPPDITTELIAAARVAADLDTRMERLSDQVRQTD +KDDDAAASWEDDGGPAFEDEGDDDGPDGDAPGTSTG +>MOLHKGIG_02186 +MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE +ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV +IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV +EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD +RDDDAAAAWEDDGGPAFEDEPTVEPGEARPGDAPGASTA +>NAFOICDF_00489 +MPRDVDHPPPADDPAPVERPAPGGRGVTSASTALEALRATPLTDLTQLPGEVADALASLR +TDFERFDLEYRSALLQVETRLETLQDEFTHLHEYNPIEHIATRVKSPESLLRKAASRGLS +LDLDALRSGVTDIAGARVIVSFTEDVYRVFRQFTSQPDIRVLEVEDYIRDPKPSGYRSLH +CLVQVPVHLTTGTVPVTVELQFRTIAMDFWASLEHKINYKFAGHVPPAITTELAAAARVA +HDLDARMERLHQAVHDAGAGPDEHDDEDDWVGHA +>MHAAABBN_01900 +MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE +ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV +IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV +EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD +RDDDAAAAWEDDGGPVFEDEPAAGPGEARPGDDAPGASTV +>LFPAFLNI_02131 +MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE +ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV +IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIQVTV +EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD +RDDDAAAAWEDDGGPAFEDEPAAGPDGTDPGEARPGDDAPGASTV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000452.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000452.fa new file mode 100644 index 0000000000000000000000000000000000000000..07eae2ab4f105a23ab2fafa0a914f4798f90deeb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000452.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00565 +MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR +AWSGVTPGRDVHRVVRAMEVQYEAPVVYGPELTAKVWIARIGTSSYTLRHELWQDGRRCV +LCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT +>MOLHKGIG_02185 +MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT +ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV +FVQVDPAAGRPVAVSDEERAAFERVLIPAED +>NAFOICDF_00490 +MSDSQPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALKAWDEGDVGRDVMRVVR +AMTTEYERPVEYGPELTAKVWVRALGRTSYTLHHELWQEGVRCVTCDAVMVHLDPETGAP +LPHDDARRARLQAVLVPAEG +>MHAAABBN_01899 +MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT +ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV +FVQVDPAAGRPVAVSDEERAAFERVLIPAED +>LFPAFLNI_02130 +MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALAAWATTT +ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV +FVQVDPAAGRPVAVSDEERAAFERVLIPAED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000453.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000453.fa new file mode 100644 index 0000000000000000000000000000000000000000..3028a21684e9ca69494ae770b167d9751d366f33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000453.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_00567 +MTSPDRAAPPAPPTPAFGPAPEAPAADNAAPARRRLQVVSLRPEGLSEDAVGRVAELLAE +AFAEDEFTLGLLPADRRAERLARMFALDVHDALRPARAAGGEAGPRGAVDVALDPEDGTL +LAAAVWDGPDAPRGTTVPGALAALPARLRVHGRRTWDAARTDAACERARPAAAHWHLTQL +GTAPAARGRGAASALVRLRQRRAARAGVGIHLEASSAEAVPFYARLGFRETGTVRAHGTR +DLTAMWWEAQA +>MOLHKGIG_02183 +MTSPDPAPPRPRVHVLTLRPDGAREDTARRVGIVLAEAFATDPYTLGLVPEDRREARLER +KFTAAVRHGLRTGADGAPLGAVDVAVDADDGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA +VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGAVPSARGRGAASALVRHGQRRASGLP +VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA +>NAFOICDF_00492 +MSDAARRPRPLVTSLRPAAAADHPDAAAVAGMAGALAEAFAEDPYTTSFLPPDRREERLR +DYFDLLVRESLDAAARGHGAVDAAVDPRTGEVLGVALWERPGAPRPPAGLLGALRPAVPT +AARRWRAFGRHALDHVRTVAACQAVRPSEEHWYLLELGTVPSARGRGAGRALLERRRREA +RAAGVGIYLESSSAESTRFYEHVGFRPHGTATVHGADDLTTMWWKD +>MHAAABBN_01897 +MTSPDPAAPRPRVHVLTLRPDGAREDTARRVGAVLAEAFATDPYTLGLVPEDRRGPRLER +KFTAAVRQGLRAGADGAPLGAVDVAVDAADGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA +VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGTVPSARGRGAASALVRHGQRRASGLP +VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA +>LFPAFLNI_02128 +MTSPDPAAPRPRVHVLTLRPGGAREDTARRVGAVLAEAFATDPYTLGLVPEDRREARLER +KFTAAVRHGLRAGADGAPLGAVDVAVDADDGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA +VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGTVPSARGRGAASALVRHGQRRAAGLP +VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000455.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000455.fa new file mode 100644 index 0000000000000000000000000000000000000000..1cb8f70ee77a1dd14e809df5070376e983903c31 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000455.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_00569 +MLRLARPRSRRAPQGLGGRLVRAVAARPVPPVRPRARLAWHVSGALPLIGCLTSFPIGMS +KDSMVIPGVGYQGGFSAGWHHALNQPAYFTWLSNALVAGTSLTLATRRTAPTSDAFWAVR +TAGLGSVMVTGIVYNSVLRGREQDTVLYRFNDTLQHIVNPVLAPAVWALFDPRGQITPRR +AGLASVIPLAWAALTMARGPRIDWYPYPFLDVPRHGARTVGVVLAGILAGFTGLMGLLGG +LDRRLGGR +>MOLHKGIG_02181 +MPLSTLRVSLPSVRRTRPAPQGVRGRIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI +GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE +APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL +CDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA +GFTGLMGVLGTVDRRLGLA +>NAFOICDF_00496 +MPAWLARFTRPRPAPRPSRAARAGWWAAGALPLVGCLTSFPIGASKPTMVIPGVGYHGGF +EAGWQHALNQPAYFTWLSNAMVAGTSLTLAARRDAPTSDAFWALRTAGLGSVMVTGIVYN +AVLRGMEQDTLLYRFNDAVQHVVNPVLAPLVWAAFDPRGQITYRRAGLAAVVPLMWATAT +LVRGARIDWYPYPFLDVPRLGWRGVGAAVSVVLAGFSAVLGLLGQVDRRLGTR +>MHAAABBN_01895 +MPLSTLRVSLPSLRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWHVSGALPLI +GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE +APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL +FDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA +GFTGLMGVLGTVDRRLGLA +>LFPAFLNI_02126 +MPLSTLRVSLPSVRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI +GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE +APTSDTFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL +FDPRGQITPRRAGLASVIPLMWAAVTMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA +GFTGLMGVLGTVDRRLGLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000456.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000456.fa new file mode 100644 index 0000000000000000000000000000000000000000..90d63bd13b08d11c1a114741a8a0c304f6638d3d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000456.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00572 +MTRTVIIGGHGKVALLAAPLLAEAGHDVTSIIRNPEHAAEVEAAGAAPLVLDVERAGEED +LVQAFRDADNVVFSAGAGGGDPARTRAVDHDAALATMRAAEAAGVRRYVMVSYLGASLHH +GVPEDDSFHAYAQAKAEADEALRDSGLAWTILGPAALTLEEPTGRITVDPDLDTPDAPKG +EVSRGNVARALVAVLADPTTVGRKIDFVDGDTPVAEAIRGA +>MOLHKGIG_02180 +MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE +LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH +DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTDEEPSGRITVDPDLSDSDAPQR +GASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD +>NAFOICDF_00499 +MDILIIGGHGKIALLTAPLLADAGHTVTSAIRNPEHADDVRTAGAEPLVLDVEHSSPAEL +EAAMRGRDVVVWSAGAGGGDPERTYAVDRDAAIASMDAARAAGVRRYVMVSYRGASVHHG +VPEDSSFFAYAEAKAAADEHLRGSHLDWTILGPGALTLDEPTGRVQVDPQGPSEELPGTS +RGNVARMIAAAVDSGASIGRQVEFVDGDTPVDDVFRR +>MHAAABBN_01894 +MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE +LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH +DVPEDDPFYAYAQAKAEADEALRDSGLAWTILGPGTLTDEEPSGRITVDPDLSDSDAPQR +GASRGNVARAIVAVLNEPGTVGRKIDFVDGDVPVAEAVRGD +>LFPAFLNI_02125 +MTRTVIIGGHGKVALLAAPLLAEAGHDVVSLIRNPDHAEDVRAAGAEPLVLDIEKADQEE +LVHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH +DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTEEEASGRITVDPDLSGSDASQR +EASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000461.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000461.fa new file mode 100644 index 0000000000000000000000000000000000000000..928e98470f04615dfc0e09ecc938426abd7e353a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000461.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00577 +MATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAALEKVEGAERPVTWSEAAGI +DAEAVASVRPDVILAAYSGLTREDYDRLSKIAPVVAYPKDVPAFGTPWQQSTRMIGQALG +KDAEAEALVEDVEGRIAAAAQKHPDLKDATFVYGTVDPTAADQISVYTLVDNRPRFLESL +GMKQAPVVAENSPKDQAFFFTWSPERADELESDVLVSWALDASVADAIEADPLLSALPAV +QKDGLVLQVDQQEVLSVSAISPLSIPFALERIVPPIAEAAARSRG +>MOLHKGIG_02175 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH +VYGTTEIPQRPTRVATVSWVNQDVTLALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG +AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS +WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHADLQGASFVYGTIDPAAADQISIY +TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA +IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG +>NAFOICDF_00504 +MPQSPSRRSVLAAGGSGLALLLAACSTGPAGSSVPSSSPASSAGSAAASSSASGSAAYPL +TVEHVYGTTEIPARPERVATVSWVNQDVALALGVVPVGVPAVEFGGNADKSTDWFDAKLK +ELGGPTPVQWSEADGIDAEAIAAVKPDVILAVYSGLTREDYDRLSKIAPVVAYPKDVPAF +GTSWQQSTEVIGRVLGKEREAAALVADLERQIADAGAEEDGLAGASFIYGTLDPAAADQI +SIYTAADNRPKFLELLGMELAPVVAENAPEDGAFFFTWSPERADELESDVFVSWAASADV +ADAIEADPLLGAIPAVEKGGLVLQVDQQEVLSVSAISPLSIPYALEKVVPPIAEAARAAK +G +>MHAAABBN_01889 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH +VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGVAAVEFGGNAEKSTDWFDAKLAETEG +AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS +WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY +TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA +IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG +>LFPAFLNI_02120 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH +VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG +AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS +WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY +TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA +IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000462.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000462.fa new file mode 100644 index 0000000000000000000000000000000000000000..cdf33685009b7db4904b39fe3a25480fe8c57f62 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000462.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00579 +MSRIQSTTSPSSMAELKKVLPELSHPDGSPVRVLVVDDEPMIADLLSMGLSLCGWDVVVA +HDGASAVEQGTARRPDLAILDVMLPDMDGLEVLERLRAHWPEVPAMFLTAKDATEDRVAG +LASGGDDYVTKPFSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGQVI +DLTATQYNLLKFLMANVRTVLSKERILQEVWGYDFGGRANIVELYISYLRKKIDADRDPM +IHTIRGAGYVIRPA +>MOLHKGIG_02173 +MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA +GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP +FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF +LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR +PA +>NAFOICDF_00506 +MTSAEHTVSPASMAELRESLPDLTHQDGSPVRVLVADAEGLEADLLSMGYSLLGWETVVA +KDTAAAVQEGTARRPDLALLDAGLPDGGGLEVLARLRAHWAEMPAIVLASPAEAEDRIAA +LLAGADDVVAKPFAVEEILLRSHHLVRRAGLNASTGEELVVGDLVMNTRTHEVTRGGDLI +ELTATQFNLLKFLMANVRTVLSKDRILQDVWGYDFGGRANIVELYISYLRKRIDAGREPM +IHTVRGAGYVIRPAEG +>MHAAABBN_01887 +MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA +GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP +FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF +LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR +PA +>LFPAFLNI_02118 +MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA +GRPDLAILDVMLPDMDGLDVLERLRAHWSEMPAMFLTAKDATEDRVAGLAAGGDDYVTKP +FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF +LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR +PA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000463.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000463.fa new file mode 100644 index 0000000000000000000000000000000000000000..8cc8e14905c8050a73dc8605626dbab46f14f444 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000463.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_00582 +MNSDHLRALVSAVDHGTFDAAADALRISGSAFSQRVKALERQVGQVLLARTVPVRPTPAG +ERMLRLARHTLALEEEALASLGRGDGGRVPVRVAINADSLDTWWELVLREAATWDDVVLQ +LRTEDQEHTAALLRDGTVVAAVTDDPTPVSGCTSTPLGTMRYHAVCASFLLEMHRDERGR +LDLATLPRVDYGLRDGLQRTVLRRAARGRAAFDPPHHLVPSVQSYLRAVELGLGWGMLPS +AQLPPGVLEGRHPDLEPVPSLGTVDLTLHWQRWSAGTAALDRLTDAVLRAAPSVADAAD +>MOLHKGIG_02170 +MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERMLRLARQTLALEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG +LGWGMLPSVQIPPGVLEGRHPDLETIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP +SAGDTAD +>NAFOICDF_00508 +MNSDHLRALAAAVDEGTFDAAAAWLGISGSALSQRIKALEGQTGQVLLTRTVPVRPTEAG +ERMLRLARQTLPLEEEALAALGRGTGRRAPLRVGVNADSLETWWTPVLREAATWDDVVLH +LHAEDQGHTPELLRQGTVVAVVTDDPTPVTGCTVTRIGTMRYHAVAASFLLDLHRDAHGR +VDVATMPVVDYGPRDGLQRTMLERAARGRVSVPRPPHHLVPSVGAYASAVGMGLGWGMLP +TGQVPPELAAGSHPDLELVPELGTAEVPLYWQRWSAGTPALDRLTAAVTAAAPAG +>MHAAABBN_01884 +MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERMLRLARQTLVLEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGTLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG +LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP +SAGDTAD +>LFPAFLNI_02115 +MTTPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERLLRLARQTLALEDEALAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG +LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP +SAGDTAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000464.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000464.fa new file mode 100644 index 0000000000000000000000000000000000000000..17346e7513ca51015981c03dcfda9009a6a301e6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000464.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_00583 +MTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLIVCFLGDVALLALGAAGIGVV +AERWPWLVTALTVAGVVYLVWFAAGALRSAVRGQRTLAAAAEAEGPAVGLTDGEIAALTG +ELPLIDPATGRLSADFTGRTAEGRAVPVGAGVGMGRGHDPLGDESRTVGGIPVGNPRLCG +TRPGERGADGRSGGVAVKQRVQPRRVVLSAPQTPLPRIVLLALSVSFLNPHAVLDTVVMM +GTFAQTYGPGKWVYVGGAVAASLVWFTALGWGGTRLAPYMNTPRTWRIVDAAVGVLMLVI +AAKVGLTLL +>MOLHKGIG_02169 +MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLGFAAGALRSAWRGDRTLSTAAADVEGTG +HGPDRIDLAVLTGELPLIDPVTGRLAEREPAGAGVGHHDDGAPGFGAPSGGGSVTVRQRV +QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWAYVGGAVAA +SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL +>NAFOICDF_00509 +MTVFSAGFLTYLALIVAIGAQTLFLLRQVVRGDRAWTAIGVCFLSDIVLLLAGAAGVGAA +AERAPWLVPALTVAGVAYLVWFGVSALRSAHRGDRTLAGAAAEVEDDAWAPTAEEVAAMT +GSLPVVAAGPDAGADAATAPAGTGGGVALRTRPVSTTAPASAAPRPALTPLPRLVLLCLS +VSLLNPHAILDAVVMMGTFAQGYGADKWLYVAGAVASSALWFLVLGWGGAKLAPLMNTPR +TWRIVDGAVGVVVLGIAGKVALTLF +>MHAAABBN_01883 +MARTWGDSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADAAGTG +HGPDRIDLAVLTGELPLIDPATGRLAEREPAGAGVGQHDDGAPGVGAPSGGGSVAARQRV +QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWTYVGGAVAA +SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL +>LFPAFLNI_02114 +MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGVGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADGAGTG +HGPDRIDLAVLTGELPLIDPATGRLADREPAGAGVGRHDDGAPGVGAPSGGGSVAVRQRV +QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWVYVGGAVAA +SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000465.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000465.fa new file mode 100644 index 0000000000000000000000000000000000000000..66d4bef1b1072d522373cbff1824c1e14dc38d97 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000465.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_00585 +MLAAVLTLATPFLIGAATDRIVAAIAGETTVEDAVVAVTWLAVAFLAVEVTTTLVVSVGG +YWGDVMAARMRTILSTRYFDQLLHLPQRYFDTAITGRVTNRLNRTINELTQFLQFFANNA +FTMLITTTAVLVITAFYWWPLAILLAIVFPVYMWLTAKTSAKWQVWEGEKNIEVDMASGR +FAEVVSQMSVVRAYNRQDHELAGFRERFTRTVGITRKQSRFWHGMDAWRRLALNVVFGAM +YLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSRDYFEVLAEER +ERAGGAGPQGRGAAAVAAGQPRADDDGGTDVRWGGAAPSRPAQPRADVVPGDGTGGMPAG +PSADVVPAVRFDEVSFAYDPDASRPVLDRVSFEIPQGQRVALVGESGGGKSTIAHLLMGL +YPVTGGRIEVFGQDVAELDLAELRERIAAVFQEPSLFSGTVRENIAYADPAASDERVRAA +AEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDT +KSERLVQGALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAESGGIYA +QLLRLQKAGTKEARKMLKEYGLSG +>MOLHKGIG_02167 +MTSLLRILRFAPQLNRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV +TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT +GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAILLAVVFPVYMWL +TARTSTKWQVWEGEKNTEVDIASGRFAEVVSQMSVVRAYNRQDHELSGFRDRFLRTVGIT +RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM +SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAVAGASAESAGADAPRVPAEPRADVVP +GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL +LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV +RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA +LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG +IYAQLLELQRAGTQEARKMLKEYGLSG +>NAFOICDF_00512 +MRALLRILRFAPQLNPLYLGIAVCSVLAAALSLATPFLIGAATNRIVDAIAGRSTLDDAV +AAVTWLALAFLAVEVATTAVVSVGGYWGDVMAARMRAALSGRYYDHLLHLPQRYFDTAIT +GRIVNRLNRSITELTQFLQFFSNNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL +TAKTSAKWQGWEGEKNTEVDIASGRFAETVAQMNVVRAYNRQDHELAGFTERFRRTVGIT +RKQSRFWHGMDAGRRLALNLVFGVMYLIVFVRTARGLFSVGDMVILLQLMNMARQPIFSM +SYLVDSAQRAVAGSKDYFGVLAEERERSGGAALPAGLGSAEAPTTTTATGVVVRDRAEAP +TGAPVRAGADVPAVRFADVTFAYDPEAERPVLDGVTFDIPQGAKVALVGESGGGKSTLAH +LLMGLYPVGSGRVEVFGRDVAGLDLAVLRGQVAAVFQEPFLFSGTIRENIAYADPDASGE +RVRAAAKAAFADGFVEEFEHGCEQLIGERGLRLSGGQKQRIAVARAVLKDAPVLVLDEAT +SALDTKSERLVQSALDDLMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAQS +GGIYAQLLRLQKAGTKEARKLLKEYGLSG +>MHAAABBN_01881 +MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV +TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT +GRVVNRLNRTINEITQFLQFFANNAFTMLVTTAAMLVITAFYWWPLAILLAVVFPVYMWL +TARTSAKWQVWEGEKNTEVDVASGRFAEVVSQMSVVRAYNRQDHELTGFRDRFLRTVEIT +RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM +SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAAASASAESAGADAPRVPAEPRADVVP +GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL +LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV +RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA +LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG +IYAQLLELQRAGTQEARKMLKEYGLSG +>LFPAFLNI_02112 +MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAIAGETGVAEAV +TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT +GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL +TARTSAKWQVWEGEKNTEVDIASGRFAEVVSQMGVVRAYNRQEQELSGFRDRFLRTVGIT +RQQSRFWHGMDAGRRLALNAAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM +SFLVDSAQRAVAGSKDYFEVLAEERERAGGAVLAVASADAPRVPAEPRADVVAGAPDVPA +DVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGAKVALVGESGGGKSTIAHLLLGLYPVT +SGRIEVFGQDIAGLDLAALRGRIATVFQEPSLFSGTVRENIAYADADASDERVRAAAQAA +YAHRFVAAFDDGYDQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDTKSER +LVQAALDELMVGRSSLIVAHRLSTIASVDRIVTLRAGRVEEVGSPAELAESGGIYAQLLE +LQRAGTQEARKMLKEYGLSG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000467.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000467.fa new file mode 100644 index 0000000000000000000000000000000000000000..94b027d0145ae55aba9e949e3fc7a7b524e5c544 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000467.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_00593 +MWTVALSQLRAQPRRYVSLVLAILIGTMFLAASFLVSASAQATLRTTLGNTYSAADLVVL +PEPSDHADEDPTAAFPGLAGTPAEPGALGRVDGVEEAYATQFTWAGGSAGGTEFTATLLP +VPGDVSLLPVTLTEGAFPAADDARGVTLDTGTAERTGVAVGDEIALTGAPGAGGETATVV +GLTTRSPDPTLSSGAQIWAAAPVIAAVNPPQDGEAGGSGAYSPHVLLRLTDGADRDAVAD +AAAAVLAQEGVAASVTTPDEAVRDTLAEAGGGTDVFGWVLGGFAALALLVTALVIGNTFQ +VLVAQRTRDLALQRTLGSTAGQVRGSVLTEAVVVGLVGSVLGVALAVVGLLAGVAFVRSA +FDLPTLTFGMDPAGLAITVVVGVLVTLVAALSPAVAATRVSPLQALRPREEVTVASRVGV +VRTVVGAVLAVGGTALMLWGAFRPEPLTAVGGGALSFIGVLLLATLFVPAAVRGAAVLAR +PAGVPGRLAGLNATRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDL +VLSLPADGDAARAAEAVAARDDVAAVALALPVGATENGSPVLATPGADLRKVVAELPDGE +DGLGDPGTAFVPGWVDEDTVTATVAGTEQTFSAVRAGDLSSGVYVEADSLRAAGWDGSPL +ATDGVEVPGQLLVALAGDVPVDRLQALSEDITAAAGEGASIIDGGAPTRAVYAQVIDVML +WIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLPRGGLRGMIAIESVLIAAV +AALLGCVLGVFYGWAGSQLILGELVETVGRGGTVLPTIPWLELALVVGVAAVAGLAASLL +PARRAARLSPVAGLATV +>MOLHKGIG_02164 +MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL +PGGSEDVSDLAGTGAEPGPLARLDGVEEAYALRMAWATARAADAEFGTTVMPLPRDPALA +GLTVTAGTLPAADDARGVTLDAQTADRHGVAVGDVVTLAGESGPAPATTPLDAVVTGLTQ +PSPDPMLSGQAQVWASSAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA +GVDVDVATPDEAVRSAVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD +LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG +LHPAGLAVSVAVGVAVTVLAALAPAVAATRVAPLEALRPKDEVTAGSRGGRVRAAIGLVL +AVGGTALMLGGVSVREPVSAIGGGALCFVGVLLLARLFVPAAVRGAAVLARPAGVPGHLA +GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD +PARAAEAVAATEDVQAVALATPVGTTENGSPVLATPAADLRAVVARLPEGVTGLGDPGTA +LVPDWVEADPVRAEVAGAAQTFAPVRAGSLSSGVYVAAEPLREAGWDGAADAAVPGQLLV +ALDPGVPVDRLQGLSEDVTRAAGDGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI +ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGAIAIEAVLIAAVAAVLGCALGVCYG +WAGAQLVLADLSATAGAGTAVRPVVPWLELGLVVAVAALAGLAASLLPARRAARLSPVAG +LAAV +>NAFOICDF_00516 +MWTVALSQLRARRRRYASVVLAVLIGTMFLAASFLVASTAQATLRTTLGSVYAGADLVIQ +PEDDPETSADASGPPPGQRLAALAGTPETPGALARLDDVAEAWAPTPGFAEAAAPGGGTP +RPAAVIPAPAHPDLLGVRAVAGALPDPADARGVAVDEETARALGVGVGDELPLTGEPTRA +PVRATVTGLTSVSPDPMLSSQAQVWASRPVAQDLAPDGQVPYTTAVLLRLAPGADREAVA +EAAARALHDDGVPAAVQTPDQAVRDQLASLSGGTDLLGWVLGGFALLALVVTALVIANTF +QVPVAQRTRELALLRAVGAEARQVRGAVLLEAVATGLTGAVAGVVLAVGLTAAVVAVARG +ALGADALTLGVDWLPLAGAVALGTAVAAVAALGPARAATRVAPVQALRPVDEAPVRSRVG +LVRAGLGLLLAVGGAALMWWGAWGSAFAAALGGGVLSFLGVLLLARLFVPGAVRAAAVLA +RPAGVPGRLAGLNAVRHRRRTAATASALLIGTTLVALVLTGGRTAQIRLDALLDEEYPVD +LVVSVPAGGDLAAATRALGAVDGVGSVAAASPVGATVNGSPAYAVEADALRSVVAALPDG +QDRALGDGASVLVPAWAGATTEVVVDGRVSGLASVRGSGLTTGVFLTPETAEWVRRHGVA +ADAGTASDAAGPAAEDQAVAGLVLVAAADDVSVNRLQEMSAALTAAAGAGASIVDGGAAE +RAVYAQIIDALLWIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLTRGGLRG +MIAVEAVLVAGVAAVLGCGLGVLYGWAGSQLVLGQLVAQLGEDRALVWPEVPWAELALVV +AVAAVAGLLASLAPAGRAARLSPVEGLATV +>MHAAABBN_01878 +MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL +PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA +GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ +PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA +GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD +LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG +LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL +AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA +GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD +PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA +LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV +ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI +ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG +WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG +LAAV +>LFPAFLNI_02109 +MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL +PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA +GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ +PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA +GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD +LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG +LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL +AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA +GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD +PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA +LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV +ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI +ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG +WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG +LAAV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000468.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000468.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f25d87fbfcc11f1edaff67e5f9d0e477920b92d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000468.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00594 +MSTTADSHSAHSTPPGAGASGPGMPSSSTTTTTAPAASARALTKTYGRGDAEVHALRGVD +VDFAAGAFTAIMGPSGSGKSTLMHCLAGLDTPTSGSVVLGGTEITGLGDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRKPDRAWLDEITATLGLTDRLKHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDSATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELLDPTVESVTNALAALSAPGAADAAGTFDAPADGGR +>MOLHKGIG_02163 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLLHCLAGLDARTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRALGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR +>NAFOICDF_00517 +MDITSPRSAAHDAGAHALATPLAHAAAPPAPAVSARGLTKTYGRGDAAVHALRGVDVDVE +TGRFTAIMGPSGSGKSTLMHCLAGLDTPDAGVVTLGDTVITGLSDAALTRVRRDRVGFVF +QAFNLVPTLTAEQNIVLPMELAGRTPDRAWLAEIVDRLGLSDRLAHRPHELSGGQQQRVA +VARALLTRPDVVFGDEPTGNLDSATGAQVLDLLRRATRETGQTVIMVTHDPVAAAAADRV +VLLADGALAGELHAPTAERVAEALTALQQGRPLPQGRPLPQDGGR +>MHAAABBN_01877 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR +>LFPAFLNI_02108 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000469.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000469.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f83baebc32d9ba2b9808b4476a3be5a3cfac856 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000469.fa @@ -0,0 +1,14 @@ +>ACLBLIBL_00596 +MTAAVVILGLSLFTQVEGLPRLLVTAASGLLAGAVTWSVTQPVLEDEVLHG +>MOLHKGIG_02161 +MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA +LTAGAGLLAGAVAWATARPVLEDDAPGD +>NAFOICDF_00519 +MSAAPAPSPAAPAVPPVTAVPPAAREPEGTSPSDRERERGDAECLAFFLALVTAALVMAG +LALATDLGPLLRVLLSLGASGLAGALTLAFTRPSLED +>MHAAABBN_01874 +MTGSILDHPTPTTSRASDPAAEQAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA +LTAGAGLLAGAVAWATARPVLEDDAPGD +>LFPAFLNI_02105 +MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA +LTAGAGLLAGAVAWATARPVLEDDAPGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000470.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000470.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7692a5082ff477c41cc2bcdf828137d52ea77fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000470.fa @@ -0,0 +1,46 @@ +>ACLBLIBL_00599 +MNPLHRIDQWMRAHPVRTDVLVSVLLFAVLGLTPWVMLGSLAGPTPGSIVASILIALALI +APWAFRRVRPVASAAAVAAAAVAHLVAGPEFSLALVLVPMTVYNLAANAPRWASFTGLVA +ALLGGVANGIRVGLFPDPAMRPDGVYEPVDPSLEALLVMVFGCAAVVLTAWAFGDVVRHR +RLAVRALEDRNRRLETMALQERRLAASDERNHIAREMHDIVAHSLQVIISQADGARYAAA +AKPELAVATLDTIGLTGRAALADMRQLLGVLRETGETVAGVPGVAPDDGAPGPAAGASDE +GAAGAADEGAAGAADEGAAGAGTAGAGTTPGAGRTRLPADVASRDGRGARQPPGHRPQPT +LADVPALIETMRLSGLEVSLLETGAPRRPLPPGGELAAYRIVQEALTNTLRHGGPQASAF +LTLAWTGRGLDVQSDDDGRGADADPGTRGSGHGLRGVAERVALFGGTVETGPRAGAGYRV +SAHLPYSAV +>MOLHKGIG_02159 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVYNLAANAPRSVSVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR +NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA +AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA +SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV +QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA +LFGGTLETGPRVGAGYRVSAHLPYSAV +>NAFOICDF_00521 +MNPLRRLDVLLRRHPVRTDVTAAVLLTLVLVLAPLVMLGGGVGSPAAWQTAGTVVAGLLM +TGAWGLRRVRPVAAAGVTVAGALLHLAVGPEFTIALAMVPATVYNLAAIGPRWASLAGLA +TGLAGGLANGLKVWLFPPRFTTPDGVQVQSPAEPVAMVVMAVLCGMAVLTAWAFGDVVRN +RRLAVQALEDRARRLETQALQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYAA +AAKPELAVETLETIGQTGRSALADMRQLLGVLRGPAEPTGGPDRARRDPAAPDGHRAPPG +LADLPALFQTLRLSGLEISLLEQGSPRRDLPAGGELTAYRTVQEALTNTLRHGGEGAHAF +LTLRWTARGLEIQADDDGRSQADAETTGSGQGLRGIAERVALFGGTMEAGPRVGAGWRVW +AELPYADV +>MHAAABBN_01872 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSMSLLMVPLTVYNLAANAPRSISVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR +NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA +AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA +SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV +QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA +LFGGTLETGPRVGAGYRVSAHLPYSAV +>LFPAFLNI_02103 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVCNLAANAPRSVSVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLVVLTAWAFGDVVR +NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA +AAAKPALAVTALETIGQTGRSALADMRQLPGVLRETGETVAGVPGVTDDDTRRPADPAPD +RADPTGTRPDVVAAPDGRGARLPPGRRPQPRLADLPALVETMRLSGLEVSLLETDTPRRA +LPAGGELAAYRIVQEALTNTLRHGGPDADAFVTLAWTARGLDLQIDDDGRGAAADPATRG +SGQGLRGAAERTALFGGTLETGPRVGTGYRVSAHLPYSAV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000471.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000471.fa new file mode 100644 index 0000000000000000000000000000000000000000..44b19f8cc5029f464fcfb6e95a36ef0cb1653b8f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000471.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00600 +MSAAQLPDDVVRARLIPPARVLAAPMAGGPSTPELVAAVVRAGGSGFLAGGMRTAAQVRE +QVDALRGLLGGGDGSVDGSDAARRWGVNLFVPDAVNTAIPAADRTERARAERRAAVAAYR +ERLAAEGERAAGGAAAEGAGGAPTLPSPDDVTPDPARERAEFAAMLTAAEEQAWPLVSFT +FGLPEPAVFARLAAAGIPAGVTVTDADEARSARAHGAAFLVVQGHRAGGHRGTLDPAADP +VERELPSVLAQVRAVVGTRVPVVAAGGVGAAAHVRSLLAAGADAVAAGTAFLLAAEAGTS +VAHRAGIRRCAAGEGFVGPDGAARTVLTRAYTGRWARTLATDFAAAHPDAPAAYPELNAL +TTGLRAAAATAGDLERVHLWAGTQAHTAREAGAADVVAGLTP +>MOLHKGIG_02158 +MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA +QVDALRALLGAERPDRWGVNLFVPDAVNTAIPAAARTEAARSARAAAVAAYRAGLTADGA +ADLPAVADVVPDPDAERADFEAMLVAAEEQAWPLVSFTFGLPAADVFARLAAAGVPAGAT +VTDAAEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPTRAELPTVLAAVRDVVGTGAAS +AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA +DDGRARTALTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAVGDLERVH +LWAGTEAHRVREAPAADVLASLTP +>NAFOICDF_00522 +MSSTTVPSVPAPVPAPLDPPVPVLAAPMAGGPSTPELAAAVIRAGGGAFLAGGMRSAAQV +REQVDGLRALLTAPEEAGRFGVNLFVPDAVNTAVAASARGGAARIARAQAVASYRERLAP +LAADLGAELPSVLTVTPDPDAERAAFEDMLAAAEEQSWPAVSFTFGLPAPDVFARLDAAG +IPAGVTVTSPAEAMAAVASGARFLVVQGPKAGGHRATLDPQGRPGITDLRTLVFAVRHAL +GPAAVPLVAAGGITDGAQVRPLLEAGAVAVAAGTAFLLTPEAGTSAAHRTALRQASAGVA +FAHPDDGAASTALTRAYTGRWARGLVTPFMDEHHDAPAAYPEVNGLTGPLRRAAAEEGDL +EHVHLWAGTGAHRVEEVGAAEVLASLAPRAEP +>MHAAABBN_01871 +MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA +QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARAAAVAAYRADLTADGA +ADLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT +VTDATEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPPRAELPAVLPAVRDVVGTGATS +AVPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA +DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH +LWAGTEAHRVREAPAVDVLASLTP +>LFPAFLNI_02101 +MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA +QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARTAAVAAYRAGLTADGA +AGLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT +VTDATEARAALDHGAAFLVVQGHRAGGHRGTSDPAAEPTRAEMPTVLAAVRDVVGTGAAS +AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA +DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH +LWAGTEAHRVREAPAADVLASLAP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000472.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000472.fa new file mode 100644 index 0000000000000000000000000000000000000000..81bf94a43c20f47eb239a8fcf2f1ed0e0d308348 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000472.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00601 +MQVLLALTPILLTLALLLTRLPAWVAPAAGGVLAAALAPTVFGVDPGVLAAEVGRGVPTV +VEILAIIAGGITLSRVMEHSGAHARLALWLSAGNGPTLATALLMVHGIIPFLETVTGFGV +SLIVGVPLLLGLGFTAFRSALLAVLALTIGPWGSMAPGTLMGARLYDLDFQAVGVTAALF +NLPASLVAGAATVLLLRGAQGMRGDGEPARTVPWLAVGLLSGAAQWALILGANLSVGTAP +AGAVGTFVLTVAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVFGTTVEDALGLTGVLSVVG +TPALWSFVAVGAGVALLGLGPHARRTVPGEAARLWVGTAIPNALYVAFGLTLSAGGVSQA +LAGALSGMGPAYLAAIPVIGAFSGFVTASNTGAMALMGPLQMDTGAALGVPPTWTNGLHN +AAAGWGIIAGPARIQVAHAMAVGAQTPEMPGWAVSRRALLAVLLPAMVVGIALMSLLGLA +VLPRV +>MOLHKGIG_02157 +MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL +LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV +SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF +NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP +AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG +TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA +LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN +AAAGWGIVAGPARIQVAHGMAAGAQSPHMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF +LLPR +>NAFOICDF_00523 +MQVLLALAPILLTLGLLMTRLPAWAAPAAGSVAAVVLGLTVFGVDPAVLGAAVGHGVPTV +LEILAIIAGGITLSRVMEHSGAHARLGGWLSAGNGPTLATALLMVHGVIPFLETVTGFGV +SLVVGVPLLLGLGFTAYRAALLSVLSLTIGVWGSMAPGTLMGARLAGLDVQEVGVTAAVF +NLPASLVAGVATVLAVRGARGLRDDSAPARLAPWLGVALASGTAQWALILGANLLVGTAP +AGAVATFALTLAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVLGTTAEDALGLTGPLSVVG +TPALWSFVAVGVGLRLLDLDAAARRTVPRESLRLWRGTAVPNALYVAFGLVLSAGGASPA +LAGALSGLGESYLAAMPFIGAFAGFVTASNTGAMALVGPLQMDTGAALGVPPAWSNGLHN +AAAGWGIIAGPARIQVAHGMAAPAQTPDMPGRAVSPRGLVAALLPASLAGVAGMSLMGWL +LLPR +>MHAAABBN_01870 +MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTVFGVAPGDLGGAVGAGVPTL +LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV +SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF +NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP +AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG +TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA +LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN +AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF +LLPR +>LFPAFLNI_02100 +MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL +LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV +SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF +NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP +AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG +TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA +LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN +AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF +LLPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000473.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000473.fa new file mode 100644 index 0000000000000000000000000000000000000000..64bfc6c0905964e603c86f5bbd455086d5b5690d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000473.fa @@ -0,0 +1,100 @@ +>ACLBLIBL_00609 +MDGVVTDTAGVHAQAWKELFDEALPAVGALPANAAAVAADPEALRPFDAAADYLHHVDGR +PREDGVRTFFHSRGLRVPEADSPEAATTPQLTVLALAERKQGYFEQVLARDGVRVFPEAQ +DLLEKLRAKGVPVALVTSSKNSRAVLGAGGVLDFFPVIVDGHTAIERGLPGKPDPAMFWE +AARELGVDVADAMVLEDAVSGVKAAADGRFGLVIGVDREPDLGKGRLKGAGAHLVVQDYG +TLCLEQRTTTPFDPAWVLRWDEFDPASEGTREVLCTLANGYWGTRGAVPGTRISDVHYPG +TYMAGVFNRLTSMVQGRAVDTEHMVNIQDWTPLVVTPRGGRPLLPGEETLVDFSQEMDLR +RGVLSRTMAFEDEQGRRTSLHTRQFTSLANRHLAAIELTVVAENWTGELTVRSTIEGRVA +NLNVSDDRTLANQHLEPSQAREIDGETVLLETTTSQSRIDIAVATRTRQMAPVGHHEPIR +RPVDGSDLRVGQDIRLHVEEGVPLVIEKIAAVATSHDHAQASVWESAVKDVQRANNFRNL +LTLHEQRWGTNWDRFSVRIDIAEPYRHQRRSAAAAEGAEYAPPVVDAGRSASVGSAVPMG +KDGASLRQQLALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLT +LRRPEITRGILMYRYRRLNEARANAQAEGWAGAMYPWQSGADGSEETPTELWNPRSRMWM +PDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEVSRFFMSMALHNADTDRYE +IHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLSETARLVRWLDTLDDGLPEIMEIT +EEEIERWEDVSARLTVPFFEDGEEAGILAQFEGYQDLKEFDWEAYRAKYGNIGRMDLILQ +AEGDATNRYKLSKQADTLMLGYLFSAEELDGILRRMGYELPQEAFERMVTYYEARSTHGS +TLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTREGIHLGLMAGTVDTVIRCYA +GLETREDVVRVDPRMPSQLPGASFTIRFRQQPVQIHMRRSEVTVRAGSGMWHDVPMIIAG +QEHTLSPGAEITVPLG +>MOLHKGIG_02154 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP +ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL +TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV +LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG +LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDHFDPASEGTR +EVLSTLANGYWGTRGAVPGTRISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT +PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR +HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE +TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKVAA +VATSHDHASASVWESAVKDAQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHHRRS +TAAETGGEYAPPVVAAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD +ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA +GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI +SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL +TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF +EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSSEELDR +ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL +SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ +PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLD +>NAFOICDF_00533 +MTQTLTPVDQQDRNARRHRLRRYRAVIFDMDGVITDTAGVHAAAWKELFDQALPAVGALD +ANRAAVAADPGVLRPFDPEADYLHHVDGRPREDGVRAFFASRGLTVPEVDDADAPVDLTV +LALAERKQGFFEKVLERDGVRVFPEATDLLEKLRDKGVPVALVTSSKNSRAVLTAGGVLD +YFPVIVDGHTAIERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFGLV +IGVDREHGEGGKPRLKDAGAHIVVKDYGTLRLADRTTAPFDAAWVLRWDHFDPATEGTRE +VLCTLANGYWGTRGSIPGTRISDVHYPGTYLAGVFNRLTSMVQGRQVETEHMVNMQDWTP +LQVIPAGGRPLIPGEETLLDYHQEMDLRRGVLSRSMRFEDAQGRITTLHTRQFQSLADRH +LGAIELTVEAENWSGDLVVRTLVDGRVANLNVSDDRTLANQHLEPVAAREVDGETLLLET +VTSQSRVHVAVAARTRQMAPKGHHQPIRRPVEGSDLMVGQDIHLHVEQDVPLVLEKVAAV +ANTHDHALASVDASAIKKVQRAQNFRNLLTLHEQRWGMNWDRFSVRIDLAEEHRNQRRST +AVLAEGEEFEAPVFEAGRSASVGSAATMGKDGASLRQQLALNLHTYHVLQTAFGKRRDLD +ASVGARGLHGEGYRGHIFWDEIFVYPMLTLRRPEITRGILMYRYRRLNEARANAQAEGWA +GAMYPWQSGSDGREETPAELWNPRSHMWMPDNSHNQRHVSLDIAYSVLRYIEITKDASFI +SDYAAEMLVEISRFFTSMTLHNAETGRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL +TSWVLSETARLLRWLDTLDDGLPEVMEVTEEEIARWEEIAAKLTVPFFTEGPEAGILAQF +EGYQDLLEFDWEGYRAKYGNIGRMDLILQSEGDATNRYKLSKQADTLMLPYLFSGAELEQ +ILGRMGYELHQEALERTVEYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL +SDTQGGTTREGIHLGLMAGTVDTVIRCYSGLETRDDVVRLDPRLPRQLPGARFTIRYHQQ +PVVIHMTQRDVTVTAGEGMWHEVPMVIAGREHTLEPGGEVTVALG +>MHAAABBN_01867 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP +ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL +TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV +LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAASDGRFG +LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR +EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT +PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR +HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE +TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA +VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS +TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD +ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAEGWA +GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI +SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL +TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF +EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR +ILRRMGYELPEEAFERMVTYYEARSTHGSTLSRLVHAWVSARTDPDRSWDLFTEALESDL +SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ +PVVIQMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLG +>LFPAFLNI_02097 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP +ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL +TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV +LDFFPVIVDGNTALERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG +LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR +EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT +PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR +HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE +TATNQSGIHVAMATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA +VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS +TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD +ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA +GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI +SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL +TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF +EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR +ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL +SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ +PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGDKLTVPLD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000474.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000474.fa new file mode 100644 index 0000000000000000000000000000000000000000..26d3c23ecbb5ce92896cb0b877419e9fdfbffca3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000474.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_00610 +MQCHHYDAGRCRSCALMGVPYGVQLTDKDAAVCARLDAAVPAEAWLPPQASAESGFRNKA +KLVATGTAAAPRLGILDPEQHPRHHDGTGHDLRDCGLYEDGMEAAFHAIAETIPAAGLEP +YDVAARTGELKSVIVTLSPDRELMVRFVLRSAARLDALRAAVPGLRSALAGLGTPAAVVT +ANLHPEHVALPEGPDEVHLAGDPTLRMELNGIGLRLRPQGFFQTNTDVTRRLYATAAAWL +AEAAAADGTPVHSAWDLYCGVGGFAFHLARPVAEGGAGVAEVWGLETSEDAVAAARDTAA +ELGLAGAVRFTAGDATRALSPGRREPSEALSSGKREAWDALSSGSREPSDAGAHPDDDAA +PAAMPDAVVVNPPRRGIGPELAARLQDSGVPHVLYSSCNAASLAKDLAAMPAYRARRAQV +FDMFPQTGHAETLVLLSRA +>MOLHKGIG_02152 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADALDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFEACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF +SAGDATSALSFEKRRAPEALSFEKRRSRPDAVVVNPPRRGIGAELADALEDSGAPTVLYS +SCNPTTLAQDLARMPSYRVARVQLFDMFPQTLHAEVLTLLTRR +>NAFOICDF_00534 +MQCPHFDAGECRSCALMGVPYGAQLADKDAAVRARLAEATDARTRWEAPAASAESGFRNK +AKLVVTGTAAAPRLGILDPRQHPRHHDGTGVDLRDCGLYEDGMEAAFHAIAGAVTAAGLE +PYDVAARTGELKNVIVTRSPDRELMVRFVLRSADRLEALRPEVPALREALAALGTPAAVV +TANLHPEHVALPEGPEEVHLAGDATLRMELNGIGLRLRPQGFFQTNTDITQRLYATAAAW +LAEAAAEGGTPVERAWDLYCGVGGFAFHLARPVAEGGAGVAEAWGLEVSAEAIEAAREAA +AELGVAERVRFTAGDATTALAAPGGTRPDAVVVNPPRRGIGAELAGRFEESGVPFVLYSS +CNAATLATDLTAMPSYRVARAQVFDMFPQTGHAETLVLLARR +>MHAAABBN_01865 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF +SDGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS +SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR +>LFPAFLNI_02095 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLTMRLNGVGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEAGLPAAAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF +SAGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS +SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000475.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000475.fa new file mode 100644 index 0000000000000000000000000000000000000000..097360627e65bca50ec5adf34939cdea566c3cd0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000475.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00611 +MTAFDRLPLPAEPQTPHDRLRRRVAAAVAERGEAAVAGLAVRLLTGSVTPADVTSGAARA +LTGDDGDLTAGATGALALGHAWHRSALPALTSALSAPEPDVRSAAHLVLAARAGSLRADV +AVDRALVDAVRAGCADPDPQVRASAASALGALAGPQDLEAALPVLTGMVMDVDADLATAA +ELALDHLAERLDRPDLRVGAEG +>MOLHKGIG_02151 +MTAFDRFPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA +AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG +>NAFOICDF_00535 +MTSRDLPLPVEPQTPHTRLARRVEAAVSARGEAAVAGLAVRLLTGAPTPEDVTSGAARDL +IGDDGELTPGATGALALGVVWHRGAAGALAAALDAPEPEVRAAALLVLAARADRLRADAQ +AGRALVEAVTARASDADPQVREAAASALGALARAEDLSAVEPVLSALVMDVDPELATAAE +LALAHLAARLDRPELDPTPQA +>MHAAABBN_01864 +MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA +AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG +>LFPAFLNI_02094 +MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPEDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVIASRAGSLRRDA +AVDRALVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000476.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000476.fa new file mode 100644 index 0000000000000000000000000000000000000000..5d7ef9f6fb5c7625c7820788bd0d7d1edc03779e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000476.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00612 +MKPAGALALEFRADSFDHPGGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +SVPVDHRAVVQARVVHTDGADVHVQTRLLLPEVKDESGDPVVATSSLVVYSAEEDGARVT +VPAWVPSTPGQIERDEQASRSTVARRAVERGMARLPFPSPGQAPEEMSTLAFLAPASEAT +VGGTMNAGAILRWLDEAAAVCAARWTGHESVVAVFGGGVRFVRNILVGDLVRVDALLVNT +TERSMQVALRVYAGRPTGVQPRLVAHSIAVMVDVSAEDKAQPVRQYVPESEGARSLQEAA +VQLVRLRSEVGAAWTETRRSPESR +>MOLHKGIG_02150 +MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT +VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA +IELVRMRSEVSAAWTEMRRSTDPR +>NAFOICDF_00536 +MMRSGALSLDFRADSFDHPSGLVDAGTAIGWIDKVGYAVAASWSGTYVRARYMGTMQFRH +PVPVDMRVTVQGRVVRTHGAAVHVQLRLLLPEVLDDDGRPVVSTSTLSVYYAEEDGQMLQ +VPEWTPSTPDQIERDERARVSSVERRGIEQVMARLPFPEPGQEHEEMTTLAFIAPMAEAS +VGGTVAAGAVMRWLDEAAGVCAARWTGHENVVAVFAGGVRFVRPVKVGDLVRVDALLVHT +SERSMHVALRVHAGPRHQRDHRLVAHSIAVMVDVTREGRAESVRPYAPGSPAAHRLEESA +VELVRLRSEAGAVWSDPS +>MHAAABBN_01863 +MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT +VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA +IELVRMRSEVSAAWTEMRRSTDPR +>LFPAFLNI_02093 +MRPPGALALEFRADSFDHPTGLVDAGTVVSWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEDGVPVT +VPAWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEGQAQPVRQYVPESESARRLQETA +IELVRMRSEVSAAWTETRRSTDPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000480.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000480.fa new file mode 100644 index 0000000000000000000000000000000000000000..a31ae97ea71a48359e3dc6e861eb8b898ecc60c9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000480.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_00621 +MLWTLLRRPRRPDLGAVTAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTDRIWDLGLV +MLGVALVQVVAAIVAVWFGAKVAMGIGRDLRRAVYTRVDGFSAEELGRFGAPTLITRGTN +DVNQVQMVTLMGLNFMVAVPIMAIGGIIMAVREDPGLSWLVWVSVPVLLVIVAWIVAKLM +PLFQRMQDDIDRVNGVMREQVMGIRVVRAFVREPHESARFSGANAALTRTSVLIGRLFVL +LGPVITMILHLATAAVLWFGGHRVADGLVEVGALTAFMQYLLQILMAVMMGTFMMMMLPR +AVVSAGRIGEVLDTVPTLAEPVNPVTPADPRGAVELRDVTFAYPGAEAPVLDGVSFTVAP +GSTTAIIGATGSGKSTLVNLIPRLYDATSGQVLIDGVPVTELARAELTRAVALVPQKPYL +FSGTVAENMRFGAPEATEEEIWAALETAQAAGFVRERTTGEGETAAGGLDSRLSQGGTDV +SGGQRQRLSIARALVARPRILLFDDSFSALDVATDARLRGALDATAAGTTRIVVAQRVAT +ITEADQIIVLDEGRVVGRGTHAELLAGNETYKAIVDSQVREEELA +>MOLHKGIG_02148 +MLWTLLRRHGRRYRGDVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV +MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN +DVNQVQMLTLMALNFMVAVPIMAVGGIVMAIREDPGLSWLVWVSVPVLLVIVAWIVARLM +PLFQQMQDNIDDVNGVLREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR +AVISARRIGEVLDTVPTLGEPVRPVTPERRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP +GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL +FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT +ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA +>NAFOICDF_00546 +MLWTLLRRHLNPYAGAVTAVIVLQLVSTLAMLYLPSLNARIIDEGVARGDTARIWDLGLV +MLGVAAVQVVAAISAVWFGAKASMGVGRDLRRAVYTRVDGFSAEELGRFGAATLITRGTN +DVNQVQMLTLMALNFMVAVPIMAVGGIVMAVREDAGLSWLVWVSVPLLLVIVGFIVSRLM +PLFQRMQDDIDAVNGVMREQVMGIRVVRAFVRQDHEAARFTDANQALTDTSVRIGRLFVL +LGPVITMVLHLATAAVLWFGGHRVDQGLVQIGSLTAFMQYLLQILMAVMMGTFMMMMLPR +AVISARRIGEVLDTAPTLGEPVHPVTPERREGRVELRDVTFAYPGAEAPVLDGVSFTAEP +GTTTAIIGATGSGKSTLVNLIPRLYDATSGQVLVDGVPVTDLARAELTDAVAIVPQKPYL +FSGTVRDNMRFGAPEATDEQIWAALETAQAADFVRERTTGEGETAASGLDSSLSQGGTDV +SGGQRQRLSIARALVADPRILLFDDSFSALDVTTDATLRAALDASAAQTTRVVVAQRVAT +ITDADQIVVLEAGRVVGRGTHAELLAGNETYRQIVDSQVREEELA +>MHAAABBN_01856 +MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV +MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN +DVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWLVWVSVPVLLVIVAWIVARLM +PLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGERVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR +AVISARRIGEVLDTVPTLAEPVRPVTPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP +GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL +FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKAETAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT +ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA +>LFPAFLNI_02086 +MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV +MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN +DVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWLVWVSVPVLLVIVAWIVAGLM +PLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHEARRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR +AVISARRIGEVLDTVPTLGEPARPVSPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP +GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL +FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRVLVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT +ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000481.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000481.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb8cc6f4edffff0425def27322a3fa8ca25544f7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000481.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_00622 +MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFA +PERTGLILVSLMVLVAVVLNVWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQG +QGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQLFMWLQGRVLNDLVMRIVFRL +REDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM +FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVF +GRQADMAERFDERNEAMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMT +LGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFELLDEDEQDSDAEVARRASDD +DVAEPADASVRETGASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLVAEPGQT +IAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGG +TIRENIRYGRQDATDEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIA +RAFLAQPSLLILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVME +HGDIVEQGNHAELLAARGAYHRLYMSQFKGGEDDGGGAASGEDAR +>MOLHKGIG_02147 +MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV +AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP +GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY +FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALIAL +PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE +ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN +QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPARTFVRETAPSEGTFVRE +TAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLVAEPGQTVAIVGPTGA +GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYG +RLDATDEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSL +LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGS +HAELLAAKGAYHRLYMSQFKGGEDDDGAASRDDAR +>NAFOICDF_00547 +MSEQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLV +AVVFNVWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTP +GQGIDFDALARLILTVLGMYVVAQGFMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSH +FDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMMFWLSWELALIALIAL +PVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERND +AMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN +QPLGQVAGMSNMLISGVASAERIFELLDEPEEEPDDVVAARADDDVAHLPQPVAGRVEFE +HVRFSYTEAKPLITDLNLVAEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVD +TRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEATDEEVLAAAKATYVDRFVHTLP +DGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAALR +NDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGEDEH +HDDGAPASR +>MHAAABBN_01855 +MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV +AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP +GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY +FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL +PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE +ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN +QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE +TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA +GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG +RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL +LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS +HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR +>LFPAFLNI_02085 +MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLV +AVVFNVWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP +GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY +FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL +PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE +ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN +QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE +TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA +GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG +RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL +LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS +HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000483.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000483.fa new file mode 100644 index 0000000000000000000000000000000000000000..258b86dd5e1cda7a3e93fd61b0eba4d4deb1fd83 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000483.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00627 +MSKVTRWAALVLTLVLVAALAFWAGRATLTPPAQADQRPSEDAVVTVAEQELGRVITLGV +SVAREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVIAVQGELPQWRALDEGATG +SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAAGTVELGQLVVLESLPAA +LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWEAV +AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL +RTQPGGAVVVTVVQDGVEEERTVTVRGSADGLAVVDGVDAGETVRVLNGAP +>MOLHKGIG_02145 +MTRPLRWATLAGVLLIVAVLAFWAGRATLTPPAQAEQRPSEDALVTVAEQELGRVITLGV +SVTREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVITVQGELPQWRALGEGATG +SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAADTVELGQLVVLESLPAA +LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAIIPAGTAVTVPHGEHEWEAV +AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL +RTQPDGAARVTVVRDGVQEERTVIVRGSADGLAVVDGVDAGETVRVLNGAP +>NAFOICDF_00551 +MTRPARWAALVLAVVLVAALAFWAGRVTLTPPAQAEQRPSEDAVVTVAEQELGRVITLGV +SVTREQAPAAVNALSGVVTRAGQSGEVAAGDVLYAVAQKPVIAVQGELPQWRALGEGATG +SDVTAFQRMLTATGTKVKATGTWDEATATAWNAWLTTRGYPAADTVELGQLVVLESLPTA +LSVDAKATAVGGTLAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWKAV +AGESISDEQGLIRITLTAPDGGVVCGEDCDTLPADPTTSLLSQVSVVPPVSGPVVPVSAL +RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR +>MHAAABBN_01852 +MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV +SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG +DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP +LSVDAKTTAVGTTLAGGENVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV +AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL +RTQPDGAATVTVVRDGAAEDRAVTVLGSADGLAVVDGVDAGEQVRVLNGTR +>LFPAFLNI_02082 +MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV +SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG +DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP +LSVDAKTTAVGTTLAGGEKVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV +AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL +RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000484.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000484.fa new file mode 100644 index 0000000000000000000000000000000000000000..cfef8452c0ceb05d78eaa7d9a5d40ac734bb2f40 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000484.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00628 +MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA +GVVRLGDVEASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLERRVLE +ERARALLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL +VLDALAETAAEGRTVVVATHDPAVVARADEVVRL +>MOLHKGIG_02144 +MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA +GVVRLGDVDASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLSRRELE +GRARILLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL +VLDALAEAAGEGRTVVVATHDPAVVARADEVVRL +>NAFOICDF_00552 +MTGPATPGTPAAPGTPAALAVEDLRFAYTRAAEELFDGLTHAFTPGGVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL +>MHAAABBN_01851 +MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL +>LFPAFLNI_02081 +MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPVVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000486.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000486.fa new file mode 100644 index 0000000000000000000000000000000000000000..5d3030206e2fa62d7ebbb4e329d066e3edfb766e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000486.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00632 +MALFSQPVFINLPTTDTERIREFWTSLGAQAIEDFSDENSVCIELTESTFAMYLSPGYYT +DFIGDREIADCMTTNSALMALTVGDAAAVDALADRAIEAGAAEVPLPVDLREEMVDSGMH +SREIVDPDGHQWEFVTA +>MOLHKGIG_02140 +MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT +DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH +SREIVDPDGHQWEFVTA +>NAFOICDF_00556 +MRTRWSTVLVMALFSQPVYINLPSTDTERIREFWTSMGADIDEDFSDENSVCVQLTESTF +AMYLSPGFYTDFIGDREIADCLTTNSVLLQLTAPDRGAVDALVRAAVEAGGSEVPLPDEL +QEDMTATGVHSRQVVDPDGHQWEFMAA +>MHAAABBN_01848 +MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT +DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH +SREIVDPDGHQWEFVTA +>LFPAFLNI_02078 +MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT +DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH +SREIVDPDGHQWEFITA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000487.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000487.fa new file mode 100644 index 0000000000000000000000000000000000000000..0da6cfd1db9985a5f19b5c276de8050cd77295f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000487.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_00633 +MPAGWPGRTPGPRTAPDWEPGRFHWGDAVVVLAYAGLMLFGLGLPLAMLLGLVPGDLAAF +DLVRDGFTVNMVSYAILTALVLIVAWRPLVTSLRVFRTGTWWKILLLPAVWFTCILVNVL +VLSLIGEAQTSANQAALEEMSAQAPPVLMILMTVVGAPLVEEYLFRHLLVGKLSRWVNVW +VCAVVSMLAFTLLHFLGTGGQFDLVETVPYLTLAIAITVTYILMGRSFGYAVLLHMVNNG +IAIAMLYLVAPLLPDVLPEPTAPAAALSPLLALLG +>MOLHKGIG_02139 +MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW +TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV +VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE +EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT +GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP +GPTAPTTALAPLLALLG +>NAFOICDF_00557 +MSVPPPGPHDAGALPPPGSTAPTSAAGEAPEGWPPAGWPGRASAGGAPQGWPPSGWPGRT +ASARTAPSWEPGRLHWGDAAVVVLYVLMMVVGLGYLLAVLLGLAPRDPAAMDVMDGFRVN +LVSYAVLVVAVLAVSWRPLVASLRVFATHTWLKILLLPALWLVTVLVNALLLSLIGQAQT +SANQAALEEMTTQAPALGMVLMTVVGAPIVEEYLFRHLLVGKLSRWINVWVCAAISVAAF +TLLHFLGTGGDFQWVETVPYLTLAVTITVTYVLIGRSFGYAVLLHMVNNGIAIAMLYLVA +PLLPSAPAPVGPGALLSPLLALLG +>MHAAABBN_01847 +MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW +TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV +VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE +EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT +GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP +GPTAPTTALAPLLALLG +>LFPAFLNI_02077 +MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW +TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV +VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE +EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT +GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP +GPTAPTTALAPLLALLG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000489.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000489.fa new file mode 100644 index 0000000000000000000000000000000000000000..779ffec033e1870b931b7df707a7328ee2ec5ed3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000489.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00635 +MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAAPGLTWMKVSLALYLAFSGSAMWEYLR +REPVPVAMRSPLSMAAAASMLGVIVLLFLGTPAGVGLAAAAALVLGGAAELVAWARHRRE +FIPARDQLWTGLVGLLSGLGVAFGALQGFGPHALLGIAGGGAIIIGVLLLVSGLGFHHEV +RRDRGTAKGL +>MOLHKGIG_02137 +MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR +RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE +FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV +RRDRGTARGL +>NAFOICDF_00559 +MTSPQTPLEISSEVFKPVLIRAGVALIFGLTTVFVQNPGLTWMKVAFALYLVFSGSALWE +YLRRDPVPVGMRSPLSLAAAAWMLGTVVLVIMGSPAAVGIVVGLALLAGGAAELTAWARF +RREFIPARDQLWTGLVGALSGLGVLVGAVQGFGPHALLGIAGGGAIIVGVLMLISGLGFH +HEVRRDRGTAKGL +>MHAAABBN_01845 +MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR +RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE +FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV +RRDRGTARGL +>LFPAFLNI_02075 +MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR +RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE +FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV +RRDRGTARGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000490.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000490.fa new file mode 100644 index 0000000000000000000000000000000000000000..c05e59e8ac72a45e5b5f94329f312650532dfd93 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000490.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00636 +MSAPSPRPSADRAGTGRPARGGLRTTVKGPLVFSAVLGVIGGVIAGITASGGTQNPLRID +IALIAFGVFFMTSLVVVAMLQLAARENPDHLSAGSGINRSSEETFQKAAAERRAQVARER +REQDGTGGDAPRA +>MOLHKGIG_02136 +MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRID +IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAARER +REQGGTGGDAPRA +>NAFOICDF_00560 +MSAQSPRPSDDRTRPGAGRPARGGLRTTVKGPLVFSAVLGLVGGVVAALTASGGTANPLR +IDIGLIAFGVFFMTSLVVVAMLQLASRENPDHLSRGSGVNRSSEETFQRRAAERRAKAAA +ERRAAQGDAGR +>MHAAABBN_01844 +MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD +IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER +REQGGTGGDAPRA +>LFPAFLNI_02074 +MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD +IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER +REQGGTGGDAPRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000491.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000491.fa new file mode 100644 index 0000000000000000000000000000000000000000..e47e2987b7e849afd8b93b0264b4f82bcd935d8d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000491.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00638 +MLSPRTLARLSSVAAFLNTAPGPRGGQEAPERFTAATQLPALVPELQEGEVRLRLAAAAA +VRARELRERLTRVWALAATDESAAVERVNELLAEAGPLRLTAGGDVVGLAPAQVPADAVE +RLAAMATLALAETAMDGELARLRVCEGEDCENALVDGSRNRSKRFCDEANCANRTHVRSY +RARLAEAAEAAPATDPAGPEEAEGTEAVVDEAAPADEPLQETEKEKKERRKAQKKARKKA +EKKAGKKKSDKKKSDKKKD +>MOLHKGIG_02134 +MLSAPTLTRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +VRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE +RLAAMAALALAETAMDGELVRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY +RARLAEAAEAAPATDPAGPEEAEAPEAVADEAAPADKPRQETEKEKKERKKAEKKAEKKA +RKKAEKKARKKKSDKKKD +>NAFOICDF_00561 +MLSPHTLARLASISAFLNTAPGVRGGQEAEERLTAGTQLPALVPELQEGESRLRVAAAAR +TRAHELRARLTELWAAADAEDVPAAVAAVNELLAETGPLRLEVSDGSADLAPAQVPADAV +ERLTAMAALALTEAALEGELTRLRVCAGEDCENTLVDASRNRSKRFCDAANCANRTHVRS +YRARLAEAEDTQADVEAADAAPLPEVAPEADPQDATDLEAIEAAEGVESAVQEPVKKDST +KDKKSKSEKKARRAAKKKAEKESEAAAEGKKGKREKSKKSEKHKKKAAKD +>MHAAABBN_01842 +MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +VRGRELRGRLAEVWALAAGDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE +RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY +RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA +EKKAGKKKSDKKKD +>LFPAFLNI_02072 +MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +GRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE +RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY +RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA +EKKAGKKKSDKKKD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000493.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000493.fa new file mode 100644 index 0000000000000000000000000000000000000000..711c921213a3adfc1bd18a145029cffa5c9480eb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000493.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00648 +MLPDPSPTVTVDGLLLRPLRTADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAADA +RGDVEPGRVPASFYVGVDEAGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR +LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVETGLDGAPFPEPKLRFD +VPTTAA +>MOLHKGIG_02132 +MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA +RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR +LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD +VPTTAA +>NAFOICDF_00564 +MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA +RGDVEPGRVPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR +LLRGALTLLAAHGVSTALLTCDETNTASVATIRACGGVLRDRVEAGLDGAPFPVPKLRFD +VPTTAA +>MHAAABBN_01840 +MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA +RGDVEPGRVPASFYVGVDEAGHLVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR +LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD +VPTTAA +>LFPAFLNI_02070 +MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA +RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR +LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD +VPTTAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000494.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000494.fa new file mode 100644 index 0000000000000000000000000000000000000000..991425c14d5e47ab6b7db9e185b6a417fedab3ed --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000494.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00649 +MTVPSSSAEHAPALEARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQDAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>MOLHKGIG_02131 +MTVPSSSAEHAPALEARPEMPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>NAFOICDF_00565 +MTVSSSSAEHAPALEARPELPGETVSRVAMTPAALALIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVRLGTFVVPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>MHAAABBN_01839 +MTVPSSSAEHAPALEARPEMPGETLSRVAMTSAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>LFPAFLNI_02069 +MTVPSSSAEHALDARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGSAP +MCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGRGS +GFSVEAPEGKRFLIRSRLMAGSG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000496.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000496.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a9b928025be61b4602c189d54882110c290e0e6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000496.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00651 +MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP +LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE +VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKIISYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>MOLHKGIG_02129 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +AALDAAWKAAPAWGATSPAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP +LAIDHFRYFAGAIRAQEGRLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE +VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>NAFOICDF_00567 +MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAIRETLNADLP +LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE +ICTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>MHAAABBN_01837 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP +LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE +VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>LFPAFLNI_02067 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADLP +LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASVMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE +VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000497.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000497.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d07792590f96c8c2506cdea6f31367a7e3a1e33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000497.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00652 +MTTMKAAVVTQFGKEADVQEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSAD +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD +>MOLHKGIG_02128 +MTTMKAAVVTQFGTEADVTEVERPTPGQHEALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD +>NAFOICDF_00568 +MTTMKAAVVSQFGKEADVKEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWGACGHCQYCRTGWETLCEEQINGGYSMN +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD +>MHAAABBN_01836 +MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD +>LFPAFLNI_02066 +MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000498.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000498.fa new file mode 100644 index 0000000000000000000000000000000000000000..b64adcc690928fdc34bfe2a593ca90e49c50dc06 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000498.fa @@ -0,0 +1,32 @@ +>ACLBLIBL_00653 +MTQTTSTPVRLRAPDGFVLAARHFTPTTTTPPASPAGTVVIASATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESREPFAVARRARWADWGVLDADAVLGWARTHLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRR +LGWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDA +ALDRADSYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVVPAAA +R +>MOLHKGIG_02127 +MTQTTSTPARLRARDGFVLAARHFAPTTAPQARPAGAVVIAPATGVKATYYRRYAEFLAG +HGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG +FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPVVTLARGHLPGRRL +GWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTEAA +LDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVAPDAAR +>NAFOICDF_00569 +MTQTTSTLVRLRARDGFVLAARHFAPTTTPPARPAGAVVIAPATGVKATYYRRYAEFLAG +HGFHAVTFDYRGVGESRAPFAVARRARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG +FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHALMPMVTLARGHFPGRRL +GWLEDLPRGVALDWARSRRDFTASARTVAGRDELRRRLAAFTADALIVAPVDDDFGTDAA +LDRADSYSPGRRTVRWRVRPEELGVGEIGHFGLFHARFASTFWPATLEWLRDGVAPAGAR +>MHAAABBN_01835 +MTQTTSTPVRLRARDGFVLAARHFAPTTTTPPARPAGAVVIASATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESREPFAVARRARWADWGALDADAVLGWARTRLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPAITLARGHFPGRR +LGWLEDLPRGVALDWARSRRDFTASARTTAGRDELRRRLAAFTADALIVAPVDDDFGTDA +ALDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPAFWPATLEWLRDGVAPAAA +R +>LFPAFLNI_02065 +MTQTTSTPARLRARDGFVLAARHFAPTTAPQARPAGAVVIAPATGVKATYYRRYAEFLAG +HGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG +FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRRL +GWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDAA +LDRADAYSPGRRTVRWRVRPEELGVTEIGHFGLLHARFAPTFWPATLEWLRDGVAPDAAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000500.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000500.fa new file mode 100644 index 0000000000000000000000000000000000000000..63ae6e440ba7ba875e047d98994c46502a41974f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000500.fa @@ -0,0 +1,14 @@ +>ACLBLIBL_00655 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAAELFRGARATSFALTRQVEDPARY +RLLIGWRTLEDHTVGFRESEAFGQWRALVTPHLAQPPAATHWESVAAAF +>MOLHKGIG_02125 +MSAGQGATTAGPVIESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPARY +RLLIGWRTLEDHTVAFRESDSFLAWRALVTPHLAQLPAATHWSAV +>NAFOICDF_00572 +MEDPARYRLLIGWRTLEDHTVGFRESDAFLAWRALVTPHLAQPPAATHWSAV +>MHAAABBN_01833 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDKGATSFALSRQVEDPARY +RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV +>LFPAFLNI_02063 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPAHY +RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000502.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000502.fa new file mode 100644 index 0000000000000000000000000000000000000000..be3c7d4e99223965072fcf306b50c2f77209e9a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000502.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00659 +MTTTDLKITGMTCGHCVASVQEELGEIAGVTAVDVDLTAGGVSTATVTSESPLDPAAARA +AVEEAGYRLVEG +>MOLHKGIG_02121 +MTTTDLKITGMTCGHCVASVQEELGEIAGVSAVDVDLNSGGVSTATVTSEAPLDPAAARA +AVEEAGYTLVEA +>NAFOICDF_00576 +MTTTDLKITGMTCGHCVASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLGPAAARA +AVEEAGYTLVEG +>MHAAABBN_01829 +MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA +AVEEAGYTLVEA +>LFPAFLNI_02059 +MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA +AVEEAGYTLVEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000503.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000503.fa new file mode 100644 index 0000000000000000000000000000000000000000..ccc9b9e4a88aa8a2899d113355a26d265bf023d6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000503.fa @@ -0,0 +1,18 @@ +>ACLBLIBL_00660 +MSTLPTTTDAHDGADPCAGAHPPHAAHRDKDAHLTRLRRIEGQVRGIHRMVDEDVYCIDI +LTQVAAVTKALQAMSLNLTSEHLRHCVAEAAVEAEASGRTELIDEKVAEATAAIGRLLR +>MOLHKGIG_02120 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR +>NAFOICDF_00577 +MEHDRHAGPGYSPQREAYLKRLKRIEGQVRGIHRMVEEDVYCIDVLTQVAAATKALHAVS +LGLVEDHLRHCVAEAAVQAEAEGRTELIDEKVAEATAALGRLLR +>MHAAABBN_01828 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR +>LFPAFLNI_02058 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000506.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000506.fa new file mode 100644 index 0000000000000000000000000000000000000000..1fd609f7a4f9e7e57f4926a53b01df50d86177ef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000506.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00663 +MSINTVHHLPAAPSPLMQRHVLKRVEETLARRFEGVATAEAVRATVREVASELKRSARMT +MFLPALTEREAARRLQAGAPAHEPLAAAA +>MOLHKGIG_02117 +MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI +TTFLPALAEREATRRLQAATPAHEAMAVAA +>NAFOICDF_00580 +MTATLTTQHHMPVHPDTTMQQRVLERIAGTLIRRFDGSVPAADVRTTVAEVTAELEAEAR +LTTYLPALTEREALNRLEAMAAAPAHMTITHARHAA +>MHAAABBN_01825 +MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI +TTFLPALAEREATRRLQATTPAHEAMAVAA +>LFPAFLNI_02055 +MVRQPKEVLTVSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREV +VADLKRGARITTFLPALAEREATRRLQAATPAHEAMAVAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000507.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000507.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f66fcb3a68bc913ed88574bbace8c00065253d6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000507.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00665 +MSDYQPRRPGSNPAPARRTDRAGKPALGRPKRGLIDESEARQLAEDRERMRRAGVGHQLS +APKRREAATAERPQVMPQTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLAERQAKA +KEIGLPAFRAKQLSVHYFERYTTDPEQMTDLPKDKREVIAEAFFPPLLTEVRRMETDRGD +TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE +QIVRANQVIAEGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPAPEG +LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID +AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW +TASEKDVTREFVERLNAAGIPTTLRDTRGKEIDGACGQLAAGDEDA +>MOLHKGIG_02115 +MSDYQPRRPGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS +APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA +KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD +TIKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE +QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG +LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID +AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW +TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD +>NAFOICDF_00581 +MEGMSDYTPRRPGSKPTPARQKDRAGKPALGRPRRGMIDEPEARQLAEDRERMHRAGVGH +QLSAPPRRAAEVDADRPQVMPKTEGWQQPMGPDGRPQLQFKQPRVSQPPQHLADMTLAER +QAKAKEIGLPAFRAKQLSVHYFEHFTTDPEQMTDLPKGKREEIAEAFFPPLLTEVRRLTT +DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA +EIVEQIVRANQVIAEGGLGGTRRDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP +APEGLGMSARHVTLSTVGLVPAIKKLAQEGVPLTFALSLHAPDDELRDELIPVNARWKAD +EAIDAAYEYFLATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP +GSIWTASEKDVTREFVDRLNAAGIPATLRDTRGKEIDGACGQLAADDEDVAARA +>MHAAABBN_01823 +MSDYQPRRPGSKSTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS +APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA +KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD +TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE +QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG +LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID +AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW +TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD +>LFPAFLNI_02053 +MSDYQPRRTGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS +APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA +KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD +TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSPAEIVE +QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG +LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID +AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW +TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000508.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000508.fa new file mode 100644 index 0000000000000000000000000000000000000000..87e0544540c6ec1dbc6c2144ab414c8ffb4279e4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000508.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00666 +MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAEETGTLWFMTRAASDVASD +ASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVRV +DVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF +>MOLHKGIG_02114 +MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD +APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV +DVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF +>NAFOICDF_00582 +MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ +DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR +VQADSAEYWDGGGAASVVEIVKAKVTGGEARPGDHDTVEF +>MHAAABBN_01822 +MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAEDGGTLWFMTRSTSDVAAD +APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVRV +DVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF +>LFPAFLNI_02052 +MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD +APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV +DVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000510.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000510.fa new file mode 100644 index 0000000000000000000000000000000000000000..8b0b2cc19d149d9a1154b575830eaedf74b33e08 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000510.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00668 +MATKDLTLEEFGTTVSENDTVLVDFWADWCGPCKQFAPVFDAASEKHEDIVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPAPALDQLLEQVKGLDIAEVRAMAEQQAG +EAEAEPSQDEAVQSTASHLDEVNGR +>MOLHKGIG_02110 +MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDIAEVRRLAEEQQG +QQGDAEPGQDEAVQSTAAHLDDVNGR +>NAFOICDF_00585 +MATTDLTLEAFGTTVSENDTVLVDFWAEWCGPCKMFGPVFETASEKHQNVVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGQALDQLIDQVTALDIAEVRAMAEQQGA +QDAEPSEEEAVQSAAAQLDDVNGR +>MHAAABBN_01817 +MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGAALEQLLDQVKGLDIAEVRRLAEEQQG +QQGDAEPGQDDAVQSTAAHLDDVNGR +>LFPAFLNI_02050 +MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHDDVVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDVAEVRRLAEEQQG +QQDDAEPGQDDAEPGQDEALQSTAAHLDDVNGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000511.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000511.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3d1f02b9514d578ddab8950b25fcefb9868aab1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000511.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00669 +MQTPATPSPHDRPSPVVRPWMAAPDLPIAGPDGVERVVLLSPAGEAVGTEAKAAVHRRTE +DGGTPLHLAFSCHVYDDAGRFLLTRRALGKKAFPGVWTNGFCGHPGPGESPAQAVLRRAP +QELGAEVSDVVEVLPDFRYRAADASGMEEHEICPVFQARMHGDPAPERDEVAEWCWVEPA +DLAAALAAVPRAFSPWLVEQWQQGAFEAR +>MOLHKGIG_02109 +MQTPATPSPHDRPSPVARPWMAASDVPVAGPDDVERVVLLSPAGEAVGTEAKATVHRRTE +DGGTPLHLAFSCHVYDEAGRFLLTRRALGKAAFPGVWTNGFCGHPGPGEPPAEAVLRRAP +QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA +DLAAALAAVPRAFSPWLVEQWQQGAFDPR +>NAFOICDF_00586 +MQQGPSDPRTVEEVEERVVLLGADGAPIGTEAKASVHRNAADGGTPLHLAFSCHVYGPDG +RFLLTRRALGKKAFGGVWTNGFCGHPAPGEAPAEAVLRRAPQELGVGVREVTPLLPGFRY +RAADAGGVEEHEVCPVFRAECDGDPVPERDEVAEWCWVEVADLTAALASVPRVFSPWLVM +QWEQGAFGPR +>MHAAABBN_01816 +MQTPATPSPPDRPSPVARPWLAASDVPVAGPDDVERVVLLSPEGEAVGTEAKATVHRRTE +DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPGPGESPAEAVLRRAP +QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA +DLAAALAAVPRAFSPWLVEQWQQGAFDPR +>LFPAFLNI_02049 +MQTPATPSPHDRPSPVVRPWMAASDVPVTGPDDVEHVVLLSPAGEAVGTEAKATVHRRTE +DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPSPGESPAEAVLRRAP +QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA +DLAAALAAVPRAFSPWLVEQWQQGAFDAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000512.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000512.fa new file mode 100644 index 0000000000000000000000000000000000000000..2db9f4e872dae93ed89e9ae9694a847323c37e01 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000512.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_00672 +MSAGREGVVAELEAALSRAAGLAPESAAFAELLAGLRTHAGAGKLIRPRLVELGWRAAAD +GPVPAAERPAVDRLGAAFELLHTGLLVHDDVIDRDVVRRGERTVHEATRRRLAARGVPEA +EAAHAGTAVALIGGDVLLVEALRLAMTCTPDPGRAAPVAAVVLDAATASAAGELEDVLLG +LARHTGEEPEPERILAMQRLKTAHYTVSAPLRVGGAAGGGGSRRRRGAGEAAAPTWAWPT +RWWTTCSGCSAPRSRPASPPTATCARARPPCSPRTAAATPPSAPCSTPAPATPEELEAAR +RALEAAGAREHALQVAEELTRRAAEHLAVLPLGEAACAEFADACHAVLTRSS +>MOLHKGIG_02107 +MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL +GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE +ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE +LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA +DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA +DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS +>NAFOICDF_00588 +MNPLAAGIGGAAPWSASAATPGLDDAGRARAAVRAELDRVFAETPLCADAPDSFHLLWAR +LREAVSGGKLVRPRLVDLGWRTVRRAPASSGVPRGGTGEEEAADLRAVARVGAAFELLHA +ALIVHDDVIDRDDLRRGRPTVAEQYRRDAVRDGVPAGEAEHVGRSAGIIAGDLLLTAAFR +LAAASGARVRAAEAAESVFRAASAAAAGELEDVLLALHRHTGHHPEAGRILTMERLKTAG +YSFEEPLRAGALLAGADPAHAEALAEAGALLGVAYQVVDDVLGTAGDPAVTGKPHDADLR +EGKATLLTAHGRRDPRARAALDRVARAERHGEDLGELAAAVAEARAALVDAGSVEHALGV +AEELVDQARALLDALPMAPAERAEFAATCGQILQREA +>MHAAABBN_01814 +MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL +GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE +ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE +LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA +DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA +DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS +>LFPAFLNI_02047 +MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL +GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE +ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTVRAAEAAAVVFDAAAVTAAGE +LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA +DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA +DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000513.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000513.fa new file mode 100644 index 0000000000000000000000000000000000000000..00f9dfcabed30a8fd7574c5742a79276381c4c9e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000513.fa @@ -0,0 +1,32 @@ +>ACLBLIBL_00673 +MPADAPLYTRTARAAAGRVIRRYSTSFSWACRTLPREARRDVEAIYAMVRVADEAVDGVA +QAAGLDSQRVRAALDDYERACEAAMASGFSTDLVLHAFGDVARRHGITPELTRPFFASMR +ADLGVSEHGAESLAAYIHGSAEVVGLMCLQVFLSLPGTRARTPAEREAIRAQAARLGAAF +QKVNFLRDLAADHDGLGRTYLTGAAPDELTEARKAELVAEVRADLAAALPGIRALDPRAG +RAVALAHGLFAALADRIETTPAAELARRRVRVPDAQKARIAARVLAEQAGLAVARRRRGG +RR +>MOLHKGIG_02106 +MAAPTPSPAALYTRTAHTAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV +DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF +ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL +GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD +PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR +>NAFOICDF_00589 +MTGTTTPPAPAGPECGTVRARTGETDLELYTATALRVAGEVIGRYSTSFSWACRVLPPDA +RRDIAAIYAMVRVADEVVDGAAEEAGLPVARVAAGLDAYERACEDAMDTGFSTDLVLHAF +ADVSRRHGITAELTRPFFVSMRADLTVAEHGEDSLAAYIHGSAEVVGLMCLQVFLSMDGT +RADGPADRAALRAAASRLGAAFQKVNFLRDLAADHDALGRTYFSGAAPEALTEERKAELL +ADLDADLDASLPGILALDPRAARAVLLAHGLFAELSRRLAATPAAELARRRVRVPDPVKA +RIAVRVLAASPVGIGRRGRPLPAGCAEDLAAHQDGDRRP +>MHAAABBN_01813 +MAAPTPSPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV +DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF +ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL +GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD +PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR +>LFPAFLNI_02046 +MAAPAPIPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV +DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF +ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL +GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD +PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000514.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000514.fa new file mode 100644 index 0000000000000000000000000000000000000000..019ce8a8592dbe0f00eaec67a7f0a35aab7c7d9f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000514.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_00674 +MSAAPNVASGAAAHDDGPRAVVIGGGFAGLATAGLLARDGHRVTLLERNDGLGGRSGRWS +AEGFAFDTGPSWYLMPEVIDRWFRLMGASAAERLDLRRLDPGYRVYFEDHLDAPPVDVRT +GHAEELVESLEPGAGERLRAYLDSAGRVYELAKEHFLYTDFRRPADLARPAVLRALPSLG +PQLLGGLRAHVAARFRDPRIRQILGYPAVFLGTSPDRAPAMYHLMSHLDLRDGVQYPIGG +FAALVDAMADLVREAGVEVVTGAEATRIEVEDAERRRRRRGRVTGVVVRQDGTERRLSAD +VVVAAADLHHVQTALLPPAQRVAESAWDRRDPGPSGVLVCVGVRGALPQLAHHTLLFTAD +WEDNFGRIERGEDLAADTSLYVSRTSATDPGVAPDGDESLFVLVPAPAEPGWGRGGIRVR +EGDGWRVEREGDAQVEAVADRALDQLARWAGIEDLHERIVVRRTIGPGDFAADVHAWRGS +MLGPGHTLAQSAMFRPSVRDADVAGLLYAGSSVRPGIGVPMCLISAEVVREELRHAARRD +ALRAQRRGRSQDDDDGARRGRVAAS +>MOLHKGIG_02105 +MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT +GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE +SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR +SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM +AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG +VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR +GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV +PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT +YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI +SAEVVRDELRHDARRVRPAGPGGSGT +>NAFOICDF_00590 +MTPTTPAARPAAAPSGSRRVVVIGGGFAGLATAGLLAQDGHRVTLLEKNPVLGGRSGRWS +AEGFTFDTGPSWYLMPEVIDRWFRLMGTSADEALDLRALSPAYRVYFQEHAADDAAAPGD +GSTPGARAPLDVVSGREESLALAEELEPGAGGRLAAYLDSAERIYALAKRRFLYTDFQDL +TELLRPDVLRALPALAPQLLGDLRGFVARRFEDGRLRRVLGYPAVFLGTSPGKAPAMYHL +MSHLDLADGVQYPIGGFAALVDAMAELVRAAGVEIVTAAEVTAVDVVSDPRPRGRLPRLL +DGAPRPWEPRTPAGGRRRSGHVRGVSWRDAEGGSHRLDADAVVAAADLHHVQTALLPGDQ +RVAERTWDRRDPGPSAVLVCVGVRGRLPELLHHTLLFTEDWDENFRRIDEGEDLQEETSL +YVSMTSATDPGVAPEGDESLFLLVPAPAVPEWGRGGVRTPEEDRAGDAQVETVADRALAQ +LARWAGVPDLGERIVVRRTWGPADFTADVHAWRGSLLGPGHVLRQSALFRPPVRDPRVAG +LVYAGSSVRPGIGVPMCLISAELARDAVSGVRPGGAAPGAPAMAGR +>MHAAABBN_01812 +MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT +GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE +SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR +SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM +AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG +VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR +GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV +PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT +YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI +SAEVVRDELRHDARRVRPAGPGGSGT +>LFPAFLNI_02045 +MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT +GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE +SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR +SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM +AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG +VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR +GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV +PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT +YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI +SAEVVRDELRHDARRARPAGPGGSGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000515.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000515.fa new file mode 100644 index 0000000000000000000000000000000000000000..23ca785430d3a6b361545799fe8c3928c100b484 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000515.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00675 +MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPTWLVVLGTVFFLVPYNLAMYGINDVFDF +ASDLRNPRKGGVEGSVLADPAVRRRVLRWSCLVAVPFVAVLAGWSIARGQWDALAVLAVS +LFAVVAYSWAGLRFKERPFLDAATSATHFVSPALYGLVLAGAAFTPALWALLGGFFLWGM +ASQMFGAVQDVLPDREGGLASVATVLGARPTVWLAAALYAGAGLLMLGTEWPGPLAALLA +VPYVLNVLRFRAVTDATSGAAHRGWRLFLPLNYVTGFLVTLLLIGWALARGGV +>MOLHKGIG_02104 +MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF +ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS +LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM +ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA +VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA +>NAFOICDF_00593 +MIRTLFWASRPVSWVNTAYPFLAAVLLTGGLPWWLVALGGFFFLVPYNLAMYGINDVFDF +ESDLRNPRKGGVEGSVLADPAVRRRVLAWSALTPAPFAAVLAGRSVLRGEWAAVAVLAVS +LFAVVAYSWAGLRFKERPFLDAVTSSTHFVSPAVYGLVLAGAEFTPALWSLLGGFFLWGM +ASQMFGAVQDVVPDREGGLASVATVLGARPTVLAAAALYAAAGLLMLPTDWPGPLAALLA +APYLLSTLRFRHVTDATSGEAHRGWRTFLWLNYLTGFLVTLLLIWWALVR +>MHAAABBN_01811 +MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF +ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS +LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM +ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA +VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA +>LFPAFLNI_02044 +MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF +ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS +LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLVLAGATPTPALAALLGAFFLWGM +ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA +VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000518.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000518.fa new file mode 100644 index 0000000000000000000000000000000000000000..5432d9935a2dfb60409cba97ab2acaf1c7c32a04 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000518.fa @@ -0,0 +1,54 @@ +>ACLBLIBL_00680 +MGGRLIPELLAAGFDVRAGARNPSDLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLY +LVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDTIPVAELSDHMRSRALV +AERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLY +YLLQACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIG +TVTPIPVAVALPLAASLAEEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDV +TFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVWPVIESVGGANGWYSTP +MLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRA +WLQMSTEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTT +GGERRRPRSLARALVDRLPLRRNPLDRGASA +>MOLHKGIG_02099 +MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA +GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI +ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV +IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI +GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA +EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS +DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL +TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ +RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL +PLRRNPLDRRARGAGGAQSRD +>NAFOICDF_00594 +MSTPSTSRGSGLTSAAASGDTPAGTGATTASLSPLGLALPDGHDRRVLVTGATGYVGGRL +IPELLAAGFRVRAGARTPRDLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSM +GAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAGKPVEELSDHMRSRALVAERLE +AAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQA +CALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPI +PVKVALPLAASLAEDAVVEDHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEAD +VYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVWPVIESIGGRNGWYSTPLLWKV +RGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQLT +TEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARR +RTRGLVRALADRLPLRRSPLDRRAG +>MHAAABBN_01806 +MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA +GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI +ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV +IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI +GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA +EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS +DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL +TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ +RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL +PLRRNPLDRRARGAGGAQSRD +>LFPAFLNI_02039 +MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA +GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI +ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV +IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI +GNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA +EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS +DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL +TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ +RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL +PLRRNPLDRRARGAGGAQSRD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000522.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000522.fa new file mode 100644 index 0000000000000000000000000000000000000000..65891a0b6ed2f95739465b31afc9c1029cfbe10b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000522.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00697 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGERAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHDLAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAVGRGTPSSSAVPRPA +PAHHRTTRVRTPERTR +>MOLHKGIG_02086 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA +PAHHRTTRARTPERTR +>NAFOICDF_00607 +MTAVHHPTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDTTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHDLATRQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGTPSSSAVPRPA +PAHHRTTRVRTPERTR +>MHAAABBN_01791 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA +PAHHRTTRARTPERTR +>LFPAFLNI_02025 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSIRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPSSSAVPRPA +PAHHRTTHARTPERTR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000523.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000523.fa new file mode 100644 index 0000000000000000000000000000000000000000..94c3e65e7de00f11adb448bf6baa55538539f457 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000523.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00698 +MSHATLAPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDKHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEASRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLVATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR +>MOLHKGIG_02085 +MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR +>NAFOICDF_00608 +MSHATLVPSTVPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERETG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDTEETR +>MHAAABBN_01790 +MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR +>LFPAFLNI_02024 +MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000524.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000524.fa new file mode 100644 index 0000000000000000000000000000000000000000..23645faccc1719c174d5616ef5d066de425d7f9f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000524.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00699 +MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGQLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPASVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGQEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDVVETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE +>MOLHKGIG_02084 +MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE +>NAFOICDF_00609 +MTTLIPTTLVGSLPKPGWLAEEETLWSPWKLEGERLREGKLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGVKANNDWKATLGEEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE +>MHAAABBN_01789 +MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE +>LFPAFLNI_02023 +MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGERLHEGKLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAAGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000525.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000525.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e5dd13323c13aaf653309590c01f94647df99aa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000525.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00700 +MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQQSSPELWGRLIAAVFALDGVEEGHS +TVSPATSRAVHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG +>MOLHKGIG_02083 +MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS +TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG +>NAFOICDF_00610 +MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS +TVSPATSRAVHLTGRPKERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLPPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG +>MHAAABBN_01788 +MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS +TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG +>LFPAFLNI_02022 +MDPDASPRVRLTADDPRPGSRPVTSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS +TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000527.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000527.fa new file mode 100644 index 0000000000000000000000000000000000000000..c071e472f0921f25cd5d9d50e5cb4307de490c74 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000527.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00703 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALHPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPTAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>MOLHKGIG_02081 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>NAFOICDF_00613 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASILWFTALGYGARLLARVLADPKAWRV +VDLVIAVVMAVLAVRLIAGSGVWG +>MHAAABBN_01785 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>LFPAFLNI_02019 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000528.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000528.fa new file mode 100644 index 0000000000000000000000000000000000000000..e46507a0e0170818660c87f8ae6eb73c6f6d4efa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000528.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_00704 +MNLDQLQVLLRRGTPCEPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPAD +VLGTWFGPVLAEAADWDDLVLDLHVEDQDHSAQLLRRGEVLAAVTTEPQPVQGCAAEPLG +SMRYVPLVAPALLARHAAGDVVDLGAMPMMRYNVKDDLQRLALSDAGLDVAPPTLPVTRL +VRLTRAVREAAQRTLEPG +>MOLHKGIG_02080 +MNLDQLQALRAIADEGSFEAAAYELDVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG +IGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADWEDTVLD +LHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAGPLGSMRYVPLASPALLARHAADDVV +DLGAMPMMRYNAKDDLQRLALSGAGLDIAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV +EDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG +>NAFOICDF_00614 +MNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG +VGLVRVARHMRVLEQEAWAGLGRMAAGRSVTSLAVPADVLGTWFGPVLAEAADWDDTVLD +LRVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARHAAGDVV +DLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV +EDVRAGRLVRVPGLDDVLVPLYWQATTLPVTRLARLTQAVREAAQRTLERG +>MHAAABBN_01784 +MPKLCFMNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPC +EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW +DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALRARH +AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML +VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG +>LFPAFLNI_02018 +MPKLCFMNLDQLQALRAIADEGSFEAAAYDLGVSASAVSQRIRALEREVGQVLLRRGTPC +EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW +DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARH +AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML +VGAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000529.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000529.fa new file mode 100644 index 0000000000000000000000000000000000000000..d56fc5fdf5e1cfce5fb6180d8cc4397dca4ac93a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000529.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_00711 +MDTSTAPGADHGRAADDISYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYAIIQLGN +PRSVTKLISEINFRSSARQGDMIEMGLRAVEFGRTSLTMRAKVRNIISGEVILTIEKIVF +VSLDEDGNPVPHGYTDITFDRDRLPQDTAR +>MOLHKGIG_02055 +MDSTLFTRSADRAAHNDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN +PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF +VSLGEDGKPVPHGFTEITYDRDRLPLDNPL +>NAFOICDF_00726 +MATHHAPNLTAHEDDDVSYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYSIIQLGNP +RSVTKLISEIEFSASARQGDMIEMGLRAVKFGRTSLTMRAKVRNIVTGEVILTIDKIVFV +SLDEEGRPQPHGYTDITYDRDRLPLDTSR +>MHAAABBN_01761 +MDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN +PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF +VSLGEDGKPVPHGFTEITYDRDRLPLDNPL +>LFPAFLNI_01989 +MPAATVKPSTGTSRQVASGVAGSGWGRMVIGRVPPVWSVADPSGDPTARSSTSPHRAPSL +VPASASLYRGAMDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEE +AAIYATLQLGNPRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTG +EMILTIDKIVFVSLGEDGKPVPHGFTEITYDRDRLPLDNPL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000533.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000533.fa new file mode 100644 index 0000000000000000000000000000000000000000..24b0647321993d3373fe4f89946a3102b0a0cf92 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000533.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00760 +MPTSDTLASGRPAHSTDDRRPRRSSAGSGLARVAVFAALMAVLGLVPPVPVAGIPAPIVL +QNLAVTLAGVILGPWRGAAAILLFNVLVALGLPLLTGGRGGLGVFVGPSSGFILGYVVAA +AAVGLVFWALTGRARPGLRPGRVLAAALVAGLVGMVVLYAAGAVGFIVAAHMEPGAAVLA +MGAFVPGDTVKVVLAALLVTGLWKAYPRAFR +>MOLHKGIG_02058 +MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV +AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG +FILGWIPSALIVGLIFWALTSRARPGLDAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA +GMEFGAAVLSMAPFVPGDLIKLVVSVILIVGLWKAYPRAFR +>NAFOICDF_00723 +MTSPSAPQTAVVDAPATHRPRRSPGADLARIAVMAALIAVLGAMPGIPVPGIPTPITLQT +LGVMLAGLVLGAWRGAASVALFHLLVALGLPLLAGGRGGAAVFVGPSAGFLWGWIPGAFV +VGLLFHLYLRGRRDGRNTGGLVAAALTACVVGGIAVIYLFGIPGMNLFGGVPLDKAAIGS +LAFIPGDLLKAVVAALLAAGLWKAYPRAFA +>MHAAABBN_01764 +MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV +AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG +FILGWIPSALIVGLIFWALTSRARPGLGAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA +GMEFGAAVLSMAPFVPGDLLKLVVSVILVVGLWKAYPRAFR +>LFPAFLNI_01994 +MSTSVPSSHDGHVRPAATTTADRPADAGRPRHGSAGGSLARIAVMTALMAVLGLVPPIAV +AGVPAPIVLQNIAVILAGVILGPWRGAASMALFNALVALGLPLLTGGRGGLGVFVGPSVG +FILGWIPSAMIVGLIFWALTSRSRPGLSAGRIALAAAVAGLIGGVIMVYVFGAFGFVGVQ +GMEFGAAMLSMAVFVPGDLTKLVIAVLLCAGLWKAYPRAFR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000535.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000535.fa new file mode 100644 index 0000000000000000000000000000000000000000..81aec9a3e8a3a5bf548e89a5a7be6cd5093a6edc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000535.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00764 +MISLYVPGDSPLHRAPAGLKLALFAAWALAVTLAPPTPWTAGAAVGMALAAYLTGFGPRR +GAAMLGRDLRALWVFYAFLFAAQWLFADLTAAALMVGRVLGLVLAAQVLTRTTRIAELVG +VAEAVLAPVERIPWLGPRLARVGLRPERVGLAMGLVLASIGHLRSVAEQVRQAQASRGVR +MAPWAWVLPLLVLSVKHADDVGDALAARGIE +>MOLHKGIG_02056 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSRWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLHALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMAG +VAEAMLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID +>NAFOICDF_00728 +MLSLHVPGDSPLHRCPAGAKVAALAVWALVVTLAPVSALTAGASVVVGVGAYLLGFGLRR +GVRLLAADLRGLWVFYAVLFAAQWLFTDLPTAALTTARVLGLVLAAQVLTRTTRIAEMAG +VAEAVLGPVTRIPWLGPRLARAGVRPDRVGLAMGLVLASVGHLRGLAEQIRAAQAARGVR +MAPWAWVLPLLVLSLKHADDVGDALAARGID +>MHAAABBN_01762 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG +VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID +>LFPAFLNI_01990 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG +VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000536.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000536.fa new file mode 100644 index 0000000000000000000000000000000000000000..8a9da88ffa51cf2291f54394988f9a4090414d7d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000536.fa @@ -0,0 +1,79 @@ +>ACLBLIBL_00769 +MTPPAPAPPPAAAPGALSGVSGLTSAEVAEREAAGLTNRQSKDTSRSLAEILRVHVLTLF +NLAIALCAVVVISLGRWLDLLFSLAAIANVVIGVVQEYSAKRKLDRIALLHQDDAVVVRD +GARVSLPMARIVRDDVVVLRRGDQVPVDGEVLASDGLDLDEALLTGENDPVPKAPGDAVL +SGSSVVAGTGLMRATAVGPASHAARLSAEARRFSAIRSELRGALEKVARWLTIGLVPIIA +VIVHGQMTAVGGWAHALAQPREAALEPALIASVAAVTSMIPQGLALMTTIAFAVSALKLA +QHEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFHELLAPASASPSTSTSTDDDGAPA +DVDAAARAVLAWFGADPDANPTAAALHEPFADAPPHEPADHVAFSSARRWSAVAFGPEVG +AATGTWLLGAPEALLGDADARPGEAGTGRDDVAAVRAQADALSDEGLRVLLLARTDAPLA +GNALPAGRVPAAVVTFRENVRPDAAETLGYFHAQGVRTVVISGDSPRTVAAVAREVGMDV +PGHARDGRTLPEDPEALADVMAEHDVFGRVSPDQKKAMVAALQSRGHVVAMTGDGVNDAL +ALKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPAVLGEGRQVIANMERLAHIYLTKTT +YALLFGVVFSLLAWQFPLLPRQASTVDFIMIGLPTFFLALLPNPRRYVPGFLGRALRFAI +PSGVVILLSMVALQVYVRLAADHVDLAQQQTAFMITLTLVGLWVLSVMSRPLTRRVVLLV +LAMYAVLAAVVLVPASRWYHQMEVPPADVLVAALVIAAVGCALIELIHQVHRRHVARVLA +AAGA +>MOLHKGIG_02053 +MASPSPASAHPSAPESGTGLGFTGVEGITGLTASEVAEREAAGLVNVQSRDTSRSLGQIL +RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ +DDVLVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP +KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT +IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF +AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLAAPASADASPDAH +DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA +FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG +DALPAGGVPVAVVTFRENVRPDAAETLGYFHAQGVRAVVISGDSPRTVAAVAREVGLEVA +GQAYDGRTLPDDPDALADVMEEHSVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA +LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY +ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP +SGAVILLSMVALQTYVRLTAGDVDLARQQAAFMITLTLVGLWVLSVMSRPLSARVVVLIL +AMYAVLAAVVLVPVSRWYHQMEVPPTDVLVAALVIAAVGCGLIELIHQVHRRHVARMLAA +AGA +>NAFOICDF_00126 +MTHTPPSPAPAADAGPAALAGLTSAQVAERVAAGRVNVQPKDTSRSFGTILRSHVLTLFN +LVIALCATVIVVLGRWFDLLFSLAAVANVVIGVVQENSARRALDRIALLHQDGVLVVRDG +ARREVRIEEVVLDDVVVLRRGDQVPVDGAVLTSEGLDVDESLLTGESDPVPKAPGDAVLS +GSAVVAGTALVRATAVGADSHAAKLAVQARRFTRAHSELRAALEKVARWLTIALVPIVAV +ILHGQVTAAGGWSRVLGSEDQPALEAALVATVAAVTAMIPQGLALMTTISFALAALKLAR +RAVLIQEQPAVEILARVDTVCLDKTGTLTEGGIVFHGAHAPVGAPALPHDDDAAVALDPG +ARAVLAWFGADPDANPTAAALREPFPAAPASSPTGVVPFSSVRRWSAVTFGPDADAAHPG +MAGTWLLGAPEALADAAHLGPERTAALTEACTAPADRGLRTVLLCRASDAPAGETLPAGR +EPVAVLTFAEDVRPDAAQTLGYFREQGVAVKVISGDSPRTVAAVARAVGMEVPGDAVDGR +TLPADPAELADVLESHEVFGRVAPEQKQAMVAALQSRGHVVAMTGDGVNDALALKTADLG +IAMGNAAPATKAVSRMVLLDGRFDRLPDVLREGRQVIANMERLAHIYLTKTSYALLFGLV +FSLLAWPFPLLPRQASTADFLMIGAPTFFLALLPNPRRYVPGFLRRALLFAVPAGVTIVA +AMLAVSWYARHLSSKPVDTAQLQTASLITLTLLGLWVLTCISRPLRPLMCGVVAGMYALL +AAAVLVPASRWYHQMELPAPDLLAASLAIALGGCVVVEAVHRIHHARVTVPGRRAAEG +>MHAAABBN_01759 +MASPSPASAHPSAPESGTGLGFTGAAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL +RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ +DDVVVIRDGARVPLPMARIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP +KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT +IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF +AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH +DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA +FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDAPLIG +DALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA +GQAYDGRTLPDEPGELAAVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA +LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY +ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP +SGAVILLSMVALHAYVRLTAGDVDLARQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL +AMYAVLAAVVLVPASRWYHRMEVPPTDVLVAALVVAALGCGLIEVIHQVHRRHVARVLAA +AGA +>LFPAFLNI_01987 +MASPSPASAHPSAPESGTGLGFTGVAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL +RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ +DDVVVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP +KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT +IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF +AVAALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH +DDGAPAEVGDGPRAVLAWFGADPDVNPTAAALREPFTAVPAVDPVAQVAFSSARRWSAVA +FGPEAGAAAGTWLLGAPEALVDEWHLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG +EALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA +GQAYDGRTLPEDPGALADVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA +LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY +ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP +SGAVILLSMVTLQTYVRLTAGDVDLPRQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL +AMYAVLAAVVLVPASRWYHQMEVPPTDVLVAALVIAALGCGLIEIIHQVHRRHVARVLAA +AGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000539.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000539.fa new file mode 100644 index 0000000000000000000000000000000000000000..5f25555c5923c95e14378956d2601b31ff77d293 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000539.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_00780 +MDVQQFFADLSDVPWLLTTLDLIGIFFFATSGALLASRKEFDLVGSMALALLAGLGGGFT +RDILLDRGLPASLENPIYLAPPVLVSLLVYVKALHPNRLNLTITLFDAGGLALFTVSGVL +IAHSMDVHPVSTVVVAMVAALGGGVLRDIVANEVPSIFDPRGVYVMPTFVGATVATIAAM +NGVLNAFTGFLIAFLIFAVRMLAYRYQWRLFGADISQDKESLDRLRRLATQAQDAAARRV +ERARERRLRSASGPGGMDVGEAEAIADRAVHHPPAPAGYHYDAVEDAYTRDHAFDDDGEP +GSASYGPRQEYEDQVRVDEYDPETQTITVIDPASRQQVRLDPATGVMDVTDLRTGRTRSY +DDPEHDWIADDAEDDARG +>MOLHKGIG_02036 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLARLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDADGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDEKG +>NAFOICDF_00747 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPVLVSLLVYVKLIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRAPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDSRD +>MHAAABBN_01743 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD +>LFPAFLNI_01971 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000543.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000543.fa new file mode 100644 index 0000000000000000000000000000000000000000..910f0c375231aae2326df3486d026c24c6704797 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000543.fa @@ -0,0 +1,27 @@ +>ACLBLIBL_00787 +MTELDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKWWDAPYFHAA +DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGSGWWELGILLFDP +TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW +EGRRWDSVRLALLRRDWDSARASV +>MOLHKGIG_02033 +MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA +DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP +TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW +EGRRWDSVQLAVLRRDWWPASTDG +>NAFOICDF_01226 +MDTHRSTPVVALRPVEAGDEEFLWTWIHGTPDAEWKRWDAPYFHAAEQAAPMGRAAFARS +FAPWPDDADRRIITADGAAIGLVTRHEEAPAGGGWWELGILLFDPSRWGGGIGTRALAAW +TEATLTETDAHVLTLTTWSGNARMAGAAERAGFRMCARVPESRAWDGRRWDSLRFALLRG +DHEGEQASAPEPPARRPELADLTVVTGRIPDAAALRALYDAVGWTAYTRNPDALAAGVAG +SACVATAWAGQELVGLARVVSDGHTIAYLQDVLVHPERRRQGVAGKLLDAVFAPFAHVRQ +QVLITDEEPGQRAFYEACGFRQFGGGGPVPGRTFVRFAG +>MHAAABBN_01740 +MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA +DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP +TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW +EGRRWDSVQLAVLRRDWWPASTDG +>LFPAFLNI_01968 +MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA +DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP +TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW +EGRRWDSVQLAVLRRDWWPASTDG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000544.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000544.fa new file mode 100644 index 0000000000000000000000000000000000000000..434c30aa404e9c71270d40d6bfbd646e6f26e325 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000544.fa @@ -0,0 +1,19 @@ +>ACLBLIBL_00791 +MTLTEDHHNGFGMAHGGAVFAFADSCFALTCNDPGGDGSTITVASGVDVNFLAGTRAGQT +LVAEGRLVAAAGRSAVYDITVTTDDGTPVAAFRGRSRTIPAPGR +>MOLHKGIG_02028 +MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC +FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG +TPVAAFRGRSRTIPAPGR +>NAFOICDF_00752 +MTETPHHPALVGDRVARWLGVTLEAAEKDHARIRMTLGEEHHNAFGMAHGGVVFAFADCC +FALTCNDPASDGSTLTVASGVDVNFLSGTRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG +TLVAAFRGRSRTVAVKGA +>MHAAABBN_01737 +MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC +FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG +TPVAAFRGRSRTIPAPGR +>LFPAFLNI_01965 +MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC +FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG +TPVAAFRGRSRTIPAPGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000545.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000545.fa new file mode 100644 index 0000000000000000000000000000000000000000..3472c737f66c026ea7506ef23e9d3564c80a6fde --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000545.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00792 +MLEASIPNPYTPAPLPAPADRGAQDPEETMSRDQIEALQFERLRWSLHHAYENVPAYTEH +FDAHGVHPSDFKALEDLAKFPYTDKEFLRKNYPFGAFAAQGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTDEMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS +SCVINVVEPETLARSSGKLKRIYDLRDKG +>MOLHKGIG_02027 +MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH +FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS +SCVINVVEPETLARSSGKLKRIYDLRDQA +>NAFOICDF_00753 +MLEASIPNPYSPAPVPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYKEH +FDNHGVHPSDFTALEDLELFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFRKLGLDPRESSLEVAILGAEPWTEAMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERREHATLEEAQACAAHLRMEIKTKIGS +SCVINVVEPETLARSSGKLKRIYDLRDQA +>MHAAABBN_01736 +MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH +FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHASLEEAQACAAHLRMEIKTKIGS +SCVINVVEPESLARSSGKLKRIYDLRDQA +>LFPAFLNI_01964 +MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH +FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS +SCVINVVEPESLARSSGKLKRIYDLRDQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000547.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000547.fa new file mode 100644 index 0000000000000000000000000000000000000000..524eb8de43fde2740aeea55dad8fd819a7d85acf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000547.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_00794 +MTPSRLPLLGVLAVGALALAGCAGGGAEPSSPAPSPASSSASPTTTAASSASTSPAASAS +ASSTPTATALSLDLPEELSGESATRLRAVVQDAAGPAAELGQTFSSPLERRAALEEDAAI +VDALEEDAGDDAGRRACVDATRAAREADQASGAAQAAWYAQPQTASTTGGSTDGTAASGR +PGLQVEPLGVQVAVYPDEATARSVAEAARDAAEACEGQEMSSMGVSSVEPLTGAPGETAF +TVVPVSGSIIYAVSTVVQVGDRVYAVSQGEDGAGVPEGAEERAVALVEDLEAALEG +>MOLHKGIG_02025 +MTTSRLPLLGALAVGALALAGCAGGGAEPSSPAPSSASSTTTAASSASPAASSSTAPTSP +AASASTASMGGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQT +ELRQRAAGLEQTVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAAT +TGGGPTSTPVPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLG +VESVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAAS +IVADVLAALDGEG +>NAFOICDF_00756 +MTHMTAVPSRRLRAGFALGAAALVLTGCAGGGGSASSSTAAGSPTAGGAGSSVTSPAASS +SAASSSALSLSMPDRFGNEARTGLTEAVTAAAPEGFEVTTRSVSPLERKTDLEDQATILT +DGPLEPAAEGSSASPTYTEAQQRCADAAAERFRTEAAAGGAQLRSDAMPTVAGGGYTSVR +ADVVAYPDVSAAVAALADGSAPIELCTDVQVPGAEQPTDIAPVTGIGDEAVGGELAGGRW +LAVRRGTDVVSVMVAGPGETAPAGAADQARALAEQVLEAVPAG +>MHAAABBN_01734 +MTTSRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSAPTSPAASSSTES +TGAAESTAGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQTEL +RQRAAGLEQAVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAATTG +GGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLDVE +SVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAASIV +ADVLAALDGEG +>LFPAFLNI_01962 +MTTPRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSASTSPAASSSTAP +TSPAASASTESTAGASASSSLSLEMPPALDGQRTLAVQTAVQRAAGPGSEVGLSAASPLE +RQTELRQRAAGLEQAVDAGASPAPTRSAEQQACLDATRSALERDAEAGAADLGLTAQPET +AATTGVGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLA +GLGVESVTRTEHEGGAAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDR +AASIVTDVLAALDGEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000548.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000548.fa new file mode 100644 index 0000000000000000000000000000000000000000..771adbc9ee0ab12a098c0d28340a9df900884a2f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000548.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00795 +MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD +LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL +FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE +TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY +DVVGFHVAANVSRNTGVDWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW +NLGDKDTPLG +>MOLHKGIG_02024 +MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKRVMAYDAVPAALEGIERRWAWIRQGYEAD +LGEGYDPQRFDEAIARITPTSDLGEALADADIVVEAVPENLELKRKVWAQVGELAPATTL +FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE +TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY +DIVGFHVAANVSRNAGADWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW +NLGDKDTPLG +>NAFOICDF_02090 +MTTIQKVTVFGTGVLGSQIIMQAAYHGKDVTAYDVDDKALAQLPARWEWMRGYYQRDLPD +FDAERFDKAVSSIRTTTDVADAVTDADVVIESIPENLELKKSVWAKIGEAVPERTVLLTN +TSSLLPSSFADSTGHPERFLALHFANLVWKNNTGEVMATAKTAPEHFDAVLAFAGEIGLV +PVPVRKEVPGYVLNSLLIPWLDAGAKLYQGGVSDPEDIDNVWKIATGAPKGPFEVYDVVG +FNVAYNISRVSADPLKKAFAEETLKKGIDAGTTGLGVGEGFYRYDKDGNNLGAVESWKQE +NRG +>MHAAABBN_01733 +MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD +LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL +FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE +TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY +DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW +NLGDKDTPLG +>LFPAFLNI_01961 +MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD +LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL +FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE +TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY +DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW +NLGDKDTPLG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000549.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000549.fa new file mode 100644 index 0000000000000000000000000000000000000000..96e6ace79351565a2804713ce408cfe075c55aa2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000549.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_00796 +MTVTLPSLPEILPSYVNGAWWTPQSPSKVTDVTDANTGERLTGVSTDGLDTAAAIEHART +VGRKSLGELTIHERALKLKELALYLNSRIQELYDVSFATGATQRDHAFDVDGGIGTLFTF +SGKGRRELPNSNVITDGPVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +SFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSLQLISGSARDLLDHLDYRDHVSF +TGSAATAQTLRKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPQDRVDAVVEALSARLGKVVLGDPRVEGTTMGALASKEQQGEVRGAV +QRLVDAGGQVRLGGPDASTGDADAESGAFFAPTVLSFEDARTPEVHAVEAFGPVTSVVGY +TDVEDAVALAALGSGSLVATVATDDGETARAFAAGIGAHHGRVHFLNRQTATTTTGHGAP +VPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRED +VEAGTAVHPFYKSLAELTVGDQFASGLRTVTLQDITDFAEETGDKFYAHTDEEAAMANPF +FPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITPR +VSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>MOLHKGIG_02023 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART +VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF +SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +AFVAGVPTVVKPATPTGYVAQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQGEVRGA +VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG +YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTATTTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE +DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP +FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP +RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>NAFOICDF_00757 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGELMARVSTDGIDTAGAIEHART +VGQRNLGELTIHERALKLKELALYLNSRIQELYDLSFATGSTQRDHAFDVDGGIGTLFTF +SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +AFVAGVPTVVKPATPTGYVTEACVRMMVESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAGTAQTLRQHENVLNGGVRFTAETDSLNAAILGPDAGVDTPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPEAMVEDVTAALTERLSSTVVLGDPRAEGTTMGALASKEQQSEVRKA +VQTLVDAGGQVRLGGPEGSTGDADAEAGAFFAPTVLTFADADTPQVHSVEAFGPVTSVIG +YTDVADAVRLAALGSGSLVATLATNDGATASEFIAGIGAHHGRVHVLNRQTAKTTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAVQGSPDMLTAITGVWHQGAAAQTATRE +DVEAGKAKHPFYKALDELQIGDQFASGLRTVTIEDITAFAESTGDKFYAHTDEEAAMANP +FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLDDLRFITPVTYDDAIRVTLTAKRITP +RVTDEYGEVAWDCRLHNQKDELVAQYDVLTLVAKTWPMPEAEPKA +>MHAAABBN_01732 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART +VGQQALGELTIHERALKLKELALFLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF +SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKDQQGEVRGA +VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG +YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTAATTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE +DVEAGTAVHPFYKSLAELTVGDQFASGLRTITLEDITAFAEETGDRFYAHTDEEAAMANP +FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP +RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>LFPAFLNI_01960 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART +VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF +SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQSEVRGA +VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG +YTDVADAVALAALGSGSLVATVATNDGETARAFTAGIGAHHGRVHVLNRQTATTTTGHGA +PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE +DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP +FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP +RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000551.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000551.fa new file mode 100644 index 0000000000000000000000000000000000000000..0371fa5282def7add0f2641f73acc6716322a606 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000551.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00798 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAAQILPGELVSIVDVTNGARLETYTI +AGERGSGVIGINGAAAHLVHPGDIVILIAYAQMDEEEARHIQPRVVHVDGENKIVELGAD +PADGLLDGVSRPPLSREWNEAQAEL +>MOLHKGIG_02021 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI +AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARHFQPKVVHVDADNRIVELGVD +PADGLLDGLSRPPLSREWNEAQAEL +>NAFOICDF_00759 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI +AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDAEARHFQPKVVHVDADNRIVELGVD +PADGLLDGLSRPPLSREWNEAQAEL +>MHAAABBN_01730 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI +AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGID +PADGLLDGLSRPPLSREWNEAQAEL +>LFPAFLNI_01958 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI +AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGVD +PADGLLDGLSRPPLSREWDEAQAEV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000552.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000552.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b5d2c047924e4e393777caa22fbdbc8a57bd194 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000552.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00802 +MPASARRPFRFTHRWAVPRPAAEVAALLADPLGYPTWWPSVPRARRIDGAGHDGDPRVAV +LLRGLVPVRLVMARELDDRERGRLVARLDGDLRGTVRVTVHDDDGPAGGTGGCTVAWEQE +VVLGAGRLRAAARLPGARAAMRLSHAWAMRSARRALGARALPAGR +>MOLHKGIG_02020 +MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV +RLTMERLIDDRARGLLVARLSGGLTGTVRATVHDDGAPAGHAPRCIVVWEQEVVLTSPWM +RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPA +>NAFOICDF_00760 +MSVDRPFRFTHRWSVPADARSVLALLADPAGYPRWWPAVPRVRHLGPDRAAVRLRGFVPV +RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPRCIVVWEQEVVLTAPWM +RAVDRVPGARTAMGLSHAAAMRSARRALGAKAMPTADPAPTTRP +>MHAAABBN_01729 +MSADRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV +RLTMERLIDDRARGLLVARLSGGLTGTVRVTVHDDGAPAGHAPRCIVAWEQEVVLTSPWM +RAVAHVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTSRP +>LFPAFLNI_01957 +MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRAHRLGPDRAAVRLRGLVPV +RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPHCVVTWEQEVVLTSPWM +RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTTRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000553.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000553.fa new file mode 100644 index 0000000000000000000000000000000000000000..5bd4758cb6cd6d8bdb7e45768ed96a8f66b6bcca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000553.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00804 +MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPEALEVAAHALADRIAKQDPLAVRISKRVFHLPREAHPHVDEIAQA +ILFESEAKFDRMQAFLDRKKK +>MOLHKGIG_02017 +MTDFSHFSALHVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPRGAHPHVDEIAQA +ILFESDAKFERMQAFLDRKKK +>NAFOICDF_00763 +MADFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKREPGRFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETGLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRISKRVFHLPREAHPHVDEIAQA +ILFESQAKFERMQAFLDRKKK +>MHAAABBN_01726 +MDDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKCEPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPEALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA +ILFESEAKFERMQAFLDRKKK +>LFPAFLNI_01954 +MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA +ILFESEAKFERMQAFLDRKKK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000554.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000554.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ae24ed9f9df04f31f691649ef5f57895daaaaab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000554.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00805 +MTTPSPQPQALLVGGKRTAVGRYGGALSAVRPDDLAALTIKQVIEDAGIDPAAVDEVILG +NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG +GVESMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVG +EVDGITREDADAFAARSHGRAIAAIEAGRFKDEIVPVTVKGRKGAETVVDTDEGPRPGST +PEVLAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA +PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPEIVNADGGAI +ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV +>MOLHKGIG_02016 +MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN +GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE +SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD +GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV +LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI +MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG +HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV +>NAFOICDF_00764 +MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN +GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE +SMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD +GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV +LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI +MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG +HPLGSSGSRLVVTLLGRMEREGADKGLATMCVGVGQGSAMLVEKV +>MHAAABBN_01725 +MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN +GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE +SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD +GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV +LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI +MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG +HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV +>LFPAFLNI_01953 +MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN +GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE +SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD +GITREDADAFAARSHARALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV +LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI +MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG +HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000556.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000556.fa new file mode 100644 index 0000000000000000000000000000000000000000..d751fe618a4c39750777ff9396ec6dab7836a648 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000556.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00830 +MTETTVTPATGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGQEVRRSYSICAIPKRGEIRVAVKKDIGGKFSTWANEVLEVGEKIDVMNPQGAFTSRS +HVTSLNDAEKVAAEKVAQNKNTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDAEKLTTLLDRVIDVDGTD +EWFLCGPFELVQLARETLSARGVDEDDVRFELFTTGRPENPQGHSGRVVEADPSGDNVTI +EFNLDGLSGKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTDGEYEMDENYA +LEKDEVEAGYVLTCQTRATSDSITVDYDA +>MOLHKGIG_02012 +MTETTDAPTTGKRRATFNTLEVSELRRLTEDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGTFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVPEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA +>NAFOICDF_00767 +MTETTDAPITGKRRATFNTLEVSGLRKLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAELRRSYSICAVPQRGEIRVAVKKDLGGTFSTWANEVLEVGEKIDVMNPQGAFTSRT +NVTSMNDPEAVAAEAVKQDQTHLVALAAGSGITPIMAIAKSVLAASDSARFDLIYANRSA +MDVMFAEEIGDLKDKYPARFTVNHVLSREQRVAPLLSGRIDDEKLNTLLDRVIDVENTDE +WFLCGPFELVQLARDTLSERGVAEDDVRFELFTTGKPEAPQGQSGRGVEADPSGDNVTIE +FNLDGLSAKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTEGEFTMEENYAL +EKDEVEQGYVLTCQTRPTTDSIKVDFDA +>MHAAABBN_01722 +MTETTDVPTTGKRRATFNTLEVSELRRLTDDSVEITFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA +>LFPAFLNI_01950 +MTETTAAPTTGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAENKDTHLVAFAAGSGITPIMAIAKAVLAASESSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000557.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000557.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec137df44fac024377f629a0e1cfee564cec30e5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000557.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00831 +MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARAEGEKAVVVITPTYSG +CPAMDTITTDVSRALERSGFEESEVRLVLQPAWTTDWMTDEGKAKLAEYGIAPPSARTTD +GPVMIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH +>MOLHKGIG_02011 +MTTASELRPADPAGARVWDAASTVHDPEIPVLSIADLGILREARVEGERAVVVITPTYSG +CPAMDTITTDVARALGRAGFPDAEVRLVLQPAWTTDWMTDEGKAKLNEYGIAPPVARTTD +GPVRIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH +>NAFOICDF_00768 +MTTAAELRPSDPAAAQVWDAAATVHDPEIPVLSIADLGILRDVQVEDGRAVVVITPTYSG +CPAMGTITADVTTALGRAGYPDAEVRTVLQPAWTTDWMTDEGKAKLAEYGIAPPSARTDE +GPVRVGLAVKCPRCHSLNTREITRFGSTSCKALYTCQECLEPFDYFKVH +>MHAAABBN_01721 +MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARAEGERAVVVITPTYSG +CPAMDTITTDVTRALERAGFPDAEVRLALQPAWTTDWMTDEGKAKLNEYGIAPPVARTTD +GPVMIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH +>LFPAFLNI_01949 +MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARVEGERAVVVITPTYSG +CPAMDTITTDVTRALERAGFPDAEVRLVLQPAWTTDWMTDEGKAKLNEYGIAPPVARATD +GPIRIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000558.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000558.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ab3994c11788bd0adab482ef495544e7aa2ae98 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000558.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00832 +MSFATNDSATKHSAGVAITAEEIASGEQKASEETARYALYLGDDALMLGQRLSWWISRTP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGQSEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYAFELYTRLKESTDATLAAIADKALKEVLYHQDHAALWLNRLGLGTDES +KFRMQRGLDELWPYLPELFHDDETTRPLAEQGIAVLPSSLEEPTMTRIREAIEAAGLEVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGASW +>MOLHKGIG_02010 +MSFATNDSATRHSAGVAITAEEIAAGEQKANDDVARYALALGDDALMLGQRLSWWISRAP +EIEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESTDPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEACLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW +>NAFOICDF_00769 +MSFATNDSATRHSAGVANTAEEIASGGQKASDEVARYAVYLGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWDKSEDDLAYFRDEEEFRSTRLVEAENGDFG +KTIARQLYYSVYAHGLYTRLKDSKDATLAAIADKALKEVEYHLDHAEQWVNRLGLGTEES +NARLQRGLDELWPYLPELFHDDELTRSLAEQGIAVLPSSLEESTMARIRAAIEGADLKVP +ETGAARGGDRSGQMSEYRGYILAEMQSLARRHPGASW +>MHAAABBN_01720 +MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESTDSTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW +>LFPAFLNI_01948 +MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESADPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000559.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000559.fa new file mode 100644 index 0000000000000000000000000000000000000000..79572d51ff402356e76acbe4f58c28b8da77cd39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000559.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00833 +MGENTAASNAWPLWEVFVRANRGLSHVHAGSLHAPDASLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESPQGKSYRHATYYQQSEGVPHL +>MOLHKGIG_02009 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL +>NAFOICDF_00770 +MTENTAPSNEWPLWEVFVRANRGLSHVHAGSLHAPDATMALRNARDLYTRRNEGTSVWVV +PADAVAASDPDSKGGFFESPQGKSYRHATYYQKSEGVPHL +>MHAAABBN_01719 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL +>LFPAFLNI_01947 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000560.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000560.fa new file mode 100644 index 0000000000000000000000000000000000000000..d1585f2a25795cc667b975eafb16e6655a2f4f5a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000560.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00834 +MTQTSSTTRLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDVLNDQLLEGKA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRSSYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSKQSMAWKVKRFSNDELR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDELMSVIKGNGPMNTQRLARR +IQAHEDGAWVRDAAAAYARRQAEQHAPAETHLIGA +>MOLHKGIG_02008 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPTDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA +>NAFOICDF_00771 +MTQTSSSPHLASVPSPDDAAGQENFDRLIQEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSQQSMAWKVKRFSNDELR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGNGPMNTQRLARR +VQAHEDGAWVREAAAAYARRQAEQHVPADTQLIGA +>MHAAABBN_01718 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA +>LFPAFLNI_01946 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNAQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEEGAWVREAAAAYARRQAEQNAPAETHLIGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000561.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000561.fa new file mode 100644 index 0000000000000000000000000000000000000000..a00030199d6f5232ddc27e2b4c96408ac7246c88 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000561.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00835 +MLQLIGPQHLAAALQAAGLDDDAARLLAWADPARRDRDAAQAALDELAVAQESLRGALAG +LVAAARDVRAGAAVAWRGPAAGEYADAVAEAVGAAEGLEREAGEWLALRATAEREAEDAR +QDAEARLRAAEETARAALRALAVAA +>MOLHKGIG_02007 +MPPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRAALGG +LVSAATDVRSAIQTGWRGEAAGAYGEAVRRAAALAAELEREAGEWLALRATAERDAEDAR +RNAEARQRAAEETALAVLRSLAVAA +>NAFOICDF_00772 +MLLPPTAQALLRTLVAAGLDDDAARLAVGLTDAHADLQAARAAQDALADAAEDLRDLLAL +LEELTRGVAAALDVDWRSEAGAEYGERTDGLHRTATDRQDEAREWAGLLGRARSEAEQAE +RDAELRVRRAEEGASALLRAMAAA +>MHAAABBN_01717 +MSPLIGPQQIATALRAVGLDDDAARLAAWADPARREREAAEQALADLAAAQTQLRTALGG +LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR +RNAEARQRAAEETALAVLRSLAVAA +>LFPAFLNI_01945 +MSPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRTALGG +LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR +RDAEARQRAAEETALAVLRSLAVAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000564.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000564.fa new file mode 100644 index 0000000000000000000000000000000000000000..81da425cb0805d8a012d23b537218c55b72146a4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000564.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00839 +MTDDAQLTPAAVAPHKKVGMLPPYAAGKPPVAVPGLRPYKLSSNENPHAPVAGVIERVRG +VVTGPEGAPSTLCRYPDTLSTGLREALAAHLDVPADDVVTGAGSLGALSQVITAFAGHGE +AGRGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAMLAAITDRTRVILLCTP +NNPTGPVLTTAEVEGFLAEVPEHVLVVIDEAYVEFVRDEDAVRGLDMYRKHANVVVLRTF +SKAHGLANLRVGYSVSRPEITKALRTVATPFAVSTVAEEAAIASLEHLDEVLEGVQLVVD +ERERVAAALAEAGWDVPASQANFVWLPLGERTADFAAAAQAKALSVRAFAGEGVRVSIGE +QEANDRFLEVARDFLK +>MOLHKGIG_02003 +MGRITASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE +NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL +GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML +EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL +EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL +EHLDEVLERVQIVVDERERVAAALAEAGWDLPASQANFVWLPLGERTQAFAEAAQARALS +VRAFAGEGVRVSIGEKEANDRFLEVARDFLA +>NAFOICDF_00776 +MTDVTSGSSGVAAHRKVSLLPPYAAGKPPVAVPGLRPYKLSSNENPFAPVPAVVERIHEV +VAGAEGEPSPVCRYPDPLSTALRERLAAHLDVPADDIVTGGGSLGALTQVITAFAGDGGE +DGAPDEVVFAWRSFEAYPIVVRTAGAKDVQVPLTADGRHDLPAMLAAITERTKVMLLCTP +NNPTGPVLTTAEVEDFLAQVPPHVLVVIDEAYVEFVRHPDAVDGPAMYRRHPNVVVLRTF +SKAHGLANLRVGYSVSRPEVTASLRTVAVPFAVSTVAEQAAIASLDHLDEVLERVQTVVD +ERERVVAALAEAGWDVPETHANFVWLPLGERGADFAAAAGERALSVRAFPEGVRVSISER +EANDRFLEVARAFQR +>MHAAABBN_01713 +MVPLTASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE +NPYAPVPGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL +GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML +EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL +EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL +EHLDEVLERVQVVVDERERVAAALAEAGWDLPSSQANFVWLPLGERTQAFAEAAQARALS +VRAFADEGVRVSIGEKEANDRFLEVARDFLT +>LFPAFLNI_01941 +MGRITASAARITLVAMTDDAPQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE +NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL +GALAQVITAFAGHGEAGEGDEVIFAWHSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML +EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL +EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL +EHLDEVLERVQVVVDERERVAAALAGAGWDLPSSQANFVWLPLGERTQAFAEAAQAQALS +VRAFAGEGVRVSIGEQEANDRFLEVARDFLT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000565.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000565.fa new file mode 100644 index 0000000000000000000000000000000000000000..edee8e53ce88cee112fb797df4d7ab7d81ebb259 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000565.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00857 +MAEPIHIGAAADIPEGEAVVVPAATAGTSDDVAVFHAEDGAFYAIDDTCTHEDASLAEGW +LEGTQVECPLHSAQFCLKSGEALCLPATRPVGTHPVQERDGQLYLTPGA +>MOLHKGIG_02000 +MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW +LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA +>NAFOICDF_00793 +MSREINVGPASAVPEGESLLVPNDTTGTKDHIGVFHAEDGAFYAIDNTCTHQDYALSEGF +VEDCRVECPLHGASFDLRTGEALSLPATKPVGTHRVEERDGDLWLTVEDGE +>MHAAABBN_01694 +MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW +LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA +>LFPAFLNI_01926 +MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW +LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000566.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000566.fa new file mode 100644 index 0000000000000000000000000000000000000000..df3924cb2edbb7710a905ffa9f3a3cebeb7b06cb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000566.fa @@ -0,0 +1,44 @@ +>ACLBLIBL_00858 +MSGDVDARAGAPASVVVVGGGVAGFGAVRELRRRGHTGSLALVEPQGVPYDRPPLSKDYL +TGETDAHRLLFAPPSWFAEHDVELVEEAAVRLTPGGAHPDGDPVPHRVELASGRVLEAEA +VVLATGGRPRPLDVEGATHPDLITLRTRADADALRERLHFGAEVAVVGGGFTGAEAASSA +RQALAGVTLVTATDAPALRAVGPALAARLHRMHAEHGVAVEVGRVARIEHRDDDGGAALP +AAHRLHLGDGRTVDADVVVLAGGTVPDTALAEEAGLEVADGILVDEAGRTSVPGILAVGD +TARATGSAWGPSPHWEPALRSGAAAAAALLGEEPEPPGAPWLWSDRHGCHVEAVGDMAVP +PGGASVDREARGAAVASFVLDAEGRMRGAASIDDPMTVKAARRIIDRGIVVDPQALADPT +VPLKSLARG +>MOLHKGIG_01999 +MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGEIALVDPQGVPYDRPPLSKEFL +TGDADARRLLLAPPTWFAEHGVELVEDAAVRVVPGGVHPDGGPAPHRVETASGRVLEADA +VVLATGGRPRALDVAGADHPDLITLRTRSDAEALRDRLTFGAEVAVVGGGFTGAEVAAAA +RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHVEHGVAVEVGRAAWIEHRDADGGAALP +AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD +AARARESAWATSRHWEPALRSGAAAAAALLGEQTDAPGAPWFWSDRYDAHVEAVGDMTVP +AGGRIVDREVRGVVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA +VPVKSLARG +>NAFOICDF_00794 +MTVPASVLVVGGGVAGFGTVRELRRRGFEGKLTLVDPQGLPYDRPPLSKDFLTGETDAHR +LLFAPPAWFAEHAVELVTARVDRMDLTGEHPAAVLDDGTVRAADAVVLAPGGRPRPLDVP +GGDRPGVLVLRTRADAEAIAARLHFGARVVVVGAGLTGSEVASAAREAMAEVTLVSASPA +PAAAAVGPALAARLHALHAARGVDVVQGRVLRIEHADDAPGLDAPHRVHVALADGGEAAL +DADLVVAAVGILPDAALAAEAGLELAVDGGILVDAAQRTSDPRVLAVGDAARRRDAAYAA +PAMHWEPALQDAADAAAALLGEDLPERGAPWFWSDRHGVHVEGVGAMRPPEGGRIVDREV +RGTVVASFALAADGAMVGAASVDDPMAVKAARRIVDRGIVVDPERLADPSVPVKALLRG +>MHAAABBN_01693 +MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL +TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA +VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA +RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP +AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD +AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP +AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA +VPVKSLARG +>LFPAFLNI_01925 +MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL +TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA +VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA +RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP +AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD +AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP +AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA +VPVKSLARG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000567.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000567.fa new file mode 100644 index 0000000000000000000000000000000000000000..478e578901e70a0595422762caca3c17196cb439 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000567.fa @@ -0,0 +1,56 @@ +>ACLBLIBL_00859 +MPVRHNTQPLVRDLFTTEAKAARGGRPAAGMFLSSGDCTAAEICAGAGLDYLLIDGEHAP +LSLENVQAQLRTIAGYGVPVMTRVPFLDWISIKQYLDLGAQTLLVPMIDTPEQAAEAVRA +LRYPPHGDRGVGSALARSGRWNRIEGYLQHDEEHVSLFVQIETVRGVENAAAIAAVPGVD +GVFVGPSDLSASMGLIGQQSHADVVAAVRRVIEACNAAGTTVGVNAFATDQAQAYADAGA +DFVNVGADVALMARGAEALADRWCPTPGTGADEGAGEGAGAGAGARANARPARRTDGGRP +TRPPAPHAWECGVMDDVAPAHPALAPQPGRPALRHRFADLFPELAVPWQAQETDGPELVL +LNTGLVTELGLDADWLASDDGVRLLTGEQLGPDARPVAQAYAGHQFGHYSPRLGDGRALL +LGELVPPRRTRDANDAPQALPTWRELHLKGSGRTPFARGDADGQAVLGPMLREYAVSEAM +HALGVPTTRALAVVATGRPVRRAGWQPGALLARTAASHLRVGSFQYAAALPERADPVAVL +RRLVDEAILRHHPHAAEAENPALALYEAVIAAQAELVARWMLVGFVHGVMNTDNMTLSGE +TIDYGPCAFLDAFDPAASFSSIDTQGRYAFGNQGPVAAWNLARLGEALVPVLDDDAGRAV +ELAQEALGGFQATHLAAWRGGLRAKLGLSEEVTDADVAALTDRLFPVLAAARTDWTGFWV +RLAEHVPGGRGRGRAGRGRRRTECPAECRSGRADGRRAGGGADAGPGRGRPGCRGRVAAR +LAGAGPRRGPDAGGEPRLHPAEPPARRGPHRRRGRGPGAGAPPAGGRHRPVHPAPGPRAV +RRAGPVGRGPVRDVLRDVRRGRRGLPYSRSPLPAPRPNSHRPTAFVWESGNLPPLSCGET +GVPVSHTKGDEGRTLLLTRGCGGARPLTPGRATSAARSGRRGPAGPPRSRGR +>MOLHKGIG_01998 +MTTSAPTLSSHFADTFPELALPWQAQVTDGPQLVLLNAGLAAELGLDAEWLASDDGVRFL +TGEQPGPHARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA +RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS +HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELV +SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA +AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV +AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA +DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEGGDLAPVHRLLEAVTDPFTPRPGFER +YAEPGPADGAPFVTYCGT +>NAFOICDF_00795 +MPVPALQHRFADRLPELAVPWQARPAPAPTLAALNAPLAAELGLDPAWLATDAGLAFLTG +TEPGPGARPVAQAYAGHQFGSYSPLLGDGRALLLGELTAPDGTLHDVHLKGSGLTPFSRE +GSDGLAALGPMLRELVVSEALHALGIPTTRALAVVATGGPVRRQRVLPGAVLVRVADSHL +RVGTFQHAAALVHAGRAPEDLLTRLVAESLERHHPGHADDAAPALALLRAVVAAQAELVA +RWMLMGFVHGVMNTDNMTVSGQSIDFGPCAFLDGFDPDAVFSSIDRGGRYAYGAQPRIAL +WNLNRFAETLLPLLAPDPEAAVAAAEEALGGFAPAFDAAWQGGLAAKLGLARSADSDALA +AELLRLLAQDRADWTASWANLSDLPLPADWLARWRALDPDPELARAANPLRVPRNRPLQA +ALDAAEDGDLADVERILAAVREPFTPRADASDLDVPPAPGAGGEAPFVTFCGT +>MHAAABBN_01692 +MTTSVPALSSHFADTFPELALPWQAQATDGPRLVLLNAGLAAELGLDAEWLASDDGVRFL +TGEQSGPDARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA +RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS +HLRVGTAQYAAALPEQAHPTEVLRRIVDESIARHHPHATDAEHPALALYEAVIAAQAELV +SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA +AWNLARLGEALVPVLDDDPDRAVPLAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV +AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA +EWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER +YAEPGPADGAPFVTYCGT +>LFPAFLNI_01924 +MTTSVPALSSHFADTFPELALPWQAQATDGPQLVLLNAGLAAELGLDAEWLATDDGVRFL +TGEQPGPGARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA +RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVGTGHPVRRETVLPGAVLARTAAS +HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELI +SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYACGNQGPIA +AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV +AALTDRLFPWLAAARADWTLFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA +DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER +YAEPWPEDGAPFVTYCGT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000568.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000568.fa new file mode 100644 index 0000000000000000000000000000000000000000..d58117ed3d98267ca5b84b871a977a20ce89c8a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000568.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00860 +MLDHETHVKIADELHEAGRTGTPVPLLTARYEGMEIEDSYAVQRIWAQRQVEAGRRVVGH +KIGLTSKAMQAATGITEPDYGVIFDDQVFESGHEYETARITNPRIEMELAFVLKDELRGP +HVNLFDVLRATEYVVPALEILDAHVELAGRTIVDTIADNAALGSMVLGGRPVAPDAVDLR +WVAGTLSRNQTIEETGVAAGVLNHPGNGVHWLANRLVDHGDALAAGEIVLAGSFTRPMHV +SAGDTVTADYGPLGTVTCHFA +>MOLHKGIG_01995 +MLDHETHVKIADELHRAGIDRVPVPRLTARYPQMEIEDSYAVQRIWAERQVEAGRRKVGH +KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLKDELRGP +GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVDDVDLR +WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV +YEGDTVYADYGPLGTITCRFA +>NAFOICDF_00798 +MLDHATHVKIADELFEAGRAGTPVPLLTARYADMEVEDSYAVQRIWAERRVEAGRRVVGH +KIGLTSKAMQAATGITEPDYGVIFDDQVFESGHVYETARITNPRIEMELAFVLKAELRGP +HVNLFDVLRATEYVVPALEILDAHIELAGRTIVDTIADNAALGSMVLGGRPVAPDAVDLR +WVAGTLSRNQTIEETGVAAGVLNHPGNGVHWLANRLGEHGDALAAGEIVLAGSFTRPMHV +SAGDTVTADYGPLGTVTCFFA +>MHAAABBN_01689 +MLDHETHVKIADELHRAGIDRVTVPRLTARYPEMQIEDSYAVQRIWAERQVEAGRRKVGH +KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLRDELRGP +GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVHDVDLR +WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV +HEGDTVYADYGPLGTITCRFA +>LFPAFLNI_01921 +MLDHETHVKIADELHRAGIDRVPVPRLTARYPEMEIEDSYAVQRIWAERQVEAGRRKVGH +KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLKDELRGP +GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVHDVDLR +WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV +HEGDTVYADYGPLGTITCRFA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000573.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000573.fa new file mode 100644 index 0000000000000000000000000000000000000000..338caf2f3e3cdee0c36a2b9b39200e56abdd66f2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000573.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00867 +MRHLRDHLSHRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR +FGTESLQYGPGQGTEEMRAAAAAVMAADGIPDADPELVVITPGSQAAIDTACRAFGNPGD +VVVVEDPTFVGALTTFNTWELDAVATGTDEHGLVPAALDETLTRLAAEGRRVAFLYTIPS +FANPSGALLPADRRAEVAAICERHGVLIVEDNPYGQIAFDGDPVAPIAAEHRDGVVYLGT +MSKIFSPGVRIGWALVPAELKREFYLSAESAFIHASTYSQMLSTAFVTQLDWQGHVRHVT +GLYRERAGVLVDAVREHWDPGVEFITPRGGFFLWATLPGGVDTIELMHRGIEAGAVFVPG +GAFTPVEGVHSTLRLAYPFVEAERLVEGVRRLAPVVNDAVARAR +>MOLHKGIG_01990 +MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR +FGTESLQYGPGQGTEEMRAAAATVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD +VVVVEDPTFVGALTTFATWQLEAVATGTDDQGLVPAALDETLTRLAAEGRRVAFLYTIPS +FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT +MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT +GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG +AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR +>NAFOICDF_01757 +MSTLDPAGARAHLARRATTVQQSAVRDVFDIAMDPDLVSLAGGNPWLAGLPLEELGATAA +RLVAEQGTASLQYGPGQGLECMRVAACAVMAADGIPDADPELVVITPGSQAAIDTACRAF +ADPGDVVVVEDPTFVGALTSFQTWELEAVATPTDEHGLVPADLDATLARLEAEGRRVAFL +YTIPSFANPSGLLLPADRRDDVAAVCERHGVLIVEDNPYGQIAFDGAPVAPIAAAHRERT +VYLGTMSKIFSPGVRVGWALVPEALHREFYLCAESAFIHASTTSQMLSTAFVTEYDWQDH +VRGVTGLYRSRAQALQAAIAEHWDPGFTFTPPAGGFFLWGSLPAGVDAVELMHRGIAAGA +VFVPGAAFTPVPGTHSTLRLAYSFVDEETLAEGVRRLAPVVNTAVEGAR +>MHAAABBN_01684 +MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLISLAGGNPWLADLPLDELGRIASDLMTR +FGTESLQYGPGQGTEAMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD +VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS +FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT +MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT +GLYRERAAALVDAVREHWDPAVEFITPQGGFFLWATLPVGVDTLEVMHRGIEAGAVFVPG +AAFTPVEGTHSTLRLAYSFVAAEKLVEGVRRLAPAVNESIARAR +>LFPAFLNI_01916 +MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR +FGTESLQYGPGQGTEEMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD +VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS +FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT +MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT +GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG +AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000574.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000574.fa new file mode 100644 index 0000000000000000000000000000000000000000..474f719471cc28485dad0552eb4945135f813f39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000574.fa @@ -0,0 +1,32 @@ +>ACLBLIBL_00868 +MRQRPASRAVLLVGAAAAVGLLGGCAAEPGAPAADGSAQGDALPRPEVDGYAPLTVWLTV +PAAEAVPGSTGRAYGCDDLLVPVQTVPADAPDDADAALDFLFSDERGWHGDPSLWNAVFE +TRESLTPTGHRLEGDVDVFTFTGTVTAEGECEAERIRAQLQETAAAHTSAGQVRLEVDGR +PLDDVLGLAPLALGDEVDVPESGADPSESPTEPADEPWEEPAEDPWAEPTEDTWSEPTED +PWAESEESAEPSPTAWEEPAEETWEPQDETAPTEEDAPTEWDGTVDDGSASEDVPAEVEE +PPAQDEGADAADESAPAEDAGADGAGNLGIGDPDATEPSAP +>MOLHKGIG_01989 +MRPPSPPRALRLMGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE +TEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADEQGWHGDPSLWNAVFDAR +ETLTPTGHRREGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL +DDVLGLEPLRLGESVDVPQGDPTPSGEPSDESGEQTWAPEGESPEDTWAPAEPSDETWAP +AEESSWGPAEPTQGTWSPGPEPSAP +>NAFOICDF_00805 +MRIRPTPRVRLAAVLATSAALTSGCGALTGQGLDEPKELTVHLTVPRADAASSFEGRPYG +CDDLLVPVTTAPSSGVDHGDAALDFLFSDLQGEHGDPALQNAVKATADTLHPTGHHRDGS +TEVFTFDGTVTAEDECAAQRIRAQLQETARAQSPVPDVRLEVGGRPLDEVLGLPALSLGD +PVKGGAASTPRATPTPESTPSPTATPTPTPTTVPGSSASPAPTSASPTATPAPSTSAAPS +TTGPSSASPTAETSSAAPASPDPASADPATAAPTSASATAGGASPSVEPTDGTSLRSPGA +GDATATTAPLDGLDGGAAGGTGTGGADATAPGGAPSAGAAAGAGAGSSATG +>MHAAABBN_01683 +MRPTPPSRALRLTGAVAAACLLAGCAVAPDLAEDSASDDGVPLPATEGYQPLTVYLAVAE +PEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADERGWHGDPSLWNAVFDAR +ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL +DDVLGLEPLRLGESVDVPQGDPTPSGEPSDGSGEQTWAPEGESSEDTWAPAEPSTWAPTE +ESSWGPAEPTQGTWSPGQEPSAP +>LFPAFLNI_01915 +MRPPSPSRALRITGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE +AEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADTALDFLFADERGWHGDPSLWNAVFDAR +ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL +DDVLGLEPLRLGEPVDVPRGVPAPSGEPSDGSGEQTWAPEGESSWGPAEPTQGTWSPAQE +PSTP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000576.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000576.fa new file mode 100644 index 0000000000000000000000000000000000000000..af70db45a35c5e6f0c6c43e9df046cc52dc571d8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000576.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00871 +MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW +>MOLHKGIG_01986 +MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW +>NAFOICDF_00807 +MSDDRAQSFSASTGAAADDGARGTGTTRVKRGLADMLKGGVIMDVVTPEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVCEVAETGALPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW +>MHAAABBN_01680 +MSDERARNFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGTLPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW +>LFPAFLNI_01912 +MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELRAPYELVREVAETGTLPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000579.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000579.fa new file mode 100644 index 0000000000000000000000000000000000000000..fca0dbd3af5f4838aacd20b3b148e1e091a39fb0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000579.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_00877 +MDPLIQASAPVGTFTATTDAVAGSLGLSAALGTIPLLTFFVMLLLVKAKAWQAGLVSLTA +AVLVAILAFGMPADLTLLSASQGAVFGFFPIVWIVVMALWFYQVTVLSGRFEDMRAIFDT +VGGGDIRIQAVLIAFCFGGMLEALAGFGAPVAITATMLLALGLPPLKTAVVVLLANTAPV +AFGAVGIPITTAGQLTDIPAAEIGAIVGHQAPFVAVLVPFFLVWIIDGFRGIRETWPALL +TIGGTFALGIWWASTQFSYELTDVVASLLAMASAVVLLRFWRPKGAAEADARLGITPTRP +AGDLTPGRIWMAVLPYLLVITVFGIAKLWTLGFDLPGWLASTNVRIPWPGLDGRLVTAAG +EPITGTVYSFQWLSSPGTLLLITGLLVALIYSVFTGGGRFPLRFGDALAEIGRCFWKMRW +SGLTIVLVLSLAYVMNFSGQTLAMGTAVAGVGAAFAFLSPVLGWLGTAVTGSDTSANALF +ATLQQTAAEEAGLDPSLMVAANTSGGVVGKMISPQSLAIAATAVSMEGQESKILRTVLPW +SVALLLMVCTIVFLQSNVLSWMLP +>MOLHKGIG_01981 +MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM +PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV +LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT +AGTLTGIPATHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW +LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM +AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA +SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV +MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD +PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL +QSNVLAWMLPAAG +>NAFOICDF_00812 +MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM +PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV +LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT +AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW +LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM +AVLPYIVVVAVFALAKLVPPITAALNSVTAKIPWPGLDGHLVNASGAPLASTVYKFEWLA +SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV +MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD +PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL +QSNVLAWLLPAAG +>MHAAABBN_01675 +MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM +PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV +LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT +AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW +LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM +AVLPYIVVVAVFALAKLVPSITAALNAATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA +SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV +MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD +PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL +QSNVLAWMLPAAG +>LFPAFLNI_01907 +MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM +PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV +LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT +AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW +LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM +AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA +SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV +MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD +PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL +QSNVLAWMLPAAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000580.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000580.fa new file mode 100644 index 0000000000000000000000000000000000000000..fe43fcb6333d245f423ed2df1d9daa1759ab2d6b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000580.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00878 +MRVALFATCIVDAMYPKVALATVRILERLGHEVVFPRGQGCCAQMHVNSGYLDDALPVVK +NHVRTFQGADYDVAVAPSGSCVASLGHQQPMVARAAGDEALARDAEEVAANTYELAALLT +DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGDRQERLLRSVADIDYRALPDAEECC +GFGGTFSLKNPDVSGAMAEEKIGNIERTQARLCTGGDASCLLHLGGVMSRRGTTAPDGSP +VTTLHFAEILAATRENPLDVSGPVDLSIPAQGPARRRRQKEATR +>MOLHKGIG_01980 +MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR +NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT +DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC +GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP +LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR +>NAFOICDF_00813 +MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYVEDALPVVR +NHVRTFMKADYDLAVAPSGSCVASLGHQQPDVARSCGDEGLARDAEVVASRTLELSQLLT +DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGTRQEDLLRTVADIDLRPLPDAEECC +GFGGTFSLKNPDVSAAIAEEKIEKVTASGASICTGGDASCLLHLGGAMHRREARGQDGRP +LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEAHR +>MHAAABBN_01674 +MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR +NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT +DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC +GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP +LRTVHLAEILAATRENPLEVDGPVELSIPTSAGVRRGPSARVEEARR +>LFPAFLNI_01906 +MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR +NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT +DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC +GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP +LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000581.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000581.fa new file mode 100644 index 0000000000000000000000000000000000000000..717888f98cf290778717b5b95715a99c5e03e644 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000581.fa @@ -0,0 +1,54 @@ +>ACLBLIBL_00879 +MTRTALGMPAVRPAHGHGNIVLDEPFPSAARTQLGNAQMRANIHHATHTIRGKRARVVGE +LPDWAELRQAGSALKQQVMADLPALLEQFEQRVTERGGVVHWARDAEEANRIITGLVKAK +GVDEVIKVKSMATQEIDLEHALQAEGIAAVETDLAELIVQLGHDKPSHILVPAIHRNREE +IREIFVREMPETDESLTSDPSALADVARVHLREKFLTTSVAISGANFGVAETGTLTVVES +EGNGRMCLTLPETLITVMGIEKIVPTFQDLEVFLQLLPRSSTGERMNPYTSMWTGVTPGD +GPQEFHLVLLDNGRSAVLSDPEGRPALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGA +ILSPQLTGVQEGANGSLPYASSLCGACYDVCPVAIDIPSILVHLRDQDVRATHARKKEET +RVPLPSQMDLMMKGARTVMSSGTAMSLAERGLPLGRLAAGRDATLGWLPGIAGGWTDQRD +VPSPPRQSFRNWWRGNAEHTEERVARDGGRRDVAAEDETTTTDGQEQR +>MOLHKGIG_01979 +MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG +VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL +VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR +NRREIRDIFRREMPDTDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV +TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG +PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR +KALRTEKDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH +VEEDGR +>NAFOICDF_00814 +MSTAPTRVRLGMPTLRPVHGEGEILLKTPFPESAREQLGNGQMRANIRRATHTIRAKRAG +VVGELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL +VTAKGVDEVIKVKSMATQEIGLDAALAQAGVAAVETDLAELIVQLGHDRPSHILVPAIHR +NRREIRDIFLREMPETDESLTSEPADLAEASRRHLREKFLSTKVAISGANFGVAETGTLA +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV +TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG +PIGAILSPQLTGVDAGENGTLPYASSLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR +KALRTEGDGDAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH +VEEDGR +>MHAAABBN_01673 +MSTAPTRVRLGMPTVRPVHGEGEVLLKTPFPESAREQLGNDQMRANIRRATHTIRAKRAG +VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL +VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR +NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV +TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG +PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR +KALRTEKDAAGGPLARAKTAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH +VEEDGR +>LFPAFLNI_01905 +MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG +VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL +VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR +NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV +TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG +PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR +KALRTDEDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRVAMDGVAGLDRPEDEH +VEEDGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000582.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000582.fa new file mode 100644 index 0000000000000000000000000000000000000000..8be1d6b48d76e64b1e30b488a9f7429f1f843df2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000582.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00880 +MSEATPTTVPATPTPGPGGPGGEARAAILDRIRQALQDGPTPDPVERTYRRTSEAAPGDV +VEQLVDRLVDYKAGVHREDLTTVADRVADLLGEGARYVVPPGLDPAWLPGDGQGRVRVTE +PATADAGALGVRELDELDAVVTGSTVSCSETGTIFLTGRPEEGRRAISLVPDHHVCIVPL +DTVVELFPEALARVEPTAAITMISGPSATSDIELERVEGVHGPRRLDVILLDR +>MOLHKGIG_01978 +MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE +ETVAAAIAELLGPDARYVVPAGLEPDWLPTDSRGAGRERITEPAVGHTGERAAVRGAHDG +EREPLNVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV +ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR +>NAFOICDF_00815 +MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE +ETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERITEPAVGHTGERAAVRGAHDG +EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV +ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR +>MHAAABBN_01672 +MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE +ETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERITEPAVGHTGERAAVRGAHDG +EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV +ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR +>LFPAFLNI_01904 +MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE +ETVAAAIAELLGPDARYVVPAGLEPDWLPADSCGAGRERITEPAVGHTGERAAVRGAHDG +EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV +ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000583.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000583.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c895df253f193b38ecf716f62d7358c4a84787c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000583.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00884 +MGDARPRVPVCPSSRRRRRALAALLAVVVVVHLVVLYLPGSDVPQTGFEVPGLDKTIHVL +AFAAPTWAAVRLGSSWWWALPFAVHAPVSEAVQHAWVPLRTGDAWDMVADLAGVVLGAAL +AWRAVRREVEAPGEVGEVGEAGRGDRIGGSGRPGV +>MOLHKGIG_01974 +MTVPPGSPAAPSAPASRRRRRALAAALAVAVVVQLVVLYLPGEQVPQAGFAAPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +VAARSRRIGGSGASGV +>NAFOICDF_00826 +MPARSSAPAAPPPSAARRRTLALLLVIALAAHLVVLYLPGDDVPAVGFEVPGMDKAIHVA +TFGVPALLGVLLARRVWPAAVLAVHAPLSEVLQAVQGLGRTGDPADAVADLAGVALGLLA +ARAALRRGPTGRPIGAAPGRGV +>MHAAABBN_01668 +MTVPSGSPAAPSAPASPRRRRALAAALAVAVAVQLVVLYLPGEQVPEAGFTVPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +VAARSRRIGGSGASGV +>LFPAFLNI_01900 +MTVPSGSPAAPSAPASRRRRRAVAAALVVAVVVQLVVLYLPGEQVPEAGFAVPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +LAARSRRIGGSGASGV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000585.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000585.fa new file mode 100644 index 0000000000000000000000000000000000000000..d2a07fcf87d38795d1778b1de86d44c7177bb779 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000585.fa @@ -0,0 +1,39 @@ +>ACLBLIBL_00888 +MSDGAAAVSRPGASARPSRRRRVLYYAHQHGSGHVRHAANLAATGAFDVTVVSAHPDAAR +MLLAGTPVLPLPSDVVPGHVQPERSPLHWTPVGPQIRDRFAALHDAARDVRPDVCVVDVS +VEAALFLRLAGWPVLHRRMHGERTDPAHALVYAEADGLFAHYAEELEDPAWREAHAGRTA +FLGVPDVTGRLGARATTTTATTTAAGGSAPRVAVIAGTGGGGVRAADLARAAAAVPEATW +EVYGPVAGADELQAPGGAAGSRSSDADATTGTAPTAGVALPANVTLHGWVEAPASRAAEA +DVVVVSAGHNAAVDAARSGRPVVLAPEPRPFDEQHVFAREARRAAGVPWCAWEDPDADWA +GAVRGALADPSAADRLAALLLVEPGEYRRRWEAAVEAALEATQG +>MOLHKGIG_01971 +MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL +VPGHEQPARSPLHWSPVGPEIRARFDALHAAAQRVGPDVCVVDVSVEAALFLRLAGWPVL +HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRT +TTTSTARAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA +EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF +VREIHRAAGVPWCAWEDPDADWAGAVRGALADPTAADRLAGLLLVAPDEYRRRWEAAIEG +ALG +>NAFOICDF_00829 +MSGRRLRVLHYAHQHGSGHVRHAATLIRADVADVTVATAHPDAARLLPTGTRIVPLPTDI +VPGHGQPEGSPLHHTPVGPAIQARFDALHDAARAVRPDVCVVDVSAEAALFLRLAGYPVV +HRRMHGDRTDPAHRLVYAEADALFAHYGEVLEDPAWQAEFGARTAHLGVPDADGRLGRTA +APARAGEAPRVVAVTGTGGGGVAARDIARAARSTPGARWHVIGPVRDAGGADLPENLELQ +GWVEDVPAALAAADVVVVSAGHNAAVDAAHSGRPVVLAPEERPFAEQRRFAEAVERAAGV +PWRAWEDPEADWAGAVARALGDPAAADRLAAALLRPPAEHAAGWGALLERAAASAQ +>MHAAABBN_01665 +MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL +VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVVDVSVEAALFLRLAGWPVL +HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA +TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA +EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF +VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPGEYRRRWEAAIEG +ALG +>LFPAFLNI_01897 +MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAALLPADVPVIPLPSDL +VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVADVSVEAALFLRLAGWPVL +HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA +TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA +EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF +VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPDEYRRRWEAAIEG +ALG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000586.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000586.fa new file mode 100644 index 0000000000000000000000000000000000000000..c95d13fd26d075b1f76e872997921bb11567a190 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000586.fa @@ -0,0 +1,64 @@ +>ACLBLIBL_00889 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR +PDVLHVHFGFEHFNPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR +ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVSQGDDDAPGLLPPDASDDGAAA +PARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQATVQDEDALAALRAG +CAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHI +ADQSGAWLAPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAV +YREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVPAT +GLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHPGS +VVMGRPRYLRPGWTRAVEEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLIL +ALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHL +EDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRTPTADELAVARRDDA +AY +>MOLHKGIG_01970 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR +PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR +ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGAEPGLLPPDASDD +GDGAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDAL +AALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAV +ADIGHIADQSGAWLTPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVA +AAHVAVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPD +GRVPATDLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEV +AAHPGSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHL +VWTLILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMT +PPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTA +ARRDDAAY +>NAFOICDF_00830 +MSLTVQHVPAGHPYARSVRPLDGAAAPDVEFWPDPPVPGAAEGVWWPPRALDPAWIAEHR +PDVLHVHFGFEHFTPEQLRAALDAQHAHGGAVVVTVHDLQNPHLQDQDPHRARLRVLLDA +ADAVITLTPGAAAAVEAASGRAPLVLPHPHVVPLDALPDDGAADGERPGVDRPARLLMHA +KDLRAQVDPVGLLPVLAAARDALAARGLAVEVTVDVQDGVRDEAALAELEAGAEAHGFAL +WRHARLDDAELHAALRDADVSVLPYRVGTHSGWVEMCRDLGVPVAVAEVGHIADQARAWT +TPELLAAFDPDDPASLADALAALLTAAPDARAAAPAARAAQRRRVAAAHVAVYRQALAVR +RGTAATVSVLVITGHRDAHLARVLAGLERSHRRPDQVVVVFMGQPDGAVPATDLPVTVGH +VAADHGLPLATARNRAAELATGEVLVFLDVDCIPAADTVGVLAAEVAAHPGSLVMGAPRY +LAPDWTAALAAEGVDADAAPTDGDLRRHAVPHRARTHLRPGPSEEWALVWTLVMAIGAAD +LARIDGFDEGFAGYGAEDTDLAFRARDAGLTLRISPAEAFHQHHGVHRPPLHHVADIVVN +ARRFRTLHGTWPMGGWLAAFAERGLIRWDPDGDLLELVREPTPDDVAAARVDDAAY +>MHAAABBN_01664 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPDAPAHQWWPPRALHAEWLAEHR +PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR +ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGLLPPDASDDGDGA +PVPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR +AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG +HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV +AVYREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP +ATDLPVTVGHVAADAGLPLAQARNRAAELAIGEILVFLDVDCIPAAETVGVLATEVAAHP +GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL +ILALRRADLARIGCFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLH +HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRD +DAAY +>LFPAFLNI_01896 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR +PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR +ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGALPPDASDDGDGA +AAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR +AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG +HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV +AVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP +ATDLPITVGHVSAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHP +GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL +ILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMVPPLH +HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRG +DAAY diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000587.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000587.fa new file mode 100644 index 0000000000000000000000000000000000000000..1d5593e3ad8895106ea7317c50153a4e21f14e92 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000587.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00890 +MESQPQGRVLYVIVGPPEHGVVRHARQTAAALRRVGAEVELLTAEDVAAFHGLVPLMAEA +RSLGAAVHLDVTDALFGPTAAAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRRRGEAYA +RLARHAAGVVVSSQHERALLAELVDADADVVPLPVEDRRAEAARAESVVPENMAGLDQDV +VLFGFVYPGKGHALALEALTELHRQWGPNSGAPRRLTALGPVSAGHDDLVAELTRDAEAR +GLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGRYTEEME +RLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPEHTWLDPAVDLSPGAEDCARMLFDVLRRV +HRWT +>MOLHKGIG_01969 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALQRVGAEVELLTAEDVAAFRGLV +PLLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPAGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVAGVVVSSQHERALLADLVDVAADVVPLPVQDRRAAAARAEPVVPESMA +GLDQDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR +YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEGCARMLF +DVLRRVHRWT +>NAFOICDF_00831 +MTSHAQGRVLYLSVGSRGHGVVHHGLLTAEELAQVGLDVESLHTEDATGFVGLAPVLARA +REARRAVHVDVTDSLFGPSPAAAADTLSRILPDGATVTLHDVPQPAEGEARFLERAEAYV +RIAQAAAGVVVSSEHERALLHAIVDVDAHVVPLPVEDRRAAREAVRLPEALEGLDRDVVI +FGHLYPGKGHAEAIDALAELDRQWGPSPHRPRRVTALGAVAARHEFLVDELTARAEVSGL +QFRVTGFVPDEVLDPALRAAAVPLAAHHNVSASGSLASWMSVGRRPIVPAGRYTQEMARL +RPGTLRIVQVGTSGPEYALAEAVAEAVEEPSRTWQARGTSLAPGPRACARMLAAALADVH +GWAWPR +>MHAAABBN_01663 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV +PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA +GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR +YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLGPGVDLSPGAEDCARMLF +DVLRRVHRWT +>LFPAFLNI_01895 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV +PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA +GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSIGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRTIASAGR +YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEDCARMLF +DVLRRVHRWT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000588.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000588.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a50ae6c22b7983383348ea4f5a6c74f48255467 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000588.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00891 +MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPMVGPDLPFDVVT +VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAAVAAVAEAPRDAAVVGRR +RHLAEAWLERAWADGWRPGHEVPADARLADPAWLREGYRTTDELRRADSTGYRYVISAVL +TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA +EAARVKAREALALASRIPATTARGHGLSLAGPLRVEARVRVPERADGAAAAVVAVDAVLR +AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW +SVDVRVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA +RWRRRRGGTSRVWRVPASRLGWAPVAAVPDLEAWWGGWG +>MOLHKGIG_01968 +MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPRVDPGLPFDVVT +VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR +RHLAEAWLERAWADGWRPGHEVPADALLAEPAWLRDGYRATDDLRRADSTGYRYVISAVL +TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA +EAARVKAREALVLVSRIPATTSRGHGLSLAGPLRAEARVRVPEGADGAAAAVVAVDAVLR +AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAAPEDLPPTPARGDLDAVRSVPDW +SVDVQVPLRPAAAGARPDTDAVAAWLLRLERAGVERVEVLGEPGERAERDVLAVLTCARA +RWRPRRGGTARVWRVPASRLGWAPVAAVPDLEAWWGGWG +>NAFOICDF_00832 +MTAPVAGREAAAETAGPEASVPEVSVVVPHYRAPADLERVVAALAAQDHPASRLQLVVAD +DGSPEPPVLPAGLPFEAVVVAQEDHGFRASAARALGASAAEGRILAFLDGDMLPEPGYLT +AACAAPAASVDAVVVGRRRHLDPALLESGWRPGEPVPEAARLPEPAWLAEAYQRSGDLAA +ADSTSYRYVISAVLTVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGGAFRHQPAAVA +WQAGEDFGGRGDAAERTAVKQREALRLAARITATTARGHGLSLPGPLRVGARVRAEASGD +AAAVVGVDALLAAAPGARVGVTGLGSGAARAALADPRVWIMDGGGEAARADLPPAPARGD +LGAVRGIPDWSCDVRTPLRPAAPGARPDAARAADWLLRLERAGVERVEVLGEPQAAEEPG +EAGRGERPVLAVLTCSRALWRSRRGGDSRVWRVPAARLGWAPVARDVDLEAWWGGWG +>MHAAABBN_01662 +MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVGPGLPFDVVT +VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR +RHLAEAWLERAWVDGWRPGDEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVL +TVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA +EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC +AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW +SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA +RWRRRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG +>LFPAFLNI_01894 +MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVDPGLPFDVVT +VRQPDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR +RHLAEAWLERAWAHGWQPGHEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVF +TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA +EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC +AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAADEDLPPTPARGDLDAVRSVPDW +SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPAEPGERAVLAVLTCARA +RWRHRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000589.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000589.fa new file mode 100644 index 0000000000000000000000000000000000000000..413c686b2dac5283744a9dc198bc6751b1162c14 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000589.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_00893 +MHEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP +PAFEVQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD +VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA +SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTVLTRVAERVAEHLPGDVAAQPV +PAARVLLGGVRAPLEAVVVEALDLDAEPTEDWTVGGETIPAEQLRQTHLDWYAQNPQAVE +VGMRKYADQLRLLGLAA +>MOLHKGIG_01966 +MHEDEGRRRHYGHFYGLEDLPEDDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP +PAFEAQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD +VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA +SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV +PASRVLLGGVRAPLEAPVVEALDLDAAPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE +VGMRKYADQLRLLGLTG +>NAFOICDF_00833 +MSEETPMDDQTRTAGAEPGDEGVQVRGAAERAPSSDLPADEGRRRHYAHFYGLEPLPEGE +LLTVMGGCQAEATRLLLCGEPGRAEGGTPASVRVPPMFELGPDDLPHLLALLKRTTVLVV +KPVRDDYQGLPLGLGQLESLLPAGARSIRVPALYDSSRFPWLVTLRHPTRPWEDPPVVPY +HDLRTVAEAAAEAGLIPWPAALGGPGEAGAYDAGPRLPLSAEALRGLAAESVARLRAREE +HFGTVRVSDAVADERGVGFHTVNHPDNPLLEALARTVLAELGVDKEVHAPDRLLLGHVLA +PIEEQVVDALGLQTAPRAAWRVGGAEVSDAEVRRAHLGWFRANPEALAPGLERHGALMRE +LGLLA +>MHAAABBN_01660 +MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP +PAFEAQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPKDAAVVRIPVVYD +VSRFPWQVTLRNWKVAPGAAERPGEDPPVLPYHDLRVLAEAATGRRRQVAPAAIREAAAA +SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAGHLPGDVAVQPV +PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTIPAEQLRQTHLDWYAQNPQAVE +VGMRKYADQLRLLGLAA +>LFPAFLNI_01892 +MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP +PAFEVQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD +VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA +SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV +PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE +VGLRKYADQLRLLGLTG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000591.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000591.fa new file mode 100644 index 0000000000000000000000000000000000000000..47c9e37201153390fb5000c4013c0f79de7fc8b6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000591.fa @@ -0,0 +1,61 @@ +>ACLBLIBL_00900 +MTTPATPGAASAARRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH +REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ +NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA +SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN +PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDVHLTERFDYVLSNPPYG +GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN +GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGR +VQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY +REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALETALASLRGRVWDHQPTFVL +DLKKALKEHGVTAGAPLVKALTGAIGVHDPEAQIVTNKKGEPEPDTSLRDTELVPFGRDI +HEYFAAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLDEIDAELKQLTAEIIEL +LQEVER +>MOLHKGIG_01620 +MARRAAKAKPAKTLEQTLWDAADKLRGNQEPSEYKHVVLGLVFLKYVSDRFEERREQLKD +ELAAEGIKPERIESFLEDRDEYASQNVFWVPSLARWGYVQSVAKQPEIGQQIDQAMDLIE +KENPSLRGVLPRNYGRDGLDKRRLGELVDLIGSIGFTETDDHGADDVLGRVYEYFLGQFA +GKETGKDAGAFYTPRSVVKTLVEMLEPFKGRVYDPAVGSGGMFVQSAEFVKAHGGKRTDI +SVYGQEFTDTTWKLAKMNLALRGVEADMGSHSADSFTEDLHLDLRADYVIANPPFNVSDW +WDAKLADDPRWKYGTPPKGNANFAWVQHFLHHLAPHGTAGFVLANGSLSSKSSGEGEIRQ +RLVEAGLVDCIVAMPDKLFFNTGIPVSLWFISKGRDGNGHRARKGEVLFIDARKLGAMQS +RRLRVLSDDDIAQIADTYHEWRNHDGCYEDVPGFAKSATIGEIEKHEFVLTPGRYVGAAE +AEVDDEPIDEKIERLTNELLAEFERGRELENEVRLRMGSLS +>NAFOICDF_00838 +MPSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAQHREFFAELAAKGHP +DFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTYYEFDK +TVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAASNETAGEHFTPRD +AVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMNPNAEVRLFGQELN +DQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYGGDWKASRTAVEKE +IAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSGP +SEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGKVQLIDARTFFTKL +RRNVGSKNKELSTADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGYREITVERPLQLRF +EVEDATIAAALATKPADKLPVDGRSALGAALASLRGRVWDHQPTFVLDLKKALKEHGVTA +GAPLVKALTGAIGVHDPKAEVVMNKKGEPEPDASLRDTELVPFGRDIHEYFEAEVVPHVS +GAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIELLQEVER +>MHAAABBN_01648 +MTIPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH +REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ +NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAA +SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSVLDERLRRMN +PNAEVRLFGQELNDQSYAICKSELLGKGQAADGIARGDTLKNDAHMTERFDYVLSNPPYG +GDWKASRAAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN +GSPLFTGGAGSGPSEIRRWLLESDLVDVIVALPTDMFYNTGIATYVWVLDNNKPADRRGR +AQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY +REITVERPLQLRFEVEDATIAAALATKPADKLPDDGRSALEAALASLRGRVWDHQPTFVL +DLKKALKEHGVTAGAPLVKALTGAIGVHDPKAEVVTNKKGEPEPDTSLRDTELVPFGRDI +HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDADLKQLTAEIIEL +LQEVER +>LFPAFLNI_01879 +MTTPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMDPH +REFFAELAEKGHPDFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ +NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA +SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN +PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYG +GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN +GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKPADRRGR +VQLIDARSFFTKLRRNVGSKNKELSTADRQRVLDIYRDFDAQSEDNAEFSKVLTAQDFGY +REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALESALASLRGRVWDHQPTFVL +ELKKALKKHGVTAGAPLAKALTGAIGVHDPDAEVVKDKKGEPEPDTSLRDTELVPFGRDI +HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIEL +LQEVER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000595.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000595.fa new file mode 100644 index 0000000000000000000000000000000000000000..38a4469079e89d74534f6c4bfed84c97e810cbf8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000595.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00912 +MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD +LVARAGELDLLTDGLEVPGHPVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC +AGPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG +AAGGITIVWARDTGDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA +RLPNVATFKDAVRVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER +LAQMLDEVTAMQARCVAVARLQASGRLRDEQASLLKYACTRGARRVAQTARDMLGGNGIL +LEHRVIRHFADVEALHTYEGTESVQALILGRDLTGMSAFA +>MOLHKGIG_01944 +MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPFD +LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC +ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG +AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA +RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER +LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL +LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA +>NAFOICDF_00850 +MRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLDL +VARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHCA +SPEQQERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNGA +AGGITFVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDAR +LPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQERL +AQMLDEVTAMQTRCVVVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGILL +EHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA +>MHAAABBN_01640 +MTRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLD +LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC +ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG +AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA +RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER +LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL +LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA +>LFPAFLNI_01863 +MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD +LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC +ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG +AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA +RLPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER +LAQMLDEVTAMQTRCVAVARLQAAGLLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL +LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000596.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000596.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d4acc872fbc747e637ea6d32ee6230886b85c1d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000596.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_00913 +MTEQTSPAAPTADSPSPEDTIGRLFTRAAARHPETVALRFEDRDWTYAQLLDGVHRVARR +LLATGLPRGTRVAAYGANSDAYAVLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEVL +VADAGMLERVEQVRADGGGAGLRHVWTMLPAGHAEPSLLETARDEAADATAPDVPVTATD +LAQLLYTSGTTSTPKGAMMSHRALITEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFLL +PYLSLGATVRLLATPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRKAQ +YGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEA +RVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGYI +QVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGAE +LTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>MOLHKGIG_01943 +MPDQITHPTDAAAHPSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYTQLRDGAHRVA +RRLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAE +LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETARDETLDAAAPEAEVSA +TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSMIALDFTAEDRPLVAMPLYHSAAMHVF +LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK +AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV +EARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG +YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVVGLPDERWIEAVTAVVVLKEG +AELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>NAFOICDF_00851 +MPDQITHPTDAAAHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVA +RRLQGTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGTE +LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDEALDAAAPEAEVSA +TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVF +LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK +AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV +EARVMTADGVPAAPGMPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG +YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEG +AELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>MHAAABBN_01639 +MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR +RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL +LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDETLDAAAPEAEVSAT +DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL +LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA +QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE +ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY +IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA +ELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>LFPAFLNI_01862 +MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR +RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL +LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLQTAQDETLDAAAPEAEVSAT +DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL +LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA +QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE +ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY +IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA +ELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000597.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000597.fa new file mode 100644 index 0000000000000000000000000000000000000000..1bf80102f985c4912274b5698a83f97025d6ecc8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000597.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00914 +MPEAYIIDAVRTPVGRRGKGLAQVHPLDLAAAPLREIVGRQDIDSAEYDEVILGCIDQLG +PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS +AIPLSHSNRAAAEFGFADPFTGSESWAARYGNEEISQFRGAEMMARHWNLDRDVLEEFAV +RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG +RYGLQTMCEGGGQANVTVIERL +>MOLHKGIG_01942 +MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVARQDIDSAEYDEVILGCIDQLG +PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAIMSGTADLVVAGGVQSMS +AIPLSLSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV +RSHERALAAQADSRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG +RYGLQTMCEGGGQANVTVIERL +>NAFOICDF_00852 +MGEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPIRELVGRQDVDSAEYDEVILGCIDQLG +PQAMDVARSAWLAAGLSEDVPGSTIERQCGSGQQAIHYAAQAVMSGTADLVVAGGVQSMS +AIPLSRSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV +RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAASASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAFALRRMGLGIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG +RYGLQTMCEGGGQANVTVIERL +>MHAAABBN_01638 +MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG +PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS +AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV +RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG +RYGLQTMCEGGGQANVTVIERL +>LFPAFLNI_01861 +MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG +PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS +AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV +RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG +RYGLQTMCEGGGQANVTVIERL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000599.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000599.fa new file mode 100644 index 0000000000000000000000000000000000000000..35cdd946ffada5f20fb8f701710118ba214a3e83 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000599.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00921 +MRVVAAPLAMLPGVDHGPALRMDLHPVPGGIVYVARDLVLRELGDDVRGHVHAGMVGTAQ +LHAFWSTVTVDLPPDRPVIVRLRSDRDAELLSLLEVLAPVEMRVVSYRLDESPVGTQRSS +YLLPDVDPEIVARAESPRVPLEAIEATQEEEDALRRSSGVFLSRRRTDRFLRRTLPTVTH +SLSFSDEADVADVYVDGSVLRSSRIGGAAAVGGPSMWAVQAVNGATTPLEVELEALVLGH +VVSAWAGVPGERVTIHSDSRAALALLNAARRERLTLGGARGERVRRTLRRLLAAVDLAQA +ADVRVETTWVKGHVGVQGNELADDLARAAARHAGVGTSEEDLRRRLDRLIDLHEEAEAEA +GQTPARAVAAEGHRPMPPGRRPGPRL +>MOLHKGIG_01938 +MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT +PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG +IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL +LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE +EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA +VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR +RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA +RHASVGTPEGDLPERMGQLIQLRVEDDAAG +>NAFOICDF_00855 +MDNSSTHPREGQVRSLHFDTDASSPDALLDPMWAFTGPRASRAGAPAPDGADVLARRARP +AHPGAALVRAATSLFTLPGPPGMPHRSRSAALEAARAPAGYLSPVPHRLALPRPARPRPA +PPRMRVRQDGVRVVARPLAMLPGVDHGRALRLDLHPVRDGIVFVSRHLELRELGDDVKGL +VLTGVVPAARLGYFWDTVAGDLPEGRPVIVRLRSNDDAELLTLLRAIAPPWLRVVSYRLD +ESPVGSQRSSYLLPDVDGEAVAASGAERVPLETLREAHQASAEVERASRVFLARRRVDRF +VRRSVPDLMHSLSYTDPAEVRHVYVDGSVLRGTRTGGAAAVTRSGPWAAHALPGATIPLE +AELEALTLGHLMAAWSGTPDERVLIHSDSRAALALLREAHRERLTLGDARGERIRRALRR +LLAAVDLAGSAGVEVSTLWVKGHAGTHGNELADDLARSAARNTAAGVSADEMRRRMRHVV +QLWDATTHPQA +>MHAAABBN_01634 +MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWEFRGPGAKAEEQHRPLRVVRARRPRGT +PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG +IVYVARELELRELGDDVRGHVYTGMVGTAHLSAFWSTVTVDLPPERPVIVRLGSDRDAEL +LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE +EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA +VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR +RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA +RHASVGTPEGDLPERMGQLIRLRVEDDAAAG +>LFPAFLNI_01857 +MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT +PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG +IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL +LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE +EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA +VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR +RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA +RHASVGTPEGDLPERMGQLIQLRVEDDAAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000600.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000600.fa new file mode 100644 index 0000000000000000000000000000000000000000..334eadc83bf7247ebeb0b063132bd75641ec9f73 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000600.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00922 +MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT +LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH +ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL +>MOLHKGIG_01937 +MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR +VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT +EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL +>NAFOICDF_00856 +MSTSSARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQTLLAR +VADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLHRLLV +DAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL +>MHAAABBN_01633 +MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQSLLAR +VADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLHRLLT +EAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL +>LFPAFLNI_01856 +MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR +VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT +EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000602.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000602.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ae37c5cad04719e154e150e485a68277ba5bc6b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000602.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_00924 +MDGPARGGGLLTVGLTSVPAPVGGPGAPPGAPGPAASGGRRRRRTAGGDGIGAWWLLAAV +VPVAFLLVFFAWPVGAMLWRGVSAEGVLDLGAFAEVLGRERTWRIVGQTLGMAAAGTVLA +VALGLPAAFVLHRRAFPGRAALRAVITVPFVLPTVVVGVAFRALLAPGGPFGWTGLDQST +AAVVLAMVFFNVSVVVRQVGALWASLDPRQAEAARTLGSSGWRAFRTVTLPQLAPALASS +AALVFLFCASAFGIVQTLGRPGVGTLESEIWVQTVVYFDLGTAAVFSTLQFLVVLAAVLV +SGATARRTRRALRLRDAPVRRLTRADAAPVAVTLATALLVLAPLATLLVRSFHSSEGWGL +RNYRLLASSPGAGFSGGVTPAQALEHSLRIALDATLLTLLIGVPLALLLTRPVRSAAGRR +AQRGLDGALLLPLGVSAVTVGFGFVVSLRAEAPALAASGALVPIAQAVVALPLVVRSLVP +VLGAVDPRLREAARTLGAGPLRVLATVDGPFLLRGLGVAAGFAFAVSLGEFGATSFLSSP +DYQTLPLLIVKLLGRPGADNYGMALAAATVLAVLSAGTMMACERLGPRAAASRGGI +>MOLHKGIG_01935 +MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD +ADAFTGAVDLTAFGETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA +VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG +ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR +PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLVAVVVSGVTAARTQRALRLRETPPA +RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP +ARALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV +GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP +WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN +YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL +>NAFOICDF_00858 +MPTPAPARGRRRATLRPPRGRRAAGDGLAPLWLLSAAVPVAFLLVLFAWPVAAMLWRGVA +SVDAAGDPTGGLDLSAFAQTLGAPRTWRILGNTLGLAAAGTAASVALGVPTAFALHRRAF +PGRGLARAVVTVPFVLPTVVVGAAFRALLAADGPLGWTGLDQTSTAVVMAMVFFNVSVVV +RQVGGLWAALDPRQAEAARTLGASPWRAFRTVTLPQLAPAVAGAAALVFLFCASAFGIVQ +TLGRPGPGTLETEIWAQTTVYLDLRTAAVLSTVQLAVVLAAILASGAAAARARRALRLGE +APARPLTRADAVPAAVTLAVLALVVAPILALLAGSLHSAEGWGLRNYRLLATSPGTGFAG +GVTPAQALEQSLRTAVDATVVTLVVAVPLALVLTRPVRSRAGRAAQRALDGALLLPLGVS +AVTVGFGFIVSLRATAPDLAASGALVPLAQSVIAVPLAVRALVPVLGAVDPRLREAARTL +GAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLAAADRPTLPVLIARLIGRP +GADNHGMALAAAVVLAVLSAGALLACERLRPRGAAPSGGL +>MHAAABBN_01631 +MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD +ADAFTGAVDLTAFGQTLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA +VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG +ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR +PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA +RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP +AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV +GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP +WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN +YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL +>LFPAFLNI_01854 +MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD +ADAFTGAVDLTAFRETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA +VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG +ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR +PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA +RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP +AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALVAQRALDGALLLPLGVSAVTV +GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP +WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN +YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000603.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000603.fa new file mode 100644 index 0000000000000000000000000000000000000000..37219b3d54fecc367669153f90cdd9715029800a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000603.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_00925 +MTTAPHRVRTRPRRHGALAALSVAALALTGCSVADRGGSGDQGSSSAEARTVTIMTHDSF +SLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAKDAPTVDGVYGIEDHSAHRLVSEG +VIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDTPWFQEQGLAAPTTLEQVAAPEYA +ELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTALQGGMQVDASWSDAYNTSFSGGE +GTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGVVEGAENPEGARAFVDFLLTEDVQ +AAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDAGLLDSRREDLLKEWTALHEEAAS +>MOLHKGIG_01934 +MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL +VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT +PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT +SPVASSPGLALLAATTEKYGDDGWQDWWRGLKENGGKVADSWSDAYNSDFSGGEGKGRFP +VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPES +MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR +>NAFOICDF_00859 +MSVHRTATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSSTSASG +TAAAGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSKDAPVA +DGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDPAWFTE +HGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDLLKGGA +KVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGVLTGAE +NPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDPAEIDT +EREGLLKEWTALSESAGSR +>MHAAABBN_01630 +MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSASGAGGGEPTTVTIMTHDSFNLPQE +LVQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEY +TPQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVA +TSPVASSPGLALLAATTEKYGDDGWQDWWRGLMENGGKVADSWSDAYNSDFSGGEGKGRF +PVVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPE +SMYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR +>LFPAFLNI_01853 +MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL +VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT +PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT +SPVASSPGLALLAATTEKYGDDGWQDWWQGLMENGGKIADSWSDAYNSDFSGGEGKGQFP +VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFLLTEEVQSALPES +MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000605.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000605.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c63bddd0af70e1faaa694c22f2c1e65acfecc49 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000605.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_00927 +MPAAETVPADAAGRPDARPRVPGPREQPERAWLALPRRHPVPALLDEARDAVAGLAETLA +EVLPVTVLTDPADHAVRSLIPPEVDLLAAPVDSPLLGRTGPGFVRRPEGLAAIAWRPAAG +AGGPGPRDAGVAAAVAAAAGLPLLTPMLRAPRDAWVADGEGTAVVAADPVLDGRTNPAWT +PEQVEAEFAALLGITRVAWLPPVPRIPTGPWGGAGHLGAWVRLLGGGEAAVHWRADRFHP +EHLHGAAALRILQDAPDAAGRPLRVRTVPGGALPPEHDPAEIGPRSLVDTVPLGSAVLRP +AFEDAATEEAAAAACAALHPGLRPVPFPGPPLLRLAGSLSDLVLVQPHP +>MOLHKGIG_01932 +MAAVDPAPTDARERRDLVVPVPGPEDPPERAWLVLPHRHPVPTLLEETRDAVVGLAETLA +AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFVRRPEGLAAVAWRSAAG +LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT +PGQVAAEFAALLGITRVLWVPPAPRPDTGPWGGPGHLASWVRLQGDGEAAVHWRGDRFNP +EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAEYDPAERGPRSLLDTLPLGAAVLRP +AFEDAAGEEAAAAACAALHPGRPQLSFPAPPLLRLAGALNDLVLLQPRP +>NAFOICDF_00861 +MSTPAVPEPPRAPAPWEVPERLWLALPAVHPVPGLLAEARDAVAGLAETLGAHAPVAVLT +DPDDADAARLLPGVVERVPVRGASPLPGREGPTFVHAAGTRGSVEAVHWRLPSDAAGTAG +RAAATADAVARSAGLPLRTPLFSAPAGTWAADGDGTAVVSAALLDPAVNEGWTRAQAEDA +LAGLLGAERVLWLPPVAGHAAGPWDGGGAAQPHPHPWLRFVAPGEVAVHWQPGRLHPDHA +ASAAALHALTGARDARGRALSVRTVRALPPGPDADLEARGPLSALDLLPLAPGVVLRPAH +ADPEADAATAEAAAALFPGAEQVPFPGPPLLRLLGTLSDLVLPQPPGARTRRPSPAPAHP +EGPRAAP +>MHAAABBN_01628 +MAAVDPAPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA +AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG +LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT +PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP +EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAAYDPAERGPRSLLDTLPLGAAVLRP +AFEDAAGEEAAAAACAALHPGLPQLSFPAPPLLRLAGALNDLVLLQPRP +>LFPAFLNI_01851 +MAAADPVPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA +AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG +LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVTDGEGTAVVAADPVLDGRINGAWT +PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP +EHPYAAAALRFLQGADDAAGRPLRVRTVTGAVQPAEYDPAERGPRSLLDTLPLGAAVLRP +AFEDAAGEEAAAAACAALHPGLAQLSFPAPPLLRLAGALNDLVLLQPRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000606.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000606.fa new file mode 100644 index 0000000000000000000000000000000000000000..97ea46df903214a785b3ddfe90f7258daf03d9bd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000606.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00928 +MHLIPRTLWVLARARRRPPLSIWDSASLPMRALPTDVDIAGHVNNGQYFGLFDLGRFDLM +ARSGLMRAVRRRGWLPVVQAEQIAFRRSVTLGTAFTLETRIIGLDERAVWFEQRVVVAGD +VAVRGYVCTRLRGRDGTPVGNDEVRALAVELGHDPAAEPELPGWLHDWREQVALPSARTP +LPHAWGR +>MOLHKGIG_01930 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG +>NAFOICDF_00862 +MLHLLPRTALVVVRARRRPRLGIWEASTLPLRALPTDVDFAGHINNGQYFGLFDLGRFDL +MVRAGVWDGAKRRGWLPVVQAEQIAFRRSVTLGTRFTVESRIIGLDERAVWFEQRAVVDG +DVAVRAFICTRLRAKDGTPVSNEDVRDLARELGHDLAAEPVLPEWLHGWRSDIALPSART +PLPHAWGTPAPAGV +>MHAAABBN_01626 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG +>LFPAFLNI_01849 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRHWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000607.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000607.fa new file mode 100644 index 0000000000000000000000000000000000000000..11bb142c290c928ea9296b08f14eb28cd4e16873 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000607.fa @@ -0,0 +1,62 @@ +>ACLBLIBL_00930 +MNNRLLIVATLSLGALVVVLVAAIGNGAWWVLAAIVVGLLILAVRDMTQKRHAILRNFPV +LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSLVYARSKGLDSHKAFGTERDTSEIG +YEFLLHSSAPVNAPAEAPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVQAMNKGAGL +GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNGDGTFSAEKFAAKAALPEVKGITI +KMSQGAKPGLGGMLPKEKITAEIAEAREIPMDQDCLSPASHSAFRTPREMVRFIGHLREL +SDGKPVGIKFCVGSRVDVLAMCKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT +EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ +KCHTNECPVGVATQDPRLMRALDVTDKSNRVFNYHRLTVREAVQIMASMGVTHPSQLNTR +MLRRRVDHLATRSYASIYHWLRTDELLNDPPAGWAMDWDEADGDHFGEHARVDYLTERDP +EWRSELLIPGRQEQGAPVQGSPASGAGSRVAVGDSRDTAPVTTSPLPRVSTLAEGETLYS +RSTRSHDPAREQAGVTQRVDTDGNDGLSPHAGEDPERQDGEEVTQRGTTGRVDAEPRGEG +RVG +>MOLHKGIG_01929 +MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV +LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG +YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL +GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI +KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL +SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT +EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ +KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR +MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP +QWRSELLIPGREAAGAPVQGSPISGTGSTLVDARRTESVPLTTSPMPRVSSLGEGESLCT +PGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTRRGTTGRVEGEHRGE +GRVG +>NAFOICDF_01592 +MNSKTLAAAAAALGVAGVAVRDLTQKQHALRHNFPVLARARWALETIGPELRQYIVAANN +EERPFSRDQRRWVYTSSKGKNNYYGFGTDNDVEHTSYAVVKHRTFSDVAPMSALALDPGK +ALPSAKVLGGPRGRRHAFRPNSVVNVSAMSFGSLSPQAITALNKGAALGGFMHNTGEGGL +SDHHRQGGDLMLQIGTGYFGCRDAHGNFDMEKLAAVVESAPVRALEIKLSQGAKPGLGGH +LPGAKVNAEIARIRGVEEGKDVASPSRHSEFSTVDEMLDFVERVAERTGLPVGIKSAVGD +LGFWHELADAMADGTRGVDFITIDGGEGGTGAAPLIFSDSVAFPFRVAFTEVYRIFAARG +LTDRVTWIGSGKLGLPDNALVAFALGVDMVNVAREAMLAIGCIQAQKCHLDTCPAGVATQ +NPWLAAGLDPQEKSQRLVGYVQTLRRDLIKVSEAAGVPHPALLSPDDVALVEQTRSQTPL +REIYGYERGWGVPGEEIRAEITRIMVDEDSSRADEDHLVQHEPLPQDDVDTTH +>MHAAABBN_01625 +MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV +LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG +YEFLLHSTAPVNPPEEPPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVVAMNKGAGL +GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI +KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL +SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT +EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVRRLIQGADFTMSARAMMMATGCIQAQ +KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR +MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP +EWRSELLIPGREAGGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP +HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE +GRVG +>LFPAFLNI_01848 +MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV +LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG +YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL +GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKALLPEVKGITI +KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL +SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT +EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ +KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR +MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP +QWRSELLIPGRAAAGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP +HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE +GRVG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000608.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000608.fa new file mode 100644 index 0000000000000000000000000000000000000000..34aca4425b4b02f17437f11e5f60db35030e7432 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000608.fa @@ -0,0 +1,42 @@ +>ACLBLIBL_00931 +MTPPSSAPAAARSGPSTALLWVLLAAMGAGPLFNYGISASSTVIIERLGVTSGQLGTVMT +AVFAAAAVTSLGLGRAADRLSSRAQMSIIFGGTAVALVMGAFAPSLPVLYAAAAVAGVTQ +AISNPTTNRIIRTVVPPERRIGWIGVKQSGVQAAQLFGGLFFPAASLALGWTGAALVVAV +LACVLWGFALWAAPPLPGTAPTADPDAGRASAPDVDRASAPDAGPAAARARRRDGRRRRG +TTALPASVWFFAAIAFLTGLGMQATNMYLPLFAVESLDLTLVAGGAAAAVSGVIGVFSRI +WWSRRMAVGARPTTLLAAICLGALAGVVVLLAADLAHLPALLWVGAAVHGLTVLGANVVT +NAGLMSEVPAESLGRASGANAMGMYAGFALGPLVMGVLRDLTGDYRAGFAAVGLGYILAF +LVVLLLRRHVGRRAADPRAEAA +>MOLHKGIG_01928 +MTLPAPAARRPSAALLWVLLAAMGAGPLFTYGVSASSTVVMERLDVTSGQLGTVMTVVFA +AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAVAPSLPVLYAAAAVAGVTQAISN +PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA +LWVLALVAAPPLPGAPPSATGPAGGRRRRDTSPLPATVWFSAAIAFLTGLGMQATNTYLP +LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGVVVF +LAADLLDLPALLWVGAAVHGLTVLGANVVVNAGLLSEVPAERLGRATGANSMGMYAGFAL +GPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGAA +>NAFOICDF_00863 +MGDAGAGRRLTGSSGGPAAPGGPTLGAVTASPPSRPADRAPGTLLLWTLLAAMGAGPVFN +YAVSTSSTVIIERLGVTSGQLGTVMTVVFAAAAVTSVGLGRAADRLSSRTQMAIIFFGSA +LALAVGGFAGSLWALYGAAVLAGVTQTISNPTTNRIIRTSVPAERRIGWIGVKQSGVQAS +QLFAGLFFPVAALGLGWTGASLVAAALVGLLGVVALRAAPPLPGAPAAPPTTTPDAGRPR +AGRARAPLPATVWFFAGIAFLTGFGMQATNMYLPLFAVESLDQTLVIGGAAAATSGVIGV +FSRIWWSRRMAAGHRPTTLLAGIALGAVVGVVVFLGADLLHAPALLWVGAAVHGLTVLGT +NVVTNAGLMDAVPAHHLGRASGVNAMGMYAGFACGPLVMGLMRDLTGDFRAGFLAVGVFY +LLALAVVGLLRRHTDRQGAPRAA +>MHAAABBN_01624 +MTLPAPAARRPSAALLWVLLAAMGAGPLFNYGVSASSTVVMERLDVTSGQLGTVMTVVFA +AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAVAPSLPVLYAAAAVAGVTQAISN +PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA +LWVLALVAAPPLPGAPPPATGPVGGRRRRDTSPLPATVWFFAAIAFLTGLGMQATNTYLP +LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLAVICLGAVAGVAVF +LAADLLDLPALLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAGFAL +GPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGAA +>LFPAFLNI_01847 +MTPPAPAARRPSAALLWVLLAAMGAGPLFNYGVSASSTVVMERLDVTSGQLGTVMTVVFA +AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAAAPSLPVLYAAAAVAGVTQAISN +PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA +LWVLALVAAPPLPGAPPPATGPVGGRRRRDTSPLPATVWFFAAIAFLTGLGMQATNTYLP +LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGVVVF +LAADLLDLPVLLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAGFAL +GPLLMGVLRDVTGDYRAGFAVVAAGYLLALGVVLLLRRHVGRRGAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000609.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000609.fa new file mode 100644 index 0000000000000000000000000000000000000000..df776f7e03f06868941c8bffb8b1b3a88d938593 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000609.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00934 +MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGSGFKELQENDRVEFETQDGPKGLQ +AANVTKI +>MOLHKGIG_01927 +MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGNGFKELQENDRVEFETQDGPKGLQ +AANVTKL +>NAFOICDF_00865 +MAVGTVKWFNSEKGYGFIAPEDGSADVFVHFSAIQGNGFKELQENDRVEFETQQGPKGLQ +AADVTKL +>MHAAABBN_01623 +MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ +AANVTKL +>LFPAFLNI_01846 +MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ +AANVTKL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000611.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000611.fa new file mode 100644 index 0000000000000000000000000000000000000000..dba57fc3c124b296ae857e844e51aad1672b7834 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000611.fa @@ -0,0 +1,17 @@ +>ACLBLIBL_00936 +MPHRRRRPCVPVALSVAAALGLSLSACASTTTAGVGSQSPAPSSAAGAASSAAGTSSAAP +TTSAALTTSGTAAEIAGDEAAAQAQDDAATRTALNRAVAEDGIPYAELDPSLTPVPDGAS +ILWEGLAVGAQSLRVDARAGEEYTVVLLCAEQDGSRRSLVMATVPGEDFSDVMAESPGCG +HWSAGLPAREADGPLTLTGVVPDGGPFRMVVYRSEG +>MOLHKGIG_01924 +MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE +ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA +>NAFOICDF_00868 +MTLEEYTRQNPDSDYLHPETESVLQEKVGTGTQQITVDAQEGAVLRVILLCPSDATGKTD +IHTSRGAEGEKTWMAGSEALCGGWSAATPPVEKAGPMTFSATVDNDKPFRMVLTAPAA +>MHAAABBN_01620 +MTLVEYTRQHPDADYLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVMCPSDATGETE +ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA +>LFPAFLNI_01844 +MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE +ILTSRSGGGTKTWMAGSEALCGGWSAATPPPVDEAGPMTFTATVDNDKPFRMVLTAPSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000612.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000612.fa new file mode 100644 index 0000000000000000000000000000000000000000..3901ccfb2448faddcc3a24a145d55b8fff396549 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000612.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00937 +MSGSVRVSGAVRVDAWLWAVRVYKTRSAATAAVRGGHVRVNDEPVKAAHTLAVGDRVRVR +KDQRERILEVTGLIGTRVGAPVAVTNYIDHSPPPIPRELLAVPHRERGAGRPTKRDRRKL +DELRGRASDERS +>MOLHKGIG_01923 +MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI +LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD +RR +>NAFOICDF_00872 +MGAVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI +LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRA +STGRG +>MHAAABBN_01619 +MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI +LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD +RR +>LFPAFLNI_01843 +MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI +LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD +RR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000613.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000613.fa new file mode 100644 index 0000000000000000000000000000000000000000..5c33e22168feccac4809a33cf838632f993ec003 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000613.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00938 +MEADRPRGPGPAAAVVVPRRCTPTPAPPTSLEDPVLSVTDLRQIDTAAADLSRIIPRADV +DVASTVPVVAPILEQVRTGGEAALLELAERFDGVRPPALRVPAEALAAALEGLDADVRAA +LEESIRRARLVHAAQLPQDSTVELGEGASVQNHWIPVDRVGLYVPGGRAVYPSSVVMNVV +PAQAAGVGSLAVTSPPQADHGGLPHPTVLAACALLGVDEVYAAGGAQAVAMLAHGVRDER +GGWLCAPVDMVTGPGNVYVAAAKRALQGIIGVDAEAGPSEIAVIADGTARADWVAADLIS +QSEHDPLAASVLITDSEDLVRDVLAAIEAQVPGSFHEEQIRVALTGPQSGVLLVRDLDQA +VEVSDRYATEHLEIQTRDPEAVAARIRNAGAVFVGPHAPVPLGDYSAGSNHVLPTSGTAR +HSSGLSTVTFLRLQQRIRYTETGLKELAEGISVLAEDERLPAHGVAVRARFA +>MOLHKGIG_01922 +MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV +RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW +IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL +LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA +EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA +FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV +GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL +AEDERLPAHGAAIRARFA +>NAFOICDF_00873 +MEADRTALDPQEEPVLSVTDLRELDTAAADLSAIVPRAEVDVAYTVPVVAPIIEQVRTGS +EQTLLDLAERFDGVRPPALRVPAEALTAALEGLDPAVRAALEESIARARKVHAAQVPSGS +TVELGEGAVVENRWVPVERVGLYVPGGRAVYPSSVVMNVVPAQAAGVESLVVTSPPQRDH +GGLPHPTVLAACALLGVDEVYAAGGAQAVAMLALGVRADDGDGWLCAPVRMVTGPGNVYV +AAAKRALQGVIGTDAEAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSADL +LRDVLASVEAQVPGSFHEEQIRVALTGPQSGVLLVRDMEQALEVSDLYATEHLEIHTRDA +DALAARVRNAGAVFVGPYSPVPLGDYSAGSNHVLPTSGTARFSSGLNTVTFLRSQQLIRY +GEAGLKALADGISALAEDERLPAHGVAVRARFA +>MHAAABBN_01618 +MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVVAPIIEQVRHGGEQTLLDLAERFDGV +RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW +IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL +LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA +EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA +FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEDLVGRIRNAGAVFV +GPHAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL +AEDERLPAHGAAIRARFA +>LFPAFLNI_01842 +MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV +RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW +IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL +LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA +EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA +FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV +GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL +AEDERLPAHGAAIRARFA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000614.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000614.fa new file mode 100644 index 0000000000000000000000000000000000000000..4500d40d30ce90f9c78307291677bafe5e7ccb27 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000614.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00940 +MTILVGYAPSTSADAALDTALDIARSTGERVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVDAEFRQYARGRSTVQEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYTQYGDRTPEAVSHVAETDPATRGLPASEPMLEQHPLTPVKDQDPTRRG +>MOLHKGIG_01920 +MTILVGYAPSKAADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPAAHGLPASEPMAERRRLTPVDSGDPTLER +>NAFOICDF_00875 +MTILVAYKPSETAKAALSTALDVARQTGEHVVVVNAGPGGEHRSPSLVTEAQQQEVQRLL +DDSGVSAEFRQYARGRSTADELKSVADELDPSIVVVGLRRRGGFGRFVMGSVSDELLQVI +DQPVLAVKEYRGRTPDAVSSVAETDPATHGMPSAEPGHAPRPFTGEHAADDGR +>MHAAABBN_01616 +MTILVGYAPSKAADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELGPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPAAHGLPASEPMAERRRLTPVDSGDPTLER +>LFPAFLNI_01840 +MTILVGYAPSKSADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPATHGLPASEPMAERRRLTPVDPGDPTLER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000615.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000615.fa new file mode 100644 index 0000000000000000000000000000000000000000..41e5ec1bf4aa15e5733b92eb6233f1151ca30b36 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000615.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00941 +MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDAAAHL +ERVRAAAEGRRIALILVTHRHADHTGGVDAFHTATGAPVRAADPDWCRGGAAVLTPDERI +DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS +LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLAQVSAALAELGEDEAATVTPEQ +LAPRIYPGLEGTVARVAVQTVAAHLRHLREG +>MOLHKGIG_01919 +MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL +ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI +DAAGTPMLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS +LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED +LAPRIYPGLTGTVARVAVQTVAAHLRHLRED +>NAFOICDF_00876 +MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVLFADDADAAVVLDPGPAEDAEGHL +ERVRQAAEGRRIELVLVSHRHADHTGGIDAFHAGTGAPVRAADPSHCRGGGLPLTPDEEI +VRAGVRILAWHTPGHTSDSYSFAVPESGPHGAVLTGDTILGAGTTMLDHPDGTLTDYLAS +LARLQAAGPLTVLPAHGPVPAPLDVIARDYIDHREGRLFQLRRALDGMDPARAAMVTPSE +LVGVIYPEVTGQVARVAEQVLAAHLAYLRRG +>MHAAABBN_01615 +MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL +ERVRAATEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI +DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS +LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED +LAPRIYPGLTGTVARVAVQTVAAHLRHLREG +>LFPAFLNI_01839 +MTTTTATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL +ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI +DAAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS +LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED +LAPRIYPGLTGTVARVAVQTVAAHLRHLREG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000616.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000616.fa new file mode 100644 index 0000000000000000000000000000000000000000..2fe92f960661d94604e58c4675299028ed6c5015 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000616.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00942 +MENQQTGQAADRGTIDTREGLKGNYVQSGAEFTRDTNYITDRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRAIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERLQENYFARFPDYPRGITVPAVVDVPTGDVVTNDYPQMTLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIKRVFTEVNNGVYRCGFAGSQEAYDAAYDR +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGEEVEPAHTPLR +>MOLHKGIG_01918 +MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEEGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMSALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR +>NAFOICDF_00877 +MEDQQTGQAADRGTIDTREALTGNYVQSGAEFTRDTDYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDAGGKDPVLGTERLQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWAAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPDLSGWTTEHGRADLGGDPW +GGGTAPGPVRDDERVDPEHTPLR +>MHAAABBN_01614 +MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLSTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR +>LFPAFLNI_01838 +MENQQTGQAADRGTIDSREGLKGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG +YARDLFQTPGFGDTIDFVQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000617.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000617.fa new file mode 100644 index 0000000000000000000000000000000000000000..872e71106069267eda3878db53e1eb21e052c305 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000617.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00943 +MNESTAPSEPTVRDDVAASSGHDRPEPHAGGGLHERLNWLRAGVLGANDGIVSVAATVVG +VAGATTAVAPVAIAGVAAVVGGAVSMALGEYVSVSSSSDSQKALIAKERRELAEDPEGEL +EELVGLYEAEGLSRATAENVARELTEKDALKAHLRAELGMDETGVVSPWSAAGASFVAFL +LGALLPFLTIILAPVDIRVALTFVTTLVALAGTGYAGAWLGGAPPVRAMLRVVIGGALAL +ALTFAVGAWLGTTVA +>MOLHKGIG_01911 +MSHTSEQSSPLADQVPPGGPDEPHAAEGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA +TTALTPVLLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV +QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLSFLVGAL +LPFLTVVLAPVDFRIPLTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTL +AVGSLLGASVA +>NAFOICDF_00884 +MSHSTAPAAPSSYPDEPHAQTGVHARLNWLRAGVLGANDGIVSVAATVVGVAGATTAVTP +VLLAGTAAVVGGAVSMALGEYVSVSSSSDSQKAMIAKERRELAEDPEGELEELVGLYEAE +GLSRDTAEQVARELTANDPVTAHLRMELGMAEEDVVSPLAAAGASFIAFLVGALLPFLAI +LLSPVGVRVPVTFGVTLVALAVTGYLGAWLGNAPAVRAMVRVVVGGALALALTFGVGTWL +GVGVA +>MHAAABBN_01607 +MSHTSEQSSPLADQLPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA +TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV +QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL +LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF +AVGSLLGASVA +>LFPAFLNI_01831 +MSHTSEQSSPLTDQVPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA +TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV +QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL +LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF +AVGSLLGASVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000619.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000619.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a7ba484335fb530b2b7ee7fb0820ca392cb6d1a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000619.fa @@ -0,0 +1,10 @@ +>ACLBLIBL_00949 +MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>MOLHKGIG_01909 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>NAFOICDF_00889 +MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>MHAAABBN_01605 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>LFPAFLNI_01829 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000620.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000620.fa new file mode 100644 index 0000000000000000000000000000000000000000..cdd679f441f5c50d53238a08ea792a742c6b29d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000620.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00950 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>MOLHKGIG_01908 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>NAFOICDF_00890 +MAKKSKIAKNEQRKVMVARNAEKRLELKKTLIDPNASDEAREAARVGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFREMAHRGELPGVTKSSW +>MHAAABBN_01604 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>LFPAFLNI_01828 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000621.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000621.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5bf3d9e78ed5c0e00fdde3f5f5da5607bf4c827 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000621.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00951 +MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWMAVERTERKER +TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE +>MOLHKGIG_01907 +MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER +TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE +>NAFOICDF_00891 +MAMNRKELVAAVAERSGNTQAAVSDVLDALFEAFTAQVKKGEKVSIPGWLAVERTERKER +TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE +>MHAAABBN_01603 +MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER +TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE +>LFPAFLNI_01827 +MNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKERTG +RNPRTGEEITIPAGHSVKVTAGSKLKAAASE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000625.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000625.fa new file mode 100644 index 0000000000000000000000000000000000000000..a9ef9d083fd7ab157494804d47970407c95a1dd3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000625.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_00955 +MGGGLLGTALGYGAGHASAAPAAPAASGAAGAGASPSEVMGDTGIEGEVGRAGWAEPGGQ +SARVAVSSPVGTDTVPFHGPRQAGVDTPAQAHAVFLAFDLLPDTDRLGIERMLRLLTDDA +ARLTQGRATIADTEPELAAAPARLTVTFGFGPELLARVAPDRAPAWLRPLPAFPQIDRLD +PAFGDGDLLLQICGDDRMSVAHARRMLIKAARPFAAERWAQEGFRASRGAHPTGTTMRNL +FGQVDGTANPAAQTPHLDRVVWGVGAEQVGITPWIQDGTSLVVRRIEMLLDTWDELDRPG +KERVIGRTLGTGAPLTGEQEHDEPDFVALGPAGFPVIPDISHLRRARMDVPEYGMLRRGY +NYDDPRGAIESGAGLIFAAYQADVDRQFVPVQERLAESDHLNLWTVPVGSAVFAIPPGCA +EGGFVGDVLFA +>MOLHKGIG_01903 +MPTTDPAVRPDDHHGSGGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS +TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR +QAGVDTPAQAHAVFLALDLREDADRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP +ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA +HTRRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV +WGVGAEQVGVTPWIPDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH +DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ +ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA +>NAFOICDF_00895 +MPTTDPSRRGVLFGLGAVGGGLLGGAVGYGAGAAQATPAPGGAPSGVDASPSGVMEDTGL +EGEVGRAGWAEPGGEASRVAVSSPVGTDTVPFHGPRQAGVDTPAQTHAMLVALDLLPETD +RAGVRALLRLLSDDAARLTQGRATLADTEPELAAAPARLTVTFGFGPELLARVAPERAPA +WLKPLPAFPTIDALEDRWSGGDLLLQICGDDRISVAHARRMLGKVARPFAEVRWVQEGFR +AARGTHPTGTTMRNLFGQVDGTANPQGGSPALERIVWGAGQEAADLGIAPWIPDGTSLVV +RRIDMLMDTWDELDRPAKEKVIGRTLGTGAPLTGELETDAPDLEAIGPTGFPVIPDTAHL +RRARGPEPEYGMLRRGYNYDDGAGASGTGAGLIFAAFQADVDRQYIPVQERLAASDHLNL +WTRPVGSAVFAIPPGCAEGGFVGDVLFA +>MHAAABBN_01599 +MPTTDPVVRSDDHHGPDDHHGPDGREGARPTPGGPSRRGLLLGAGAVGGGLLGTALGYGA +GHASASTAPGASAASGTGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTV +PFHGPRQAGVDTPAQAHAVFLAFDLHEDTDRVRIERMLRLLTDDAARLTQGRATIADTEP +ELAAAPARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGD +DRMSVAHARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTP +HLDRVVWGVGAEQVGVTPWIADGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPL +TGEQEHDEPDFDAVGPAGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGL +IFAAYQADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA +>LFPAFLNI_01823 +MPTTDPAVRPDDHHGPDGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS +TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR +QAGVDTPAQAHAVFLAFDLHEDTGRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP +ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA +HARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV +WGVGAEQVGVTPWITDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH +DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ +ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCTEGGFVGDALFA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000626.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000626.fa new file mode 100644 index 0000000000000000000000000000000000000000..f68deb82bc7ee1119015dd5909fac1c21d9893e3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000626.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_00956 +MLVAAAGAGALAVAAWLTGITAVRELSDPGWITRWGVPAGELVSNLAMTMAIAAIIFAAG +ILPPHAAGTERWHRSAAQRRADAQEGPLPEHPAFTRTLRVAAVSAGVWTVAALAVGILSY +SDLAGIPVTAGEGFTAGLVAYVAGISVGQAWFWVTVIAAVVTTLVIAVRSHNGLFWTGIL +AMIGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVWVGGLLVLVAISDTLVGPDGAQGR +ARAPREQGPTPLLHTALSRYSVLAGLGLVTVALSGVVNASIRMDDPAQLTSPYGMLVVIK +FLATLGLGLVGLMHRRWVIPRLDAGPDRPSPAPARRLLWQLIAVEAVVMAAVMGLSAVLS +RTAPPVPEELAPDATPARILTGYELPPELTGARWITEWRLDWLWVAIIAFLALWYLRSVW +RLHRRGDRWPVLRTLSWMVGLAVLLWATSGSPAVYGRVLFSSHMMGHMTLTMISPLFLVL +GAPITLALRALPSRTDGSRGPREWILWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFF +RFSLETHVGHEFMNVHFLLTGFLFALVMVGSDPLPSRPAYPLRLVLLLATMVFHAFIGVA +MTGSAGLIQASWFGNMGRDWGPSALEDQHIGGAVMWGIGEFPTVVMAVMVAVLWYRNDRR +NAERLDRRADRDGDAELHRWNEMYARMHGTPAAPAEPAPAAASPADPTPAASAPRPRRPG +DPRWPLSTAHPPEDPAGPEDRAAPARWPRPPSSGCWR +>MOLHKGIG_01902 +MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ +LSDPGWITRWGVPVGELVSNVAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA +APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI +SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN +SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG +LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG +PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL +PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL +WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI +LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA +LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL +EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA +RMHGTPATDAPSGAEPAARDSSTGPEEARDVR +>NAFOICDF_00896 +MPTSTAVPPATAQHPLGVPRPVLLGAAVVGVLALVLAAWFAGVTAPRELSDPGALTRWGV +PVGKAVNNAAMAVTIGALIFAAGILPPHAAGTERWHRSPRQRAQDAEEGPRPEHPAFGRV +MAVAAAAAGVWTVAALAVGVLSYSDLAGIPVSAGGSFTDGLLAYTLDISVGRAWFWVTVI +AAVVTTLAIGVRSHTGLFWTGVLAMLGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVW +VGGLLVLALISDTLVGPNGAQGRGASLRRQGPAPLLHTVVSRYSVLAGLGLVTVALSGVV +NASIRMDDPAQLLSPYGTMVLTKAGAVLLLGGIGLLHRRWIIPRLDDDGAAESPPAARRL +LWQLIAVEAVVMAAVVGVSAVLARTAPPVPEELAPDATPARILTGYELPPELTGDRWFTM +WRWDWLWVAIIAFLAVWYVRAAWQLRRRGDRWPVLRTLSWLIGLAVLAWATSGAPAVYGM +VLFSAHMVGHMVLTMIVPLFLVLGAPITLALRALPARTDGTRGPREWILWIVHSPWGAFI +TNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFIFATVMVGADPLPSR +PPYPLRLVLLLATMVFHAFIGVAMTTSTGLLQASWFGSIGRDWGPDALTDQHIGGGIMWG +IGEFPTVLMAVTVAVLWARSDTKTAARLDRRADQDGDAELARWNQMYAAMNHPGADQDPA +RGDRP +>MHAAABBN_01598 +MSAATAPARGSHPTENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ +LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA +APLPEHPAFTRVMRIAAVGAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI +SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHNGAVN +SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG +LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG +PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL +PPALEGARWITMWRFDWLWVAIIAFLSLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL +WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI +LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLQTHVGHEFMNVHFLLTGFLFA +LVMIGSDPLPRRPPYALRLVLLMATMIFHAFIGVAMTTSTGLMQASWFGNMGRDWGPTAL +EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA +RMHGTPVTDAPSGAEPVARDSSTGPEEARDVR +>LFPAFLNI_01822 +MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWMLVAAAGAAGLAAAGWLTGVTAARQ +LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA +APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI +SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN +SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG +LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG +PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL +PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL +WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI +LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA +LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL +EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA +RMHGTPATDAPSGAEPAARDSSTGPEEARDVR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000627.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000627.fa new file mode 100644 index 0000000000000000000000000000000000000000..a55243f09a08f934c3c103b55b9dc726ea5638b5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000627.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00957 +MLALTGCGAGDEPAPEQPSAPADALHGDVGGAAPAPEEGAEGLGLGDRQDERMAAAAAER +AVGFGFVRQRAAAPEEIDAAREDSRARRSDADRTTVQPAACKAPLTALDFSPISLDEGEA +TRVDVGADTFTGTGTVEVARLTGSGRQEVERHLQTVNGLLADCREMTMTVQDGDASVDYR +LAVSEAPLSEGTPAQSALVWERSLASADGPQLTAQVLTAVTADAVVMVSFVGQPEAGRKE +FTLIAEEMLAAALAAG +>MOLHKGIG_01901 +MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA +VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD +RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH +IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL +TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD +>NAFOICDF_00897 +MSADRTRPRPAVRRLAVASSGAALAAVLLAGCASGGDAAASSGAQAAGPSSSAATGGLDL +GDRVDQRRAEAAAARAASFGFTRQDAVGADQIAAARGDAADRAADDGRTTVEPARCQAPL +AALDFSPILLDQEEVSRVDVGTDSFAGTGTVEVATLDGPGRQRVEEHLQTVNTLLADCRD +MTVTTRDADGARTYRLQMSAAGLSDGSPAQSGLVWTQTPAGRDEPATAAQILTAVGPEDV +VMVSFTGQPQAAERQFTVMAEEMLAAAGTVTR +>MHAAABBN_01597 +MSADRLPPLGRPAAPRRGRLRLAAAVAAGLLALTGCGAGDGDPAAASASADGVHGDAGTA +APTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD +RTTVQPAQCKAPLTALDFSPIALDEAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH +IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL +TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD +>LFPAFLNI_01821 +MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA +VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD +RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH +IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL +TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000629.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000629.fa new file mode 100644 index 0000000000000000000000000000000000000000..fe96be4aaae3ee30b88983a6a9ee067a933028f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000629.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00959 +MTTLIVTSSAHGSTREIAERVAEVLRTSQSVETVVEDVAGAAAWLATADAVIVAAPVYEG +SLAAEARHFLDSRRAELADKPLLFLASGGGYELDPKVREKLESYGPREIAFFRGALVEER +LGWLEKLKLKVSRNENYGDYRDWDAIEAWAKSLSGHGVR +>MOLHKGIG_01899 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG +SFAADARAFLDTRRAELTDLPLVILASGGAPELARPVREKLESYGPREVAYFRGALFEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLPGAGVR +>NAFOICDF_00899 +MTALIVTASRHGSTREIAERVAEVLRTTAQTDTVVEDVAGAAAWLDTADAVVVAAPVYGD +KLEKSAKAFLDSRRAELSQKSLVILYSGASPVPNRALADQLGTYGARDVKYLRGALVEER +LGALEKLQIKLVKGRYGDFRDWNAVEHWAKGLSAHGVN +>MHAAABBN_01595 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG +SLAADARAFLDTRRAELADLPLVILASGGAPELAPPVREKLESYGPREVAYFRGALVEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR +>LFPAFLNI_01819 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVKGAAAWLATADAVIVAAPVYTG +SLAADARAFLDTRRAELADLPLVILASGGAPELARPVREKLESYGPREVAYFRGALVEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000630.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000630.fa new file mode 100644 index 0000000000000000000000000000000000000000..71ade8649d67942b8cbda3a55234fa67750dfdf0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000630.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00962 +MTQVLSGFVVVWVIIAVGFLVGRSGVLGEDARTVLSRTAFYIGSPALLFVTLSGADVAAV +LGPQLWVATLSALAAAALFLAISIPVFKQRPASERIMAALSASMVNSANLGIPIAAYVLG +DAALAAPVLIFQLAIYTPLYVAAMDVATTSEARARAAGGRPAVRRSRGQALAAQLRQTGT +NPMILGSAAGLLFSLNDWTLPGPLMQSVELIGGLSIPAMLLAFGMSLVGSRPLERAGGRR +ADVLLASGVKLLVHPLIAWVLAQFVLGLDAREVFVAVVLASLPTAQNVFVSAVRYDAGLR +VAKDTILITTIVAIPAMIAVALLLA +>MOLHKGIG_01896 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA +>NAFOICDF_00901 +MIEVLSGFSVVWVIILVGLLLGRTGVLGDEAREVLSRTAFFVGNPALLFVTLSRADVGAV +LGPQLWVACLSAFAAAVVFLGLSIPLLKGRPASERVMSGLSASLVNSANLGIPIATYVLG +DAALAAPALIFQLAIYTPVYVAVMDWATTHEAAARASSAGAAHDAGAPAPRTVRPRNPVL +AQLRQTATNPMILGAFGGLLLSFTGWTLPGPLMTSVELIGGLSIPAMLIAFGMSLAGSRP +LARDSGRRADVLLASAVKLVVHPLVAWMIAQFVFGLDARRVFVAVVLASLPTAQNVYVSA +VRYRAGETVSKDTILVTTIVAIPAMIAVALLLA +>MHAAABBN_01592 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREVRRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLPGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA +>LFPAFLNI_01816 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000633.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000633.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7ccb4fe7ec537f3bb64026d2c205c5ab5762e7e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000633.fa @@ -0,0 +1,95 @@ +>ACLBLIBL_00969 +MLVTLSALFVVALAAPAVFRWTGRQGFYLLAAVPAAGFVWLLTQLPHVFALQEALDAGRP +IPASAAHLDRSVPWVPYLDIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA +VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT +TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ +APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV +LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV +GIIDHEAGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLASLAAHGA +AHGGVWAWTPLVVMALGSVLTFAYTWRFLWGSFAVKRDEEGAPVPATRFRTRVTTLELAP +AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL +GALLALARRPFEALQERTESPLDAARGYRRLTGYVDETAVWVTGRTQTGSLRRYLGIILA +TAFLLPAAFLLFPVGRAERPLATSFLAADLIWFETPAQLLIVAIIAVATVFAVRARRRFK +AIMLVSVTGYGAAALFALRGAPDLAITQVLVETIILVTLILGLRVLPPDWHDRRTGSRRL +GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGANAVNVTLVDIRAWDTW +GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGAFGADSALGSRELSVVRSFAVD +DREGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL +ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL +FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAGRRRHPRMP +TPSTPDAPEAAR +>MOLHKGIG_01889 +MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP +VPASAARLDRAVPWVPYLETELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA +VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT +TFGGLAMLAGLIMLAHFAGSWRISGVLEAAPALMADAGLRGLLEVAVALVLIGALTKSAQ +APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHGLAMWQVLVIGVGLWTLL +LGGWRALRQTDIKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMVV +GIIDHEAGTRDLRQLSGIGRRHPALAAVAVVAGLSMAGLPPLFGFVAKESVLEGLAAHGV +AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP +AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL +GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA +TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK +AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL +GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW +GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD +DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL +ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL +FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP +TPSTPSTQEAAR +>NAFOICDF_00907 +MTVLLTALFAVALLAPVLFRRTGRRGFHLLAAAPAAGFVWVLAQLPQVFVLQDALDRGAP +VPASAAHLDTTVEWIPYLDIALSFRLDALSAFMSLIVLGVGALVLSYCASYFREHEPRHA +VFGAELLAFAGAMFGLVTTDDVMVLYTFWEITSVLSFLLIGYSGQRIFARRSAIQALIVT +TFGGLAMLAGLVMLAVQAGSWRVSGILAAAPELMERAPRGLLEAAVALVLVGALSKSAQV +PFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPGFASLASWQVLVLGVGLWTLIL +GGWRALRQTDVKLVIAYGTVSQLGFLMVANGLGTRDAALAGLAMLLAHAVFKAPLFMVVG +IIDHEAGTRDLRRLSGIGRREPALAAVAIVAAASMAGLPPLFGFVAKESVLESLAGHGEH +AGTVWGWTPLVGMALGSVLTFAYTWRFLWGAFATKDGRDSPDGEPVPETRFHSRLTAEDL +LPPGLLALACLVLGLAPGLPEALISAHTAGLAPLDAAEEPAHLALWHGITPILGVSVAIW +VLGAALAVARRPLQRLQARVAFPVEAAAVYQRITGAVDAAAVWVTGRTQTGSLRRYLFII +LATATALPALTMLVPAGEEDRVLATAFLEADLVPFTTPAQLGIAALVCVAAVLAVRARRR +FMAIMLVSVTGYGSAALFALRGAPDLAVTQVLVESIVLITVILGLRVLPPDWHSKTTGRR +RVPRLLLGVGFALVMMWVAATALGARTAERISLDMPRLAYEHGYGANAVNVTLVDLRAWD +TWGEITVLAVAATGVASLVFLEHRDKRRRDLDTVVPGSVGNYGAESALGTRELSVVRSFA +VDDRNDQWLIAGHTMAPERRSIILEVVTRFLFPAMMLLSVYLLLAGHNTPGGGFAGGLLA +GLALALRYLAGGRYELQEASRIPAGTLLGLGLGIATLTGLAPLLFGGQVLQSYKVEFHDL +WLFGDSLKIVSATAFDVGVYLVVVGLSIDVLRSLGAEIDRRGDEWQDARRRAARRRASPR +PARPRPRPVPEGRAPAARAIPAHAARHRSEEDPR +>MHAAABBN_01585 +MLVILTALFVVALAAPVIFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP +VPASAAHLDRAVPWVPYLEIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA +VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT +TFGGLAMLAGLIMLAHFAGSWRISGVLAAAPGLLADDGGRVLLEVAVGLVLIGALTKSAQ +APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPAFHELATWQVLVLGLGLWTLL +LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGVRDAALAGLAMLLAHALFKAPLFMVV +GIIDHEAGTRDLRELSGIGRRHPALAAVAVAAGLSMAGLPPLFGFVAKESVLEGLAAHGV +AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP +AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL +GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA +TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK +AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRI +ARMAVAGGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW +GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD +DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL +ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL +FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP +TPSTPDAPEAAR +>LFPAFLNI_01809 +MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP +VPASAARLDRAVPWVPYLEIELAFRMDMLAAFMSLIVLGVGALVLAYCARYFREHEPRNA +VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT +TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ +APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV +LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV +GIIDHETGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLESLAAHGA +AHGGVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP +AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL +GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA +TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK +AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL +GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW +GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD +DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL +ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL +FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP +TPSTPDAPEAAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000634.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000634.fa new file mode 100644 index 0000000000000000000000000000000000000000..2d0baef05ed5c9d7ed061384762e4517d7a43204 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000634.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_00970 +MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV +RGRDPHEYADTLPQALILTAIVIGFAVTAFLTAMIYRSWLISREDEVEVDAEDVKIASQG +AWDAEDDSELVEEHSEFMDASTDPNAHYEHTTEARPQVQHVIPAPPTAAGSREAARGRRP +EGGERA +>MOLHKGIG_01888 +MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV +RGRDPHEYADTLPQALILTAIVIGFAVIAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP +AWDAEDDAELVEESSEFLDDAADPNAHYEHATESRPHVRHASPTPPAHPGPASAVRAHRA +DGGPRP +>NAFOICDF_00908 +MTPTVDLALLAVMGVLFATGIYLLLERSLTRILVGVMLINNAAVVLLFLTSGGAGLAPLY +DADTAPEDYADMLPQALILTAIVIGFATTAFLTAMIYRSWQLRREDDVATDVEDVKIAAQ +SGWDAEDDSVLTEEDSEFMDDASDPNAEYEFATAAAPRARAVRPGRATVQGGGGRP +>MHAAABBN_01584 +MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV +RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP +AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP +EGGERA +>LFPAFLNI_01808 +MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV +RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP +AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP +EGGERA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000635.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000635.fa new file mode 100644 index 0000000000000000000000000000000000000000..b73ad5bf9d201c86fb946d836391e97568e0b997 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000635.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_00971 +MSIGSVPMTDLAPLAVMMPVLGAAVTFMLVRRPRAQVVVTVAALVLTLLLNCLLLAAVWE +GGVASVHVGGWPAPLGITLVVDRLSALMLVVSALITLAVLLYASAQGMVNRDEGGPVSIF +HPTFLILVAGVFNAFLAGDLFNLYVGFEILLTASYVLLTMGGTAQRIRAGITYVVVSVIS +SVVFLIAIAMVYAATGTVNMADLAVKLGELPSDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA +QTDIKRILSFILVSHIGYMIFGLGLATQMGLAATVFYVGHHITVQTALFLVTGLIENRAG +TANIDRLGSLAKVSPFISVLFLIPALNLGGIPPFSGFLGKVGLLRGGVEQGTGLSYTLVG +VSLLASLLTLLVVVRVWTRAFWRKVEDVEHPPAQLVAAYERTIDRGLRPRRLEPGLVLPT +AALVVMTLAFTVLAGPLFDLADAAATDMLDRTPYIASVLDEAAAERAAETLSHDPTEVHD +ARH +>MOLHKGIG_01887 +MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD +TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF +HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS +SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA +QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG +TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG +VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD +ARK +>NAFOICDF_00909 +MLGSTPLTDLAPLAVMLPVLGAAITFALVGRARAQVVVTVSALTLTLVLDCLLLADVWTG +GVAVVELAAWPAPVGITMVVDRLSALLLVVSSLITLAVLLYASAQGLINKDEGGPVSIFH +PTFLVLVAGVSNAFLAGDLFNLYVGFEILLTASYVLLTLGGTEARIRAGITYVVVSVISS +VLFLIAIAMIYAATGTVNMADLAVKLGELPHDLQLVLHVMLLAGFGIKAAVFPLSFWLPD +SYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPAEHVNGLLMGVAALTMLVGILGALAQ +SGLKRILSFILVSHIGYMVFGLALATQVGLAATVYYVGHHITVQTALFLVTGLIEQRAGT +ASIDRLGSLAKVSPLLGVLFLVPALNLGGIPPFSGFLGKVGLIRGGVEDGGVLAWVLVGV +SLLVSLLTLLVLVRAYTRAFWRKVEDVEHPTPQLVAAYERVTRRGLRPKPLSRGLVLPTA +GLVAMTLAFTVFAGPLYDLADRAAVDMLERSPYISAVLGPEAADRAAVTLSHDPSEVHDA +GR +>MHAAABBN_01583 +MSIGSVPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD +TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF +HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGITYVVVSVLS +SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA +QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTTLFLVTGLIENRAG +TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG +VSLLVSLLTLLVVVRVWTRAFWRRVEDLEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD +ARK +>LFPAFLNI_01807 +MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD +TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF +HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS +SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA +QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG +TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG +VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD +ARK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000636.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000636.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d74ca9f2bc7331f444c0df46245b6dfd766c923 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000636.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_00972 +MPGTDPARDAAGAERPARPHRVRDMVGQWPLIAVLVLLWCAVWEDYSLHVALAGLAFSLL +VMVLFPMPRIPFSGRLNPWWFLVFTAQFLGDVVRSSVEVSKVVLLRGRAARSSIVGVRLR +SHDDLVITLVSHALALVPGSIVLDVDRARSILYLHVLDATTDEDIEDFRAKALRVEAGII +KAVGTREDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT +>MOLHKGIG_01886 +MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF +PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL +IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT +REDLELVRRFPSSAPPAARPPKEEA +>NAFOICDF_00910 +MPAAETTSPASAPTRPAPGGVRSVLRQWPLLLALVLMWCAVWQDFSAHVALTGLLFSLLV +VVLFPMPPIPFGGRFHPGHALVFTGRFLADVVASSLSVTRVILTRGRTVRSSVVRVPLRS +HDDIVLTLVSHALALVPGSIVLDMDRANGVLYLHVLDATTDADVADYRAKALRVEADIIR +AVGTRADVAVLRDHPDSAPDPEGVEERRRHPAYRAELLPDTPGPVAPAPVDARPEPDAPG +GDR +>MHAAABBN_01582 +MPGSDSARRDVVRPDRVRGIVAQWPLILVMVAVWCALWQDFAPHVALAGLAFALLILGLF +PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVTGVVLLRGRRARGSIVGVPLRSHDDL +IITLVSHALVLVPGSIVLDVDRVRSVLYLHVLDATTDEDVEGFRAKALDVEAGIIRAVGT +REDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT +>LFPAFLNI_01806 +MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF +PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL +IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT +REDLELVRRFPSSAPPAARPPKEEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000637.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000637.fa new file mode 100644 index 0000000000000000000000000000000000000000..a433f43bcbee6a38ebc4ce515cb79ae1cc3e61ab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000637.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_00973 +MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAIATDVLLVVLSSGLILDMAVRRH +TDNVVLVVLAATVGFVGSVTVARFVEDRRPDHSMEDQARVPGTSDVPGGEEGR +>MOLHKGIG_01885 +MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT +HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR +>NAFOICDF_00911 +MSLPLTLAAWIGGAMLFVGAVGALYRIARGPSLLDRAAATDVLLVVLSGALLLDMGVHRR +TDTVVLVLLAAAVGFMGSVMVSRFVEDRRPEHPQEHEALVPGTSDVPAPREDA +>MHAAABBN_01581 +MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAAHRH +THHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR +>LFPAFLNI_01805 +MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT +HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000638.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000638.fa new file mode 100644 index 0000000000000000000000000000000000000000..209ba3741270103830e604e11a0870c046d708cd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000638.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_00974 +MTETATFLDWLSAALLVSGAFFTLVAGVGLLLLPDLLARMHASAKPQVLGLMLMLAGLAI +AWESWPWVPVLFLAWVTQMVTAPVASHLVGRTAYRTKHARRELLHRDELAAIARRVEPAP +ELDPRSPESRRRRRR +>MOLHKGIG_01884 +MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI +EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA +DPGPRRAGARPRGRR +>NAFOICDF_00912 +MDAAWTDWLAAALLVGGAFFSLVAGVGMTLLPDLLSRMHASAKPQVLGLLLMACGVAVLW +QAWAWVPVLVLAWVTQMITAPVASHLISRTGYRTKHVRRDLLHRDDLAAQAEPGPREDPD +AR +>MHAAABBN_01580 +MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLGI +VWRSWVWLPVLFLAWITQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVGRRAEPPA +DPGPRRAGARPRGRR +>LFPAFLNI_01804 +MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI +EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA +DPGPRRAGARPRGRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000642.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000642.fa new file mode 100644 index 0000000000000000000000000000000000000000..24205b5d42c12ec44b6b6d7cfdb7287a1573a8c3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000642.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_00979 +MSGPGPGRPVLIGVDGRSGAGKTVLADALAARLAPFARVAVLRIESMYPGWDGLAAAVDE +GGPYPAALRALHADGTAAWRAWDWHRGAPGEPTAIGPADVVVCEGVGALSVAARPLLDLA +VWLELETPARRSRALARDGETYAPHWERWAAHEEAYLARHGPRAAADLVVRLPSA +>MOLHKGIG_01880 +MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP +GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL +ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA +>NAFOICDF_00919 +MNASTEPGTARPGGPVSAPRPALIGLDGRSGAGKTTLAAALAARLAPHARVDVLHIEEMY +PGWDGLAAATADDGPYVRAVAALAAGRPAGWRAWDWHAGAPGEARALDPDALDVVVCEGV +GALCPGARPLLDLAVWVDAPEDVRRTAALARDGDAYAPHWERWARQEEAYLAAADPAGAA +DLRLST +>MHAAABBN_01576 +MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP +GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL +ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA +>LFPAFLNI_01800 +MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYQGWDGLAAAVGDDGPYP +AVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL +ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLVLRLPSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000643.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000643.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5a9880efba93fd9a7bb6b7c82129427906cd367 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000643.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_00983 +MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN +NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE +AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI +KEAGVKVSDIDHVVLVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSKEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVDKLLQDNADKLPEDVKT +EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG +DDEDIVDAEVVDEDDEKKA +>MOLHKGIG_01876 +MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN +NPERTFASVKRHMGTDWTAEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE +AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI +KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKGVNPDEVVAIGAAVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSKEDIDRMVKDAEAHADEDRKRREAADRRNQAEQSAYSVERLLQDNADKLPEDVKT +EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG +DDEDIVDAEVVDEDDEKKA +>NAFOICDF_00921 +MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGEVLVGEVAKRQAVN +NPDRTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATSGDNRLGGDDWDQRIVDWLLQQAKSKGADLSNDKIALQRLKE +AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFNDVI +KEAGVKVSDIDHVVLVGGSTRMPAVSELVKELTGGKEPNKGVNPDEVVAIGASVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSKEDIDRMVKDAESHAEEDKARREAAERRNQAEQSAYSVDKLLADNADKLPEDVTT +EVQADVDALKAALEKQDNDDEVKAAFEKLQASQVKIGEALYAQQSAEGAQPDAESGSAQA +DEDIVDAEVVEDEDEKKN +>MHAAABBN_01572 +MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN +NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE +AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFEDLTKDLLERTRKPFEDVI +KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVERLLQDNGDKLPEDVKT +EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG +DDEDIVDAEVVDEDDEKKA +>LFPAFLNI_01796 +MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN +NPERTFASIKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE +AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI +KEAGVKVSDIDHVILVGGSTRMPAVSELVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVEKLLQDNGDKLPEDVKT +EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG +DDEDIVDAEVVDEDDEKKA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000644.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000644.fa new file mode 100644 index 0000000000000000000000000000000000000000..ce538b0b9f7e10d9b41d599b8359dc314e92972c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000644.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00984 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALTQAER +ILDEAGAQAGTEAPQPAASDREAELETDLRRLQAEYVNYKRRVDRDRALAQDLGVLKAVT +ALLPVLDDLDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPSVHEAV +MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>MOLHKGIG_01875 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER +ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEYVNYKRRVDRDRDLARDAGVLKAVT +ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV +MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>NAFOICDF_00922 +MSENQNETPSPEEPVIRDRRRIDPETGQARTPGAGEDTVPAQEQGQAPQDSGDALSQAEQ +ILDEAGAAAEAEALPAAGSDREAELLEDLRRLQAEYVNYKRRVDRDRDVAKEQGVLKAVT +ALLPVLDDLDAARAAGDLEDGPFAAIAAKLMTALEGLGLEREDQEALAGVEFDPVRHEAV +MRQPHAEVPADHVVQVFRNGYARDGRVLRAAQVMVSAGQD +>MHAAABBN_01571 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER +ILDEAGAEAGTQAPQPAASDREAELETDLRRLQAEFVNYKRRVDRDRDLARDAGVLKAVT +ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTVLAGLGLERHDQAALAGVEFDPALHEAV +MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>LFPAFLNI_01795 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETDEPRVSAESAAEQAEDGDALAQAER +ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEFVNYKRRVDRDRDLARDAGVVKAVT +ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV +MRQPHAEVPADHVVQVFRNGYLRDGRVLRAAQVMVSAGDE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000645.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000645.fa new file mode 100644 index 0000000000000000000000000000000000000000..e67ae108b93400041ff88c81c74bcfaee5047cc1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000645.fa @@ -0,0 +1,32 @@ +>ACLBLIBL_00986 +MSLRAADGETIEVKIPKGIRDGQKVRARGKGAPGAAGRGDLLVTVHVREHEFFRRDGDDL +RITVPVTFPEAALGATIEVPTLERPVKMKVPAGSQSGRVLRLKGRGVERGTTKGDLLVEL +HVTVPTELNDDARAAVEALQSALAGDDPRRELARKAAW +>MOLHKGIG_01874 +MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARMYHPDQNPGDEAAEKKFKEISEAYA +VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRATQSEPDLSDL +FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG +ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF +PEAALGATIEVPTLERPVKVKVPAGSQCGRVLRLKGRGVERGKTTGDLLVELRVTVPTTL +NDDARAAVEALQSATAGDDPRRELARKAAW +>NAFOICDF_00923 +MASQDWLEKDFYQVLGVSKDASESDIKKAYRTLARKHHPDQNPGDAAAEQRFKEISEAYD +VLSDPKDRQEYDAIRSMGGGARFGAPGGFGGAGGGAGAGGFEDVFGGMFGGGGGSRTFRT +GGAQGGPDLSDLLGAFTGGGAGGFGGGQGFGGGGFGQPAPTKGADRTATTTISFRGAVEG +TTVSLRAADGETVDVRIPKGVKDGQKVRARGKGSPGTAGRGDLIVTVQVREHPFFQRDGD +DLRITVPVTFAEAALGATVEVPTLDRPVKVKVPAGSQSGRVLRLKGRGVAGAKHTGDLLV +ELQVAVPAELSAEARGAVEAYAAATAGDDVREGLAGKAQW +>MHAAABBN_01570 +MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA +VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSEPDLSDL +FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG +ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF +PEAALGATIEVPTLDRSVKVKVPAGSQCGRVLRLKGRGVERGTTTGDLLVELRVTVPTTL +NDDARAAVEALQSATAGDYPRRELARKAAW +>LFPAFLNI_01794 +MASQDWMDKDFYATLGVSKDASESDVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA +VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL +FSGMFGGAAGQTGGFGDAGYPRPRPTKGADRTATTTISFRGSIQGTTVSLRAPDGETIEV +KIPKGIRDGQKVRARGKGSPGAAGRGDLLVTVHVREHEFFHRDGDDLRITVPVTFPEAAL +GATIEVPTLERPVKVKVPAGSQSGRVLRLKGRGVERGTTTGDLLVELHVTVPTELDDDAR +AAIEALQSALAGDDPRRELARKAAW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000646.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000646.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c6e1db05567e01ea929d90f28aeae4179cd9e57 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000646.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00987 +MSARDGAARADRGRERGLDRNAPVFVVSVAAEMADMHPQTLRQYDRLGLVVPARQGGRHR +RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA +RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP +EQD +>MOLHKGIG_01873 +MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR +RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA +RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS +EQD +>NAFOICDF_00924 +MVSGVAGEHPTGAGRLRGTAGRPGRHDPVFVISVAAEMAGMHPQTLRQYDRLGLVVPQRQ +GGRHRRYSAADVEHLRAVQRLSREGVSLEGIRRILDLQREVERLQDTVVELASQVDRLHS +ASALARVFSVGLAGDVSARYAAPAAHRAAEAVQGQRRPGEGATRSAARGGLLRALPAGRA +AAPRGLTRLPAPRD +>MHAAABBN_01569 +MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR +RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA +RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS +EQD +>LFPAFLNI_01793 +MSARDGAARADRGREPGLDRNAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQGGRQR +RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA +RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP +EQD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000648.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000648.fa new file mode 100644 index 0000000000000000000000000000000000000000..289ea2c846e832ae852b6c04e29b3ff05d709ef2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000648.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_00989 +MTEQPPAPDAPSRGTPANDGRDGVLAPHERAHEHDHNRDKDPALMRREPVSFVRRGARLN +SGRQAVWDRQAQRVLVDVPRERGATSVARDARLDWDAAFGRRAPLLVDIGSGLGESTAQA +AADRPDWNVLAVEVYVPGLAALMTRVEQSGLENVRAVEANAPELMDHLLAPGSVSEVWVF +FPDPWHKKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVRMREVMEAHPEFENL +HPGRAAGEKSPLTRVRREGREAEVGAQPLPAGWESAAEDERPLRAGLGEALEAAVAEDPV +DHEGGWAPRFEGRPVTSFEAKSRRAGRLVFDLAYARR +>MOLHKGIG_01871 +MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV +WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD +WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH +KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA +GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHDGGW +APRFEGRPITSFEAKSQRAGRLVFDLAYRRR +>NAFOICDF_00926 +MTGGPENAHERDHDREKDPELIRREPVSFVRRGARMTTGRQAVWDRMAETVLVDVPRHRA +ATSVAPDAHLDWDAAFGRHAPLLVDIGSGLGESTAQGAADHPDWNVLSVEVYLPGLAALM +AQVESRGLENVRAVEANAPELLDHLLPAGSAQEVWVFFPDPWHKKRHHKRRLVNAAFADR +VARVLAPGGVLRLATDWSGYAVQMREVMESHPDFVNLHPGRAAGEESPLTRVRREGRELE +VGAQPLPAGFDPARPASELPERAGLGEAVEASLAEDPVDHDGGWAPRFEGRPLTQFEGKA +LRAGRLVFDLAYARR +>MHAAABBN_01567 +MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV +WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD +WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH +KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPGFENLFPGRAA +GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHEGGW +APRFEGRPITSFEAKSQRAGRLVFDLAYRRR +>LFPAFLNI_01791 +MTEHLPRPRPDAPDPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV +WDRQAERVLVDVPRGRGATSVDAQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD +WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH +KKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA +GEDSPLTRVRREGRETEVGAQPLPAGWERAAEEERPLRAGLGEARAGAAAADPVDHEGGW +APRFEGRPITSFEAKSQRAGRLVFDLAYRRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000651.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000651.fa new file mode 100644 index 0000000000000000000000000000000000000000..b13d1232f830c92f5947a4bd06592520a3f9df3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000651.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_00992 +MSIVQIPLRLASGAFILNSGLNKRNISEEQAAGMRDMGAQGVPYLAKLTPAQFKNFIVAT +EVGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPAMTEKDGVRPSQEGTGVAKDVFL +VGSGLAIAADSVANRSGKRRKAAKKRAARIGNARDAKVQAIRDAQDEKVAAIHAARDEQV +AALREAREELKKLRQKA +>MOLHKGIG_01868 +MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT +EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL +VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV +AALREARDELKKLRKKA +>NAFOICDF_00930 +MSIIQIPLRLTSGAFILNSGLGKRKLGEEQAAYLQNMAAKGVPSLAKLSPSQFKNFITAT +EIGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPEMTEADGVRPSQDGTAVAKDVFL +LGAGLAVTADSVVNRPGKRKKAAKKRAARISDARDAKVDAIRAAQDEKVAAIHEAREQQV +AALREARQELAKLRKKA +>MHAAABBN_01564 +MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT +EVGVGAALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL +VGSGLAITADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV +AALREARDELKKLRKKA +>LFPAFLNI_01788 +MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMSARGLPALANLSPEQFKKFLVTT +EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTAVAKDIFL +VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV +AALREARDELKKLRKKA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000652.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000652.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec40db6710bd048911a81dcfa3f0debce3d24e48 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000652.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00993 +MAQQTPQPAASAVDAAGVHVADLNKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTLL +RCVNLLEKPDSGRITVGEFDVTDEDVDLDALRRHVGMVFQQFNLFPHLSVLENCTVAQVK +VLKRSKAEAAEVARRQLARVGLAELEDRFPDQLSGGQQQRVAIARALAMDPQLMLFDEPT +SALDPETVGEVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVSMDAGVVVETGPAAALI +ADPQQPRTQDFLRRVLHPTEIDL +>MOLHKGIG_01867 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDIARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL +>NAFOICDF_00931 +MTEQTASPRPSDAGTAAGVHIAGLHKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTL +LRCVNLLEVPDSGGVQVGEFTVTDPDVDLDRLRQHVGMVFQQFNLFPHLTVLENCTVAQV +KVLKRSAAEAADTARRQLARVGLGELEGRYPDQLSGGQQQRVAIARALSMDPRLMLFDEP +TSALDPETVGDVLAIMRKLAREGMTMLVVTHEMGFAREVADRVVFMDGGVVVEQGPASAV +ITDPQEPRTQDFLRRVLNPAGVDI +>MHAAABBN_01563 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL +>LFPAFLNI_01787 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLGIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000654.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000654.fa new file mode 100644 index 0000000000000000000000000000000000000000..10cf92a021a48213b863e057399ddb46433191e0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000654.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_00995 +MGLTASAALLTGCAVLGGDSGVAGVVSDDDLSTTYNLVQPGVLTVCSDIPYPPFEFELDG +ELTGYDIQLVHAIAEELELGVNVIDSSFEAIESGASLTGCDLNASSISITEQRQRAMAFT +LPYLDDDLVLVAATDSGITDVESAKGRRVGVQAATTGDAYAKENGLNPIEFEDGGMQVQA +LQAGTVDALLGNQSVILYSLKDDERFEVVENLPTGEQLGMAVAPQNAQLGSAVNRALQQL +RNDGTVAELQERWFGLAQEDYR +>MOLHKGIG_01865 +MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV +PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI +TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV +QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL +GSAVNRALQELRNDGTVAELQERWFGQAQEDYR +>NAFOICDF_00933 +MPRTPSRALGAVGAGLSAALLSGCAVIGGDAGTTGPLAEDDLRATYRLHEPGVLTVCADV +PYPPFEFEQDGQLTGYDIDLTRKLAETMDLQLKVVDTSFEAIESGASLTGCDLNASAISI +TEPRQHVMAFTLPYLDDDLVLVARKDSGITDVASAQGKRVGVQTATTGEEYAQSQGLDTV +QFEDGGMQVQALQAGTVDALLGNQSVLLYSLKDDPRFGVVESLPTGEQLGMGVAPDNALL +GSAVNRALQTLRNDGTVAELQQKWFGTAQKDYQ +>MHAAABBN_01561 +MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDI +PYPPFEFEEKGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI +TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV +QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL +GSAVNRALQELRNDGTVAELQERWFGQAQEDYR +>LFPAFLNI_01785 +MTRIHSRLLGTVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV +PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI +TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV +QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVELLPTGEQLGMAVGPQKAQL +GSAVNRALQELRNDGTVAELQERWFGQAQEDYR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000655.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000655.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ecc50c0655cf787a4efecf76c111b97979858a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000655.fa @@ -0,0 +1,27 @@ +>ACLBLIBL_00996 +MEALEDVLLTPQTAPDGVFTDMETQAGGGGEPISTSLSLTGVTPTGACADLIEQINTQQA +PGLGGALAQYEVDPDAVTGLAGSQAGAFGMVAVTEGGTDLLAPFGELADTCGTFGDPDGV +EAAFTKVPGVPDAAHIALGNSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRA +QVEAFEKRER +>MOLHKGIG_01864 +MGALALVGCAGGGGEASSSSADASKSAPTGAGSDLTDEQEERVEALEDVLLTPETAPGGV +FTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAPGLGGALAQYEVDPAAVTG +LAGSQAGAFGMVAVTDDGTDLLAPFGKLADTCGTFGDPDGVEAAFTKVPGVPDAAHIALG +NSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRAQVEAFEARER +>NAFOICDF_00935 +MSRTATSRPRLRALLPLTATAALLASGCAAPGPAASSSATPSSSASSAAAESSSSPTVST +GPASSSDASSSAAAASSSADASATTSSSSAADLAASSPAAGGASVENPLEPLLLLATAAP +QEVFSSRTVQSGADQPLTMSLTLTGVTPTGRCQELVDEINATHEPMDVASLATYQVNPAS +PAVVDQETGAFTMIGTSTAPADLMAPYGELVSACGTLEGEQGQKAEFTAVPGVPDAATVT +MTTPGQSRKLVMTVGGASEGRDHVYMLMLGLDADVSQQVLADQVAAFQER +>MHAAABBN_01560 +MGAHALVGCAGGGGEASSSASADASESGPTGAGSDLTDEQEERVEALEDVLLTPQTAPDG +VFTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAPGLGGALAQYEVDPAAVT +GLAGSQAGAFGMVAVTEDGTDLLEPFGELADTCGTFGDPDGVEAAFTTVPGVPDAVHISL +GNSGMDTALFTMIVGGVTDGDELVYLGMVGLDEEIAAETLRAQVEAFEKRER +>LFPAFLNI_01784 +MLRPAAPARPAVALSLLAVGALALVGCGGGGGEASSSSADASESAPTGAGSDLTDEQEER +VEALEDVLLTPETAPGGVFTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAP +GLGGALAQYEVDPAAVTGLAGSQAGAFGMVAVTDDGTDLLAPFGKLADTCGTFGDPDGVQ +AAFTKVPGVPDAVHIALGNSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRAQ +VEAFEARER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000656.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000656.fa new file mode 100644 index 0000000000000000000000000000000000000000..c3418978484f3648951291673920179bc8838a37 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000656.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_00997 +MSGSTAAPRRLRTYARPRVSLLYVLRRTTHRLLELQVWDVAAAMTFFAALSLLPTVVALV +SLVSLLGVQEETVDAAAQLATEIWPSLTPDTVREWILTLGSAGTGTAAVVLGILGAVVSA +SGAVGAFHRAMHRIHDTREGRPFLQFRLVLLVETLALMVGIVLVVILVVLGGDLSLRIGQ +AVGLPEETVLTWNVVKWPVILVVIALTVTLAYRLGPNVVPPRYRPLSAGAVSVVVLLFAA +TLALGWITDRFGQFAVVGRINSAIGVLVLAWIACIVLLAGAALDAEMLRGRQLAVGVDAA +SEIQLATRHTVVLEAAERHEDRSRRLARLVAEAVREDEDLSIDATPLLSQEGRMFAIGSA +RRTAAEVSSGRPFHAAPVLDDGARLEPTSRPDD +>MOLHKGIG_01863 +MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVIALL +SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA +SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSLRLGQ +AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA +TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS +VEIQLATRHTAVLEASERYEARNRRLARLVADAVRAGEDLTIEATPLLSEEGRLLAVESG +RRDPEDVSSGSPFHADPVSHDGARLEPTPRPDD +>NAFOICDF_00936 +MPSSPVPDASTGGRAPRTYARPRASLLYVLERTWTRLVGMQVWDVAAAMTFFAVLSLLPT +LVALVSLVSLLGVEARTVETAARLATEVWPSLDAAEVSAWILNAGRTATGTPGLVLGAAG +AVVSASGAVGAFHRAMHRIYDTREGRPFLVYRLVVLLETLALIVGAALVMSLMVLGGDLS +ERLGRLLGVGRGAVAVWNASTWPMILVLLALIVSVAYRRGPNVRPPCHRPFSLGAVGAVA +LLFAAALALGWIVARFGGLALVGRLNSALGVLGLAWAACIVLVAGAAFDAEMLRARQLAV +GVESADELQLATRDTWVLRQVERQEARHLRVGRLVAEAVRTEEPVTTPATRLLAEAGSLF +AVDAAGRSASDLTSGRPFHAVPPADRAGV +>MHAAABBN_01559 +MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVVALL +SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA +SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSQRLGQ +AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA +TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS +VEIQLATRHTAVLEDFERYEARIRRLARLVAEAVRAGESLTIEATPLLSEEGRLLAVESG +GRGPEDVSSGSPFHADPVSDDGARLEPTPRPDD +>LFPAFLNI_01783 +MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVIALL +SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA +SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSLRLGQ +AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA +TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS +VEIQLATRHTAVLEASERYEARNRRLARLVADAVRAGEDLTIEATPLLSEEGRLLAVESG +RRDPEDVSSGSPFHADPVSDDGARLEPTSRPDD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000657.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000657.fa new file mode 100644 index 0000000000000000000000000000000000000000..9019ccad1e2ca4eb638104e242586a489ae98e4e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000657.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_00998 +MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS +TAASSAIRRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG +EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPENTFQSLEKYGTDLTEVARSGKLDPV +IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL +DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK +PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH +HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD +RLTMEELALEGETDPSSVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD +ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSTTEPMVSEEVTADD +IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN +RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG +YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI +LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVQFDALTVAELTRIVDL +QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDRLARGILAGE +IADGDTVVVDRAEGEEGLTVASA +>MOLHKGIG_01862 +MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS +TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG +EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV +IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL +DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK +PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH +HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD +RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD +ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD +IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN +RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG +YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI +LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL +QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE +IADGDTVVVDRVEGENGLTVTRKG +>NAFOICDF_00945 +MNPSPQFTTKSQEALSAAAMNASTASNPAVEPAHLLKALMDQRDSVAVAVLKAAGADPDV +VSVAASTAIHGLPKASGATVSEARLSPAAGAVVKAAQQQASAHGDEYVSTEHLLLGLAAD +GGEAGRALTDAGASLAALQAAFTQVRGDERVTTPDPEATFQSLEKYGTDLTAVARSGKLD +PVIGRDQEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLI +SLDLGAMIAGAKYRGEFEERLKSVLEEIKKSDGQIVTFIDEIHTVVGAGASEGAMDAGNM +LKPMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYE +AHHKVAIADSALVAAATLSDRYISGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDALRRQ +VDRITMEELALDGESDPGSVERLAGLRAEKADKEEELRALTARWEAEKASLNEAGDLRAR +VDELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAQEGQQGDVEAMVSENVTA +DDIAEVISAWTGIPAGRMLASETEKLLSMEEHLGDRLIGQKDAVRAVSDAVRRARAGIAD +PNRPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHAVSRLVGAPPGY +VGYDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVI +LILTSNLGSQFLVDQTMPEQARKDAVMDVVRAAFKPEFLNRLDEIVTFDALGVEDLARIV +DLQVASLGERLQQRRLTLDVTDAAREWLALTGYDPAYGARPLRRLVQREIGDQLARALLS +GAVQDGDTVVVDRAGEDTADGLTVAARRA +>MHAAABBN_01558 +MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS +TAASSAIQRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG +EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPETTFQSLEKYGTDLTELARSGKLDPV +IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL +DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK +PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH +HKVAIADSALVAAAALSDRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD +RLTMEELALEGETDPASVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD +ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSSTEPMVSEEVTADD +IAEVVSAWTGIPSGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN +RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG +YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI +LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVLFDALTVDELTRIVDL +QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDQLARGILAGE +IADGDTVVVDRVEGENGLTVTRKG +>LFPAFLNI_01782 +MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS +TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG +EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV +IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL +DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK +PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH +HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD +RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD +ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD +IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN +RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG +YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI +LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL +QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE +IADGDTVVVDRVEGENGLTVTRKG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000661.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000661.fa new file mode 100644 index 0000000000000000000000000000000000000000..2d9ce005e6d1e0105cd12eaef1d285fc9f3be434 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000661.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01003 +MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRAPEPELDQKPEYEDPYADLYT +DDDEDDDARAR +>MOLHKGIG_01860 +MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED +EDDDARAR +>NAFOICDF_00946 +MGRGRQKAKATKQAREMKYMSLGTDLSALERELTGGRTDAPAVEPEVDYEDPYADLYADD +DEDDDSRVR +>MHAAABBN_01556 +MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED +EDDDARAR +>LFPAFLNI_01780 +MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRSPEPDQEPEYEDPYEDLYAED +EDDDARAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000662.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000662.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b1a6147db56229933c029c8fd1ef0510002bb24 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000662.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01004 +MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLLEETRPLVITGAGVSTDS +GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNAAHRILAGWA +VRGLVSGILTQNVDGLHAQAAAEAGAPEDRLIELHGDLARVVCLHCGATESRRDLDVRLE +AANLGYLERVSIDPEAVNPDGDVTLDRHWVDEFAMVGCLRCGSVELKPDVVYFGESVPVA +RREAAEAMADDGGAVLAVGTSLAVMSGYRFVLRAERAGKDTGLINLGSTRADPKASWRWR +APVADALAWLDSRL +>MOLHKGIG_01859 +MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS +GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA +AEGRIAGVLTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE +AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPPA +RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR +APVADALAWLDARL +>NAFOICDF_00947 +MTPVRHPSQDGHQAALRSIARVVGETAPLQDPETASRGLLRMLEAGRPLVITGAGVSTDS +GIPDYRGPNGTLHRHRPMTYQEFRDDPAARHRYWARSFVGWRHMDEAAPNAAHHVLADWV +RRDVVAGIVTQNVDGLHAQAFAAAGAAPSRLIALHGDLARVVCLQCGAMEDRTSLDARLA +AANPGYLEAVTVDPDAVNPDGDVTLDQRWVDAFTMVGCRVCGSVQLKPDVVYFGENVPPA +RRDAARALAEEADSVLAVGTSLAVMSGFRFVLDAERAGKEVGVITLGPTRADPKAQWRWR +TRVAEALAWLDARL +>MHAAABBN_01555 +MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS +GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA +AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE +AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA +RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR +APVADALAWLDARL +>LFPAFLNI_01779 +MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEEFRPLVITGAGVSTDS +GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA +AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE +AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA +RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR +APVADALAWLDARL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000663.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000663.fa new file mode 100644 index 0000000000000000000000000000000000000000..b41c1d83ed6e0d64d495cf9268c0bcf8820d700b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000663.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01006 +MSMSTSTSTSLPCPQDRRPPVPARPLDVVAAGGPLFTRADLSAAGLPADRLRAADVRRVT +HGVHRRADDVPGDWGALGYAEPPVAFAPEETAAIVTASRGVASHLSALLLHGIPVPPFLV +DDGRVHVSRPHSRGASERPEVRSHARSVPEADAVVLHGIRVTSVERTWADLAALVRPGHL +DPVVAAGDAVVTGIWTPQGRLPPRATILRLRAGLARSGRFKGARTARAALELIRAGADSP +PETALRLALLHAGLPEPELQLVLHRGRRRSPDADLGWRAWRLVVHYDGDPHLDPAQQAVD +AWRNGGWARAGWSQIVATVDDARDDFRRVVAEVLAHRARLGGRAYVA +>MOLHKGIG_01858 +MATSSLPLSDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRSDHLGSWADLG +YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR +PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE +GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE +LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT +VDDARDDFRRVVAEVQTHRARLGGRVFAS +>NAFOICDF_00950 +MALESLADVLGSAPLPIRAEGPPPLGLFTRSDLRAAGLGGHRVHGRDVRRVTHGVHRLAT +DPAGDWAVLGHRCPPAPFAPEETAAIVEAAGGVASHLTALLLHGVPLPPFLAEDGTVHVS +RPHARGASGRLEVTSHARSVPAADVTSLHGIRVTSLERTWADLASLVPPGLVDPVVAAGD +AVVRHPWTPQGRSAPRTTPARLAAALDRAGRFKGVRTARRALEAVRVGSDSPQETALRLA +LVHAGIPEPELQLVLHPGRERSPDADLGWRMWRLVVHYDGASHLEPAQRAVDARRHEGWE +RAGWAQIVATVDDARDDFRRVVAEVQAHRRRLGGRVYVC +>MHAAABBN_01554 +MVTSSLPLSDIAEAGRPFTRGDLRAAGVSERLVRGADVRRVTHGVHRLRSDHLGSWADLG +YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR +PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE +GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE +LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT +VDDARDDFRRVVAEVQTHRARLGGRIFAS +>LFPAFLNI_01778 +MATSSLPLPDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRTDHLGSWADLG +YAEAPAPFAPEETAAVVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR +PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE +GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE +LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT +VDDARDDFRRVVAEVQTHRARLGGRIFAS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000664.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000664.fa new file mode 100644 index 0000000000000000000000000000000000000000..447517175d48321ff34c936e2223867dcf2356de --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000664.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01007 +MTENQNTAHDAPITYASAGVDVEAGDRAVELMKDAVKATHSPEVMGGIGGFAGMWDASAL +LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGATPLFMTDYIACG +KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLGVDEYDVAGAATGVVDADMVLGA +DRVQTGDVLIGMASSGIHSNGYSLVRRVVNAAGWSLDREVSELGRTLGEELLEPTRIYAR +SCLDLVQRLNGHDGGSGLPVRAFSHVTGGGLAANLARVLPQGLMATVERETWSLPPVFRL +LAEAGRVPQPDLERTLNLGVGMVAVVDPEIAAKSISVLVDAGIDAWEMGTIGHVTDEAAG +AGLDFVQGAKGVDGGAVLMRGAYAA +>MOLHKGIG_01857 +MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL +LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG +KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAADEYDVAGAATGVVEADMVLGA +ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR +ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL +VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA +AGLNFVQGAKGVDGGAVLMRGQYAA +>NAFOICDF_00951 +MTDAPRTETQTADALDAPLTYAAAGVDVEAGDRAVELMKDAVKATHTAEVLGGVGGFAGM +WDASALTGYRKPLLATSTDGVGTKVAIAQALDRHDTIGQDLVGMVVDDIVVVGAKPLFMT +DYIACGKVVPERVADIVRGVAEGCRLAGTALVGGETAEHPGLLAVDEYDVAGAATGVVEA +DRVLGAERVRSGDVVIGMASSGIHSNGYSLVRRVINAAGWQLDRDVDELGRTLGEELLEP +TRIYTRACLDLMDSLNGTEGGADLSLRGFSHVTGGGLAANLARVLPQGMMATVDRGTWAL +PPVFRLVGELGRVPLADLERTLNLGVGMVAVVAADAADRAVAAIEAAGIPAWVMGGIDEV +TEQAQAAGEDYVQGAKGVDGGAVLMTGTYAD +>MHAAABBN_01553 +MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL +LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG +KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAVDEYDVAGAATGVVEADMVLGA +ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR +ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL +VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA +AGLDFVHGAKGVDGGAVLMRGQYAA +>LFPAFLNI_01777 +MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL +LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG +RVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAAEEYDVAGAATGVVEADMVLGA +ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR +ACLDLVQRLNGHDGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL +VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA +AGLDFVQGAKGVDGGAVLMRGQYAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000665.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000665.fa new file mode 100644 index 0000000000000000000000000000000000000000..c36170c6f023b240061c39c826c220020d797c1b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000665.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01008 +MIASRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAASDGKRIGVYKDIGLVSQVFDESTLATFTGHIAVGHCRYSTTGANKWANAQPTLGATA +GGDTVALAHNGNLVNSGELLRMVQARDGLQLRGEMKQGNTTDTALVTALLHGEEGRKLEE +TALELLPKVRGAYCFVFMDEHTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDASIAGRSVYESRVDMGRRL +ALEGPVDADVVIPVPESGTPAAVGYAEASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFASRAELIANGAGVAEIASSIGADSLGYISEEAMIAATGQPRERLCTACFTGTYPIELA +DESERGKSVLETDAGSAAVTVMAPDGDATTVASTGCEPGPDADDEKLLTETDRTPL +>MOLHKGIG_01856 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL +ALEQPVEADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVESTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRTPL +>NAFOICDF_00952 +MISARTRRGDGRLTAALDPQEAGPQDECGVFGVWAPGEEVAKLTYYGLYALQHRGQESAG +IAASDGKRIAVYKDMGLVSQVFDEPTLAALTGHVAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVESKEGAHTLGEIKQGNTTDTALVTALLHGEKGVSVEE +TALELLPKVRGAYCFVFMTERTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDAAINGRSVYESRVEMGRRL +AQEHPVDADVVIPVPESGTPAAVGYADASGIPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAGVQEIASSIGADSLAYISEEGMIAATEQPRERLCTACFTGTYPIELA +DEKERGKAVLENGTPTAEATDVVSEDGTVTTVASTGCEPGPDSEDEKLLTQTDRTPL +>MHAAABBN_01552 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDERTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDAAIAGRSVYESRVEMGRRL +ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEKGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRIPL +>LFPAFLNI_01776 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL +ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDVDGETTTVTATGCEPGPDADDEKLLTETDRTPL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000666.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000666.fa new file mode 100644 index 0000000000000000000000000000000000000000..7998e6e82d5d35140892864c890223aa6adbfc58 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000666.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01009 +MTTGPERSQHQHAYTVRRAPRLAAVLAVALALGLVIALVITTAVHGSPTPPADPYSGIPL +SFSETFGFAALLSMLGTGVLGLVVWLLLDRRSRATTRTVVLERTDDPAAADIRLDRSAAD +ALRSRTAPTERTPEQ +>MOLHKGIG_01855 +MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL +SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG +APPARTTPTERTPEQ +>NAFOICDF_00953 +MTSGPERSTPSAPQQQEYVLRRAPRLSAAVIVSALVGVVLALLGTAAVHAGPQPPADPYS +GMPLSFASTFGYMVVAAVLACLVLGLLVWLLLDRRSRRTQRTVLLERTDDPAAADVALPR +PEAVAPAARPAADPSDGRTPEQ +>MHAAABBN_01551 +MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL +SFSETFGFAALLSMLGTGVLGLIVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG +TPPARTTSTERTPEQ +>LFPAFLNI_01775 +MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL +SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG +APPARTTPTERTPEQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000667.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000667.fa new file mode 100644 index 0000000000000000000000000000000000000000..0db87c2dbd4cfb41e1537c359ab664cdd64edda9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000667.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01014 +MTTGSVPRRRIPVPEGHAALTSWARTHAQDPAAAAALPRSTRATAVRFALEELATRVPGN +AVEVRVPPFGVAQAIPGPRHTRGTPPNVVEMDAVTWLSLATGLLGWADAVGTGAVRASGT +RADLGAHLPLIRP +>MOLHKGIG_01854 +MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRATAVRFALEELATRVPGN +SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV +RADLGAHLPLVRP +>NAFOICDF_00956 +MTTGSVPKRRVPVVEGHAALTAWARAHAEDPAAAAALPRSTRATAVRFALEELATRAPGN +SVEVRVPPFGVAQCIPGPRHTRGTPPNVVETDPVTWLSLATGLTRWNDAVASGAVRASGV +RADLAGHLPLVRP +>MHAAABBN_01550 +MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN +SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTSWDEATAAGGVRASGV +RADLGAHLPLVRP +>LFPAFLNI_01774 +MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN +SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV +RADLGAHLPLVRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000668.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000668.fa new file mode 100644 index 0000000000000000000000000000000000000000..39b6215c9af7dbf6a1d7d0fb2e530c0ae0547809 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000668.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01015 +MTQTPSATFALADAVELVHVVRNGFVESRTPGAAVVTGPDGTVLAALGPVDALIYPRSTL +KPFQAIASLRHGARLEGQEVAIACGSHRGTAAHRELAARILAEAGLSAADLQCPPDYPAD +AAEIVRFAQDLEHGAEKTPLAYNCSGKHAGFLAACVAAGHEVGTYLEPDHPLQAEVERVI +EEYCGEPVAHTGTDGCGAPAAVLSLTALARGIGKVASAPSRRDAEIHAATVANAMLEHPW +AVHGQSSSNTVVMRELGLLAKLGADGVMVMAAPDGTAVAVKALDGGTRAGNLVALALLAQ +FAPDHVDADRLPAVLETVAPKILGKGEPVGAVRLARPVLDLLD +>MOLHKGIG_01853 +MTHATVAPAGETLALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP +RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALQCPPA +WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA +>NAFOICDF_00957 +MTQTSAAPAGQTFALADAVELVEVVRGGFVESRTAGAAVVTGPDGEVLAALGPADALVYP +RSTLKPFQAIASLRHGARLEGEALAIACGSHTGSEAHQQLAARVLADHGLAPEALQCPSA +LPEVAGEVARLAAQAGTAEIATPLAYNCSGKHAGFLAACAASGHDVGTYLDPEHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVVSLAGLARGIGAVSKAPGREGAEPHAAAVARAML +AHPWAVQGPGKANTVVMEELGLVAKLGADGVMVMGAPDGTAVAVKALDGGTRAGNLVALA +LLGRFAADQVDAGRLAEVSARVAPSILGRGAPVGEVRLAAPVRQLVGA +>MHAAABBN_01549 +MTHATIAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTSPDGRVLAGLGPADALIYP +RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA +WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPTFEARA +>LFPAFLNI_01773 +MTHATVAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP +RSTLKPFQAIASLRHGAALAGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA +WPADTSEVVAQVRRDGEAAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000670.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000670.fa new file mode 100644 index 0000000000000000000000000000000000000000..050f11f3599649ac2b57528a2af9f1c9f81f6229 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000670.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01018 +MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAPAVL +ALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWVA +FPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVGA +AVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLTQ +GLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRATGGASLVAA +VERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLANVAAHARATRA +RVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAGRASRPGAGTGVGL +ASVRERLAGVGGHASVESAPGEGTVVALRVPLPAAAGRAEEDEGRERG +>MOLHKGIG_01850 +MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPAT +TLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVA +FPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAA +VAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQG +LASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEAL +ERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRAR +VTLGYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGE +ATVESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA +>NAFOICDF_00960 +MRTSDPADGPRGANGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPALAL +VGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWVAFP +LFFVALHAVHVILGRPRLALACVAAMTVVVVVASLERGTAPGAVLGPAVGAAVAVVVFHA +CRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLTQGLASIVLVS +RAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGGADRAGSALEA +ALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLANVDQHARTDR +CRVTLTWMDGEVALDVADDGVGFDPEAARARASRAAVSDPAAPRPAEEGTGVGLAGLAER +VAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA +>MHAAABBN_01546 +MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDASGPFPATT +LVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWVAF +PLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAGGVRVPAVIGPLVGAAV +AVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGL +ASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLVEALE +RAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRARV +TLGYLGDELTVDVADDGAGFDPAVVVARARAGAAGADPGAGTGVGLASVRERLAAVGGEA +TVESAPGEGTVVALRVPLAAAGAGRSADPEQTESEETA +>LFPAFLNI_01770 +MSVAPRAAAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPVTTLV +LLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVAFPL +FFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAAVAV +VLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGLAS +IVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEALERA +VTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGAHRARVTL +GYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGEATV +ESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000671.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000671.fa new file mode 100644 index 0000000000000000000000000000000000000000..28f261b27a9f30b0400e1eb6fbad98f60a0a9e33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000671.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01019 +MTVHVMLVDDHPVVRAGVRAVVEAHPDLRVVAEAADGAEALRILEAASGPVDVVLMDLQM +GEGMDGVSATRAVRERRPDVQVLILTTFDTEADILAAVDAGAAGYLLKDAPSEEIARAVR +QAAAGQKALAPQVAATLMGRMAGGADVLSAREIELLELIARGATNKAAAKELFISEATVK +THLVHVFQKLGVDNRTRAVDEARRRRIIR +>MOLHKGIG_01849 +MSVRVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM +GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR +QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK +THLVHIFQKLGVDNRTRAVDEARRRRIIR +>NAFOICDF_00961 +MSVRVMLVDDHPVVRAGVRAVLEADPELTVVAEAGDGAAALDVLQARPGEVDAVLMDLQM +GEGMDGVSATRRLRAAHPGIPVLILTTFDTEADILAALDAGAAGYLLKDAPAEQIADAVH +RAVAGRPALTPDVAERLLGRTTGATAASALSAREIELLELIARGDTNREAARALFLSEAT +VKTHLVHIFQKLGVDTRTQAVHEARARRIIR +>MHAAABBN_01545 +MSARVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM +GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR +QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIELLELIARGATNKVAAKELFISEATVK +THLVHIFQKLGVDNRTRAVDEARRRRIIR +>LFPAFLNI_01769 +MSVRVMLVDDHPVVRAGVRAVVEAHPDLSVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM +GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR +QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK +THLVHIFQKLGVDNRTRAVDEARRRRIIR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000675.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000675.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b66f128e600a2d6f282a576ca1c57c97269de5f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000675.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01026 +MRPSATAPRRLVRAGSRAAVGMGTAAALGLAWGLVEAEARVVRTHRLAVLPAGADPVRVL +HLSDIHLLPRNRSRMAWLRGLDALEPDLVVNTGDNISAAASVPLVLDALGPLLRRPGVFV +PGSNDYYEPKPANPFRYFAGPSRMDEDRARLPTEALFGAFRAAGWADLTNRGSVLSVPTR +AGTVLEVLAAGTDDPHLGLDAWGGFPAPAPAPAPAPGDAAASGPASAHDDGAARPGGDGR +FRLGVTHAPYRRVLDAMTVDGADLLLAGHTHGGQVCLPGFGALVTNCDLPRAQASGVSTW +TAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLELLPCA +>MOLHKGIG_01842 +MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL +HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV +PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR +AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT +ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA +PSAPVRFACRPEAVVLDLVPRG +>NAFOICDF_00967 +MTDAPGPRLRRLTHTAAWAAGGASALGAGALVWGRVEAEARVVRTHTVPVLPAGARPLRV +LHLSDIHLLPRHRRRLEWLCSLADLEPDLVVDTGDNISSAASIPLLLDALAPLLAVPGVF +VPGSNDYFTPKPANPLRYLRGPSELEASRSRLPTEDLFSAFRAAGWTDLTDRAADVVVGS +GPDAVRIRAAGTDDPHLGLDRWPGFDLADEGAAGDAPLLRLGVTHAPYRRVLDAMTADGA +DLLLAGHTHGGQVCLPFAGALVTNCDLPRSQASGLSSWTAAGRTVPLEVSAGIGTAPSAP +VRTFCRPEAVVLDLVPRA +>MHAAABBN_01539 +MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL +HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV +PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR +AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT +ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA +PSAPVRFACRPEAVVLDLVPRG +>LFPAFLNI_01763 +MRPAASPARRMFCAAAPAAAGLAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL +HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV +PGSNDYYAPKAANPLRYFAGPSRMDADRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR +AGTTLEVLAAGTDDPHLGLDAWAGFPGSAPDGGAGRPGDDGRFRLGVTHAPYRRVLDAMT +ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWMAAGRTVPLEVSAGLGTA +PSAPVRFACRPEAVVLDLVPRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000677.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000677.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a7d1e3c6f80b3bad9c6d9ee98ebb4f1d9bff04a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000677.fa @@ -0,0 +1,10 @@ +>ACLBLIBL_01028 +MTEQTKWEYATIPLLIHATKQILDQWGEDGWELVAVVPGPDGPNPVAYLKRPKAA +>MOLHKGIG_01840 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA +>NAFOICDF_00969 +MTQRIQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGANPVAYLKRPKDA +>MHAAABBN_01537 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA +>LFPAFLNI_01761 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000679.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000679.fa new file mode 100644 index 0000000000000000000000000000000000000000..f208a0be7ef6db09211dfa70e175164f8debdcd6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000679.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_01030 +MVLVRDGEDGPEVFLRHRPGRTPLGRVGLPGGALSEADADACAWFGPDPAHWARVLGTTD +RRCARQQVVAAVRELHDEAGVLLAGRTDADVVLDARGETWGGGGSSLEEGAESLPRMLAA +RGLGLRTDLLRPVARWHSAPHAHRRFDTAVFAAAVPPLQRPLERPETAPALQAWVSARRA +VAGPVPLPGPAGEEGVAPLDQVATPLTQVLVRRVAAHRTAAAFLLSLTQGAGHGPVPEYR +LVTEAGDDGAPRMRVERVTRD +>MOLHKGIG_01838 +MSADPAGLLLPVPGQEEDLTRQWLDRRFRQVRPARPGSSVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADSCPWYGPEPSQWARTFGTTDRRRARQHVVAAVRELHDEAGV +LLAGRSDTDVVSTARIETWGGGRSSLEEGSESLPHLLAARGLGVRADLLRPVMRWRSAPH +VHRRFDTAVFATMTPPLQSAPASEEPGPELQAWVSARRALAGPLRLPGPAGAEGTAPFDQ +VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVKRATRD +>NAFOICDF_00971 +MSAEPDAPRVRVPGHEEELTRQWLAQRHRQVRPARPASAVVLVRDGADGVEVLLRHRSGR +TPLGRIGLPGGSLVDSDADPCTWYGPAPDEWARALGLADRRRVRQHVVAAVRELFEESGV +LLAGPADMDLVQDARGETWGASRSSLEEGDESLPRLLGDRGLGLRTDLLRGVGRWLSAPH +SPRRFDTVVFAAALPPQQELVHRPEGPVLQGWFSARRLLSEPAALPGPDGWLGESGVVAL +EEVSTPMTQLVLRRVAEHRTAAGFLLSPAGCRGPVPVVKLRTEAEHDDLATGTLYTVAER +VDPVG +>MHAAABBN_01535 +MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV +LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH +VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ +VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD +>LFPAFLNI_01759 +MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV +LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH +VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ +VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000680.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000680.fa new file mode 100644 index 0000000000000000000000000000000000000000..967aab0842ee73956719df8d54dbb2926c1de6b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000680.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_01031 +MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR +TASDGRENLVAVLGPGEIFGEMALFNPAPRSATATAVSATRLAGLRHENLRRAIGSSPDV +SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE +LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR +>MOLHKGIG_01837 +MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR +TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV +SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE +LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR +>NAFOICDF_00972 +MGHNGTDIPGAPRPRLAVSQKGRARMDLEVLRKAPLFTNLDDEVFSILTSELTEVELSRG +ASAFHEGDQGDQLYVIMSGKIKLGRTASDGRENLVAVLGPGEIFGEMALFNPAPRSATAT +AVSAARLAGLRHENLRRAIASSPDVSLQLLQALAQRLSKTNESLADLVFSDVPGRVAKAL +LDLADRFGRPAADGLLVAHDLTQEELAQLVGASRETVNKALAEFVQRGWIRLENRAVVIL +DLQRLRQRSR +>MHAAABBN_01534 +MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR +TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV +SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE +LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR +>LFPAFLNI_01758 +MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR +TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV +SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE +LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000681.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000681.fa new file mode 100644 index 0000000000000000000000000000000000000000..c43ab6552f7a99de71c91cabba4bc978b23040dd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000681.fa @@ -0,0 +1,54 @@ +>ACLBLIBL_01033 +MSSTVSAPAAAPTRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI +ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTESVGWWQVLICVVIAVYYAAIIGWA +IMYTWFSVDQRWGADPETFMMGEFLQVSETPNPTFDVVSGVFWPMLAVWVITLLIMGFGV +RRGVAMASMIGIPLLVVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLKKRTNLTSSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS +VADVAGSGIGLAFIAFPTLISQAPVGALIGVLFFGSLVLAGFTSLISILEVVISAVKDKL +GWGRWTATIIVVGLAGVVSMALFSTTSGLHMLDTMDAFANNFGIVGAALVSVLLVTGVLG +SARRVTAHLNAVSSFKLGRGYVLLIGVLMPIVLAYIWLSWIMKVISEGYGGYPGDFLGVY +GWGVAIGSVVLAVVLSLIPWSRKSNLYAEEMETEIHGDLIPHNAVPEGTTPTGAIPLVPA +DHTRKEL +>MOLHKGIG_01835 +MSSTVSAPATAPKRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI +ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA +IMYTWFSVDQRWGDDPETFLMGDYLQVADDPSPSFDVVSGVFWPMLAVWVITLLIMGFGV +RRGVALASMVGIPLLIVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS +VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL +GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG +SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPV +ATTRKEL +>NAFOICDF_00974 +MSTSTGATAAPSRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYEHGGGAFVIPYLVA +LLTAGIPLLFLDYAIGHRFRGSAPMAFRRMSRWTEAIGWWQVLICAVIGVYYAAIIAWSI +MYTWFSLDQRWGDDPEGFLFSTYLQQVKDPNPSFDIVPGVFWPMVAVWGVLLLIMGLGIR +RGVALASMIGIPLLVVMFVVLVIISLTLPGAMQGLDALFTPNWAALKEPGVWIAAYGQIF +FSLSVGFGIMITYASYLKKRTNLTASGLVVGFSNSGFEILAGIGVFSALGFMAQASGVQV +SEVAGSGIGLAFIAFPTLITQAPAGALIGVLFFASLVIAGFTSLISILEVVVSAVKDKLG +WGRWTAVLVVVGISAVISISLFSTTTGVAMLDTMDAFANNFGIVGAALVAVIAVMWIARR +GGELVAHLNSVSSFRVGRVYRILVGVVMPVLLGWMWIEWIRENAATPYGGYPTDFLAVYG +WGLAIGSVVLAVLLSLIPWSHKSSLHAEESVNEIDHTAPVASKES +>MHAAABBN_01532 +MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI +ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA +IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV +RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS +VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL +GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG +SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPT +AATRKEL +>LFPAFLNI_01756 +MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI +ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA +IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV +RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS +VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL +GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG +SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPA +ATTRKEL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000685.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000685.fa new file mode 100644 index 0000000000000000000000000000000000000000..635d401f91080dbe8ea601eb5f15d36b4561c1ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000685.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01037 +MDAEQADTPTGESRLALVRRARRIDRELAATYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAATPALFARFPDAAAMAGASEAELQGLVRSTGFYRNKASAILRLSQELVERHGGEVP +GRLEDLVALPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTQDTDPVKVEHAVAE +LFPRRDWTMLSHRLIFHGRRICHARRPACGACPIARWCPSYGEGETDPEKARALLSYELK +PGREELLALMRAGLSRRELRARGHGLDA +>MOLHKGIG_01831 +METEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP +ARLEDLVALPGVGRKTEFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA +LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK +PGREELLELLRAGRTRRELRALGHGLEA +>NAFOICDF_00977 +MAPADTTTPTGETPLALTRRARRIDRALAEAYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAVTPALFARFPDAVAMAGADEVELQELVRPTGFYKNKASAVLRLSRELVERFDGEVP +DRLEDLVTLPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTEETDPVKVEHAVAA +LFPPRDWTMLSHHLVFHGRRVCHARKPACGACPIARWCPSYGAGETEPEAARALLSYELK +PGREELLARMRAGATRRQLRDEGWTLEA +>MHAAABBN_01528 +MEPEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP +ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA +LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK +PGREELLELLRAGRTRRELRALGHGLEA +>LFPAFLNI_01752 +METESTGTPTGETRPALVRRARRINRILAETYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP +ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA +LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGAGETDPERARALLAYELK +PGREELLELLRAGRTRRELRALGHGLEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000686.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000686.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0d63b739a274132c789e62aaa8cd0e33f5ee3fb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000686.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01040 +MAAVRDRLAALVERHGVPADQAPRDALTEIPASAVSTWGFDWPRAQRARPSAVLILFGSL +DDVPAHHADDRVHPDVDVLLTQRAATLRTHAGQIAFPGGRVDPEDADVVATALREAEEET +DLDPDGVEVLGVLPPVPVVVSGHVVHPVIGWWRDPSRVAVVDQAEAAAVFRMPVGDLVDP +ANRCRVARPGGRRGETPGFLVGERLVWGFTAALLDRILTLLDWDTPWDSGRVIDAHTHAP +LRG +>MOLHKGIG_01829 +MPETPASPRPTSRDAVGTSDASLAGARDQLADLVARWGAAPADAPGHHDPVSLTTVPPEA +VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI +AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD +PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL +DRVLGLLGWDVPWDDSRVRDARTHEILRD +>NAFOICDF_00979 +MSIPPLPPSSPSSARADLQRIVAEHGVAPVAGDDEAGLTTIPASSVRVWGFDWPQAARPR +ASAVLILVGELDDVPAAHDGRACGVSPAVDVLLTQRAAGLRTHAGQVAFPGGGVEAQDAD +VVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGYVVHPVIGWWRDPSRVAVVDHNEAT +AVFRVPVADLAAPANRVRVRRPGGRRGETPGFLAGDRLVWGFTAALLSRVLELAGWDEPW +AGAPLIDAGSRAVLEG +>MHAAABBN_01526 +MPETPASPHPTSRDAAGTSDASLAGAREQLADLVARWGAPPAEAPGHHDPASLTTVPPEA +VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAGRVHPHVDVLLTQRAATLRQHAGQI +AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD +PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL +DRVLALLGWDVPWDDSRVRDARTHRILRD +>LFPAFLNI_01750 +MPETPASPRPTSRDAAGTSEASLTGARDQLADLVARWGTAPADAPGHHDPASLTTIPPEA +VPMWGFEWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI +AFPGGRVDPEDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD +PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL +DRVLALLGWDVPWDDSRVRDARTHEILRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000687.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000687.fa new file mode 100644 index 0000000000000000000000000000000000000000..99579ce47df794f370ae809f120e6886a9536623 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000687.fa @@ -0,0 +1,44 @@ +>ACLBLIBL_01041 +MRRRVAEARAAAAEGQEPALAPLVAEAIGVSATDPRVAALVDELDGFGPLAGWVRAPGVT +DVLVDGSGAVWTDGAEGLLRRPQRLDPHAAQALAMRLVHRAGRRLDAAVPLADARVDGVR +VHAVLPPVSGGGTLLSLRIPAARTPSLAELAAGWPDGDLWGEALEALVRDRASVLVSGAT +GTGKTTLLAAALGCVPGDERILTVEDTAEAAPEHPHVVALQCRAANAEGAGAVGLAELIR +HALRMRPDRLVVGECRGAEVADFLTALNTGHQGAWGTLHANGAADVPARLTAMGSLAGWG +PDTVAAQARAGVDAVVHLVRDRHGRHPVELAVPDPDARGFALLPALTWTPGPGPGDGSTA +EGPGLRALAARLAGRGSR +>MOLHKGIG_01828 +MRPFVPAAPARPPRGRRRRPAPPEGGRRFPWPRTGPAEPERTQVAAPPLAAPAAGPDGLD +AAVVRRRVAEARASAADGAEPPLAPLIAEALDVPIDDPRVAALVDELDGFGPLAPWVRTP +GVTDVLVDGAGAVWTDGDGGLVRRPDRLDPETARALAVRLLHRAGRRLDAAVPLADARVG +GVRVHAVLPPVSGGGTLLSLRIPAAATPSLAALADGWPDGALWADALEALVRDRATVLVS +GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE +LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA +GWRPETVAAQARAGVDAVLHIARDGHGRHPVELAVPDLRADGFALLPALTWRPGTEATGG +RTVEGPGMPALAARLAGRSGR +>NAFOICDF_00980 +MPAWVPDAPRPARRPALLPAGLSLPAPLLPDLRRVGRRRPGSDRGEPAHVGPDPDARLRR +AVAEAQARADPHAPPPLRETVSRALADLAAEDGDTPPSGCPRPAGLRDPDAVLEELVGFG +PLAPWVRRTGVTDVLVDAAGSVWTDGVEGLVRRPLILPEPTARALAVRLIGLAGRRLDPA +CPVADARVDGVRVHAVLPPVSGGGTVLSLRVPAAEPPSLDALAADWPDGERWRDAVVALV +RGRASVLVSGATGTGKTTLLAAALGLAGADERIVLVEDTAEAAPAHPHVISLQARAPTAD +GAGEVTLAELIRQALRMRPDRLVVGECRGPEVADLLTALNTGHQGAWGTLHANAAADVPA +RLAAMGALAGWSASAVAAQARAGVDAVLHVRRDGRGRHPVELAVPAPAAHPDAPLSVLPA +LTWDGGGTRAGPGLEVLEARLSGRGHG +>MHAAABBN_01525 +MRPFVPAAPARPPRGRRRRPAPPEGSRRFPWPRTDPAEPERTQVAAPPLAAPAAGPGGLD +AAVVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP +GVTDVLVDGAGAVWTDGDEGLVRRPGRLDPETARALAVRMLHRAGRRLDAAVPLADARVG +GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS +GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVIALQCRAANAEGAGEVGLAE +LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA +GWRPETVAAQARAGVDAVLHVARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEATGG +RTVEGPGVPALAARLAGRSGR +>LFPAFLNI_01749 +MRPFVPAAPARPPRGRRSRLAPPEVGRRFPWPRTGAAEPERTQVAAPPLAAPAAGPCGLD +VAAVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP +GVTDVLVDGVGAVWTDGDEGLVRRPGRLDPETAGALAVRLLHRAGRRLDAAVPLADARVG +GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS +GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE +LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA +GWRPETVAAQARAGVDAVLHLARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEAAGG +RTIEGPGVPALAARLAGRSGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000688.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000688.fa new file mode 100644 index 0000000000000000000000000000000000000000..2cdd0eec5676907a91f410b9285ec5ff07a9185a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000688.fa @@ -0,0 +1,37 @@ +>ACLBLIBL_01042 +MSTAAPEDATEELVVVLRRWAALVSAGLTEEAAWRETVRMLPDDDGHARHAARLRAERLA +WDAAGDLSTGRDAPDVRGLRRDEHPPGDTHDASPDRSRRRWCPPWRTPPPDPGWALVDAA +LAAGARAGAAPAVVVRRLAESLEADVDAARARRSAAAGPAATARLLQWLPLGGVGLAWLL +GSSPWETVSTPFGAVVAAVGLLFWLAGRSWTRLLLRSAAREPAALTAPVVLDVLAALLGA +GRSLPAALDDLARTLPGARGLRVTSALLLWGRGWDEAWAGIGEETVWAEAAARLRPLHRS +GMAGARTLAESAAAARQQGRRADERAAEELAVRLVMPLGLCLLPAFVCWGVIPVVMALLG +AGA +>MOLHKGIG_01827 +MLVGALRRWAALVAAGLTEEQAWRETACTLPACGSGPGEAGAACCAHHRARRRAEALAWD +VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD +VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL +AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATA +ALLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER +AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG +>NAFOICDF_00981 +MIALPGRAEERAEERAQEVVEALRRWAGLTAAGMTPAEAWTAVAQASSPCGRPTPGCCPR +HEALRRAALARWGGPGRGAEGGQPRPGERSPWDLADAALAAAARAGASFSRTAARLADAL +EADVDASRARRTAAAGPRATARLLSWLPVGGLGLAWLLGMGPADLLATGFGWVLLVLGGV +LTAAGRAWTRLALRRGARPLGEASPGVVVDVAAVLLGAGRSLPAALDDVSAHLPGAADLR +VVAVLLRWGADWDEAWAPVTEEPRWAALGERLRPLHRTGMAGEAVLHQTAAALRQETRRA +DERGAEELAVRLVVPLGLCQLPAFVCWGVAPMALALLGAR +>MHAAABBN_01524 +MSPTTATGPARRSHAGRAVALLPWRAGRVPPEEETEVLIGVLRRWAALVAAGLTEEQAWR +ETACTLPACGSEPSEAGTACCAHHHARRRAEALAWDVPAAHAPTGEAARRGGTLPWRTPA +RDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADVDAARARRSAAAGPGATSRLLQWL +PLGGLGLAWLLGTSPGDLVRSPFGAVVAAVGLLFWLAGRSWTRLLLRAAAREPAAVGAAV +VLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAALLLWGRDWDEAWVGLDTDPVWAE +TAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERAAEELAVRLVMPLGLCLLPAFVCW +GVVPVVMALLGAGPG +>LFPAFLNI_01748 +MLVGVLRRWAALVSAGLTEEQAWRETACTLPACGPGPSEAGTACCAHHRARRRAEALAWD +VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD +VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL +AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRTTA +TLLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER +AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000689.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000689.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e4dbeb542b5efd953db0ee84c8650aa92af70c1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000689.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01043 +MTQLSHTVHDALATAAERHHLARVADAAADETGAITAEYGILTLAAVGFAGVLAVVLTSP +DVQSLLVELVSGALQRD +>MOLHKGIG_01826 +MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP +DVQSLLVDLVSGALQRD +>NAFOICDF_00982 +MTHNSTALTETLVPLVGPQRAAALATWAEDETGAQTAEYGILTLAAVGFAGVLAVVLTSP +EVRELLVDLVSQALQRG +>MHAAABBN_01523 +MTHRSHSAQPAVTRPSERDRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP +DVQSLLVDLVTGALQRD +>LFPAFLNI_01747 +MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP +DVQSLLVDLVSGALQRD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000690.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000690.fa new file mode 100644 index 0000000000000000000000000000000000000000..59e59b948ee25272e461223b9e271964e4714f7c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000690.fa @@ -0,0 +1,19 @@ +>ACLBLIBL_01044 +MTAEYAVLLPVIAFVLAAVLLAGAAAVQQVRGQDAATAAARILARGDGEAEARRAVARMA +GDDAALAHTADGGWVAVEVSQPGPGPLAWAEALTLTARAAAPQQHPGAAVDPDGGRT +>MOLHKGIG_01825 +MTEHPTSASPSGRRTGARTAGRPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV +QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL +AWAEVLTLTAHAAAPDQRPGTPAAGPEDRS +>NAFOICDF_00983 +MADLPAEAPRPGRLRGARAGASGTVAFRDAERGEGERGAVTAEYAVLLPAAVAVLVAVLL +AGVAAVHQVRAQDAAASAARILARGDAESLARDAVGRMAGGDAALEARTAEGWVTVTVTR +PGPGPLAAVTLSAEAVAPVQATSPTPPGRTPGITAPTGEAAP +>MHAAABBN_01522 +MTEHPTSAPPSARRTGARTAGRPRGLRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV +QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL +AWAEALTLTAHAAAPEQRPGTPAAGPEDRS +>LFPAFLNI_01746 +MTEHPTSASPSGRRTGARTAGWPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV +QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTIKGGWVTVEVVQPGPGPL +AWAEALTLTAHAAAPDQRPGTPAAGPEDRS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000693.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000693.fa new file mode 100644 index 0000000000000000000000000000000000000000..f68e929adbedad82371b6970b913d67c7b5b58bd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000693.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01047 +MSEHLDTALVDTWFAAWSRSRGYRTSPEAGRRAALRTRRPARMIPGGSGRATVDVPATWE +YVVVDPTREQLEELREALRDEEQILLTVFGDAGADPKAMGLTPQAEPERFMSMDMDPEVQ +DVEPPLLPDGYEARVDQPMEGSVRVRIMAVGASTAPEGEEELAALGWVTREDGTAVYDRI +WTSPNHRRRGLGSLVMRYLTSEVMSDGEISLGLLVASPDGRKLYEHLAWTDLGPVSIWGR +GLAADTPTAEHTGTMGA +>MOLHKGIG_01822 +MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH +MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK +AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTAPEGEEEL +AALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQK +LYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA +>NAFOICDF_00986 +MTQSIDDTLVGTWFAAWSRSRGYETRIEDGMRSALRKKRSAQRIPGGAGRAAMDIPTTWE +HVLVSPDADALAPALASLEEQPDRLVTVFGETDQDLTSAGLHSAVLPERFMSMELDREVQ +DVEPPLLPEGYEAHVDEPRPGSRRVRFYAAGALSGVPEGEEELAALGWVTFEGETAVFDR +IWTSPDHRRRGLGSLVMRHLTSEALGADDELERGLLVASPDGQKLYGHLGWTDLGPVRIW +TRADGEAPGAEHTGTMAR +>MHAAABBN_01519 +MTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPACMIPGGSGRATVDVPATWE +HVVVNPSRGELEDLREAVRDQEQILLTVFGDAGEDPKAMGLKAQAEPERFMTMDMDPELQ +DVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTVPEGEEELAALGWVTEEGGTAVYDRI +WTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQKLYRHLAWTDLGPVSIWGR +GLAEDNPAAEHTGTMGA +>LFPAFLNI_01743 +MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH +MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK +AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTAPEGEEEL +AALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQK +LYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000696.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000696.fa new file mode 100644 index 0000000000000000000000000000000000000000..df2ffc2fdd346ae6a712b44c79982b20e735db0a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000696.fa @@ -0,0 +1,85 @@ +>ACLBLIBL_01051 +MPTTPASVTASVPEGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP +ADMKKGPFGKFAVDTENGFAPYYVVHPDKKKKVTELKRELKDAVALYLATDADREGEAIA +WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAAYWGVEGTFTVAPGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGALKASAGKKVTHLDEAAASSLAQGLRGADFTVDAVED +KPYTRRPAAPFTTSTLQQEASRKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGQDAVPAQPRVYAKRNESAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRFSATAQDGRAAQFSASGTVITFKGFLDAYEEGKDAE +TEDEKAEAKDRRLPQVAEGERLVGEPIEATGHETSPPARYTEASIVAELERREIGRPSTY +APTISTIMDRGYVSKRGNALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE +LGREAWLQTFYFGAPASETGKGVEGLQQVVENLGEIDARAVNSLPITDEITLRVGQYGPY +LEKPLPADAEAGSTPPRANVPEELAPDELTPAKAEELFATAKPSERELGTDPETGRAVVA +KDGRYGPYVTEVIPEMTEEQLQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFSSMSV +DTVTLEEALRLMSLPRVVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTITQEQ +ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE +ELTAEEAYQLLADKRAKGPATRKAPARKPAARKAPAKKSAPKKKA +>MOLHKGIG_01819 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP +ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA +WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED +KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY +APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE +LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY +LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTIVA +KDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV +DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ +ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYITDGVTNITVPRGRRPE +ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA +>NAFOICDF_00989 +MPTASASTSSSVPQGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP +ADMKKGPYGKFAVDTEHGFTPYYVVHPDKKKKVTELKRELKDAEALYLATDADREGEAIA +WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVAAQYWGVEGTFTVGPDAKADGAAGSS +FTARLSTVDGARVATGRDFDDAGRLKESAGKKVAHLDEAAAASLAEGLDGKDFTVDSVED +KPYTRRPAAPFTTSTLQQEASRKLRMSARVTMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGQESVPTQPRVYAKRTENAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRFSAQAEDGRTAQFAASGTVITFKGFLDAYEEGRDAE +PEEEKDAKDRRLPQVAEGETLTGAPIQPTGHETTPPARYTEASIVAELERREIGRPSTYA +PTISTIMDRGYVSKRGSALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGEL +AREAWLQTFYFGADSADTQKGVEGLKHVVENLGEIDARQVNSLPVTEDITLRVGQYGPYL +ERRLPEGAAEGTAPERANVPEDLAPDELTPAKAEELMAAGGADERELGVDPETGRTVVAK +DGRYGPYVTEVIPEMGEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFKTMSVD +TVTLEQALQLMSLPRIVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTVTQEQA +LEIYAQPKQRGRGTAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRAPEE +LTAEEAYQLLADKRAKGSAKKPAAKKPAARKPAAKKTTTSTTTRKKA +>MHAAABBN_01516 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP +ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA +WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED +KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY +APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE +LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY +LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA +RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV +DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ +ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE +ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA +>LFPAFLNI_01740 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP +ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA +WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED +KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY +APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE +LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY +LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA +RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV +DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ +ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRDRQPE +ELTAEEAYQLLADKRAKGPATRGGAKKPATRKAPAKKTTARKKA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000700.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000700.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7f8e612b9c525c2f3f9e582e7fa9191dd1ff15e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000700.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01059 +MADPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAIERDPVLVQRFAPSLTHVVEAD +ATDPEALRQLGAQDFSTAVVGVGTSIEASVLITANLVDLEIQHIWVKAISEAHGTILKRI +GANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLGESNVRSKYG +VTVVGVKTPGEDFTYAQPDTRVGARDTLIVSGHTDLIDRFAARP +>MOLHKGIG_01815 +MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA +DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR +IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY +GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP +>NAFOICDF_00994 +MADQPRTDPNAPVLVIGLGRFGAATAEELVTQGREVLAIERDPVLAQRFAPTLTHVVEAD +ATDAEALRQLGAQDFDVAVVGVGTSIEASVLITANLVDLEIPHIWVKAISDAHGTILKRI +GAQHIIFPEKDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPTETVGFTLEESNVRQKYG +VTIVGVKTPGEDFTYAQPHTRVGPRDTLIVSGHTDLIDRFAARP +>MHAAABBN_01512 +MADTPQRTDPNAPVLLVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA +DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR +IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESKVRSKY +GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP +>LFPAFLNI_01736 +MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA +DATDPEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR +IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY +GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000701.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000701.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6d448d670b566cd91915dee92f47a698d40cec5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000701.fa @@ -0,0 +1,48 @@ +>ACLBLIBL_01060 +MSTLESSSELRTALRRSSRAVSSVVSGSPARAALSAFLLVSLVFTALLSLPWASADGRPT +ALHDAMFTAVSAVSVTGLTTLNTAEHWSVAGQVIILVAIQIGGLGILSMASLLTLAVSRH +LGLRSKLATQEAGMTTGNVGEVGRLLRVVVVTVLTCEAALAVFLVPRFAAESGSWLTGLW +HGVFYSVSAFNNAGFSLHVDGLSAVAHDPVILTVIAVGVFAGALGFPVVMVLLDKGWRYR +AWNLHTKLTVEVTLALLVLGAVLLFFFEAGNPGTNGDLGVVERIWRSLFGSVMTRSGGFA +IDDTNAHRPESLLLMDALMFVGGGSASTAGGIKVTTLAVMFLAILAEARGDREVTAHGRT +IAPETLRVAISVLALGATLVLVATLALVNIMDESLQRPLFEVISAFATCGLSVGVSAEAP +PAGKYLLAAMMFAGRVGTITFAAALALRQRRVLYRYPVERPILG +>MOLHKGIG_01814 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAAHWSPAGQV +IILVAIQIGGLGILSIASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV +LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVIIT +VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG +>NAFOICDF_00995 +MPSGALSPARRVVTAVTGVVAGSPARAALSAFALGALLFTGLLMLPAAATDGRVTPLHDA +MFTAVSAFSVTGLTTLDTAEHWTPLGQVILLAAMQIGGLGILSMASLLTLAVSRHLGLRT +KLATQESGMTTGNMGEVGHLLKVVVLTVLTCEGALAVILVPRFAALSDSWATGLWQGVFY +SVSAFNNAGFTIHEGGTAAFMHDPVILTVIAVGVFAGALGFPVVMVLVDKGWRFRSWNLH +TKLTVEVTLVLLVVGAVALFFFEAGNPATHGDMVVGQRIGHSFFGSVMTRSGGFAIDDTN +SHRPESLLLMDALMFVGGGSASTAGGIKVTTLAVMFLAIVAEARGDKEVTVHGRTIAPET +LRVAISVLALGATLVLLATLALVSIVDQPLQRPLFEVVSAFGTCGLSVGVSAEAPPAGKY +LLTAMMFAGRVGTITFAAALALRQRRVLYRYPVERPILG +>MHAAABBN_01511 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAVHWSPAGQV +IILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVLTV +LTAEAALALFLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFSLHVDGLPEIMHDPVIIT +VLGVGVFFGALGFPVVMVLLEKGWRFRQWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG +>LFPAFLNI_01735 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTALRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAEHWSPAGQV +VILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV +LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVVIT +VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHQPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000703.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000703.fa new file mode 100644 index 0000000000000000000000000000000000000000..d9b77ff9ab5073ea8c3eb8f2fdef2419c739c269 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000703.fa @@ -0,0 +1,10 @@ +>ACLBLIBL_01062 +MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK +>MOLHKGIG_01812 +MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK +>NAFOICDF_00997 +MGSVIKKRRKRMAKKKHRKLLRKTRHQRRNKK +>MHAAABBN_01509 +MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK +>LFPAFLNI_01733 +MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000704.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000704.fa new file mode 100644 index 0000000000000000000000000000000000000000..0aa0f93e982c4fdb59101991699484a6c5014851 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000704.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01063 +MSTLLPASAARVQLLVKPGCHLCEDAAATVAQVCGARGEAWEAVDGAAHPDLLERFVDEV +PVLFVDGVQRDFWRVDPARLGRLLDAPRP +>MOLHKGIG_01811 +MTADLPAATARVQLLVKPGCHLCAEAEATVVQVCDARGEAWEAVDGAAHPDLLERFVDEV +PVLFVDGVQRDFWRVDPARLGRLLDAPRA +>NAFOICDF_00998 +MAAMMTPPASAARVQLLVKPGCHLCAEAEAVVAEVCDARGTAWERVDGPAHPDLLETYAE +EVPVLFVDGVQRDFWRVDAQRLGRLLDGPAA +>MHAAABBN_01508 +MTADLPAATARVQLLVKPGCHLCAEAEATVAQVCDARGEAWEAVDGAAHPALLERFADEV +PVLFVDGVQRDFWRVDPARLGRLLDAPRA +>LFPAFLNI_01732 +MTADLPAATARVQLLVKPGCHLCAEAEAAVAQVCDARGEAWEAVDGAAHPALLERFADEV +PVLFVDGVQRDFWRVDPARLGRLLDAPRV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000705.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000705.fa new file mode 100644 index 0000000000000000000000000000000000000000..7dde9ead1b6cde3fd3f02571fdd324a246e76618 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000705.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_01064 +MSGTSPTDPQRGQNPYGQEAPGPSPYGENPYGAHPYGQAPYGQGGPAQGQPGQGHPNPGH +PAPSYADQGYPAQGGWPGQQAPGPLTAPRRPGAITASFWLILAGGLVLLASTLLAAFAMT +LPESRAMLEQQMRETYEQMGLPADQLAQMEQMTDQLLPVMSVVAAAFGVVAFLVYLLIAL +KIRKGSRAARTVGTVLAALSVLMIVTNLMMGAFNPFDLLWVGLGVAGIVMAFRPEASEYM +RLKAWERAGTR +>MOLHKGIG_01810 +MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPDPAGASPYGQNPYGAPPAAPYGAPGQA +GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFAITQPEGQ +VAIQQELDRSVEQMNLPADQAEQMRTMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG +SRAARIVGTVLASLSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKTW +QRFARR +>NAFOICDF_00999 +MSGTENSNPYGRPAGQSGPQWPDAAAQAPYGQAPDASAQAPYGAPPQGWGAPQQWGGQPG +WPAAAPVPARRPGPINAAFWLIVSAGVVFLASTVLSALVATSDAGRRELEAAMTKVWGDY +GMTPEQIREYQDMLPPMMPVMAGVMVAVGVLALLVYLLIASKIRGGSRAARTVGTVLAVL +SVLMVLAPLASGQFSPLDLLWCLLGVAGIATAYRKEATEFMRLRAWERAARR +>MHAAABBN_01507 +MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPGPAGASPYGQNPYGAPPAAPYGAPGQA +GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ +AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVVAFLVYLWVAFAIRGG +SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW +QRFARR +>LFPAFLNI_01731 +MSGTSPTDPHGSQNPYGADPYGAVPQGSTPGSPDPAGASPYGQNPYGAPPATPYGAPGQA +GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ +AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG +SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW +QRFARR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000706.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000706.fa new file mode 100644 index 0000000000000000000000000000000000000000..4034c8f59ea878bd9f1cce2274fd72686915bcff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000706.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01067 +MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG +RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL +QQERRVHFKPAAGLAGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY +CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ +LWFANEWEMPL +>MOLHKGIG_01807 +MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG +RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL +QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY +CLGLGLPFVLMALGMERGMRAVGFFTRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ +LWFANEWEMPL +>NAFOICDF_01002 +MQDNRFAEIALDGSLLAAAPVAFLAGLISFLSPCVLPLVPGYLGYVSGLGGAALDGARRG +RVALGAALFVLGFTVVFMVMNILFAQVAFRILRDLSWVMQLLGVLVILMGVVFMGGLRWF +QTERKVHVKPAAGLTGAPLLGMTFGLGWAPCIGPTLAAVFALSYTQDSSSVARAALLAFV +YCLGLGLPFVLISFGVERGMRALGFFRRHRRGVMVFGGAVLILLGAVMVTGLWTQWMVQL +QTWFQNEWVMPL +>MHAAABBN_01504 +MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG +RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL +QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY +CLGLGLPFVLMALGMERGMRALGFFLRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ +LWFANEWEMPL +>LFPAFLNI_01728 +MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG +RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL +QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY +CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ +LWFANEWEMPL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000708.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000708.fa new file mode 100644 index 0000000000000000000000000000000000000000..d3a8327ae0223c64d85bb74afc3546fb6d9ddfe2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000708.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01070 +MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA +AWEGRPGRRGRTEAADAEAEDAYTEGRFRE +>MOLHKGIG_01803 +MRIFFYGLVRVVLFVALWALFYYVMDLWMIFAVIAAAILAFAVSYLFLDRLRTGATEDLS +AAWEGRPGRRGRTETADADAEDAYTEGRFRE +>NAFOICDF_01006 +MRLFLYGLVRVVLFFVIWALCYYVFGLGMLFSTLAAVILTFAVSYLFLTRLRLDASTDLQ +NAWEGRPSRRGRTEAADAAAEDAYTDGRFPG +>MHAAABBN_01500 +MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA +AWEGRPGRRGRTEAADAEAEDAYTQGRFRE +>LFPAFLNI_01724 +MRIFFYGLVRVVVFVALWALFYYVMDLGMIFGVIAATILTFAVSYLFLGRLRAGATEDLS +AAWEGRPGRRGRTETADADAEDAYTEGRFRE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000709.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000709.fa new file mode 100644 index 0000000000000000000000000000000000000000..510d4730a376ce27714242c430178509af32fa63 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000709.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01071 +MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSRLAWAGAIGCG +LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRTLIPVLRATGVIGIVYALTFTLGVLL +>MOLHKGIG_01802 +MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAARVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG +LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGIVYAITFTLGALL +>NAFOICDF_01007 +MAATLSQWVAAARLRTLPMAVAPVIVGSAAAHALDQFRPGRALLALVVSLALQIGVNYAN +DYSDGIRGTDDARVGPFRLTVSGLVPAKTVKHAAFACFGVAAVAGLALVALSGTWWLLIV +GVASIVAAWYYTGGKKPYGYMGLGEVFVFVFFGLVAVLGTTYTQALAVNGLAWAGAVGCG +LISTALLMANNIRDIPTDREVGKMTLAARIGDGPARASYVAMLAVAVVLPLLFTGAHPWL +WLVLAAGAVAVKPCLTVLHAHERAALIPVLKATGIVGVVYAAAFALGVAL +>MHAAABBN_01499 +MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGRFHLGAALLALVVSLALQVGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFASFGLAGLAGLGLILLSGHWWFLLV +GVACVVAAWYYTGGKKPYGYLGLGEVFVFVFFGLVAVLGTTYTQAGQVSGLAWAGAIGCG +LISTALLMANNIRDIPTDRAVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPWL +LLVPLGGLLAIRPVRTVLRAQDRRALIPVLRATGVIGIVYALTFTLGVLL +>LFPAFLNI_01723 +MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG +LISTALLMVNNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGLVYAITFTLGVLL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000710.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000710.fa new file mode 100644 index 0000000000000000000000000000000000000000..721f7a7fa1e5734f84b0c1db4d35684df82685f6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000710.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01072 +MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGIAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDHAGPRLVSLVPTQLARLLAADTDPAGRTALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV +AVGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA +AAVPKTWLALDALPLLSTGKTDRQALAARFAAAG +>MOLHKGIG_01801 +MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLISLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVPAADGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAALEAHPGVAAAHVAGVPDPEWGARLCAAVVPVRPAAAPDEAVLRAHVRAALGA +AAVPKTWLLLEALPLLSTGKTDRQALAARFTAG +>NAFOICDF_01008 +MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHPAAAPDEAVLRAHVRAALGA +VAVPKTWLVLDALPLLSTGKTDRQALAARFTAG +>MHAAABBN_01498 +MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDNAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVTAVDGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA +AAVPKTWLALDALPLLSTGKTDRQALAARFTAAG +>LFPAFLNI_01722 +MPATADALARATDALAAAFDGGAPVELTADGAALPRPEARDPRRCGDPDAVAVVRSSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAAAVAPDDPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVTAADGTRAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHEAAAPDEAVLRAHVRAALGA +AAVPKTWLVLEALPLLSTGKTDRQALAARFTAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000711.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000711.fa new file mode 100644 index 0000000000000000000000000000000000000000..4038d27b3e6b3515fe76e3d4033bed57b9e4c059 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000711.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01073 +MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLVLFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP +VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG +TEKNIDAAVQAFGRRTDADPAQVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLPTPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY +LLGLVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQLGLMLFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT +GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML +>MOLHKGIG_01800 +MLALLDDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITVLAARPWSSSPRDPAP +VTDGKLRFTAAVATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG +TEKNIDAAVQAFGRRTGADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY +LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMIFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT +GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFLL +>NAFOICDF_01009 +MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGHRLALFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP +VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG +TEKNIDAAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY +LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT +GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML +>MHAAABBN_01497 +MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP +VTDGKLHFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG +TEKNIDAAVQAFGRRTDADPAQVMNPLQTAMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY +LLGLVTIPLPGGASFSLGPAAGCILVGLTLGAIGRTGPTVWEPSTEIALTLRQLGLMLFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLITAARLLGQSVDRTFGALAGIT +GQPAILDYALSRSTDVRVTEGYAQLFALIMVVKIATVPFML +>LFPAFLNI_01721 +MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP +VTDGKLRFTAAAATSALAVRDIPGISEGLVRVVALRHGGMARIAGSADRIEPGDEVVLDG +TEKNIDEAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY +LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT +GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000713.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000713.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b63ec016910adadbecda5e98cd90d0a696baef9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000713.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_01078 +MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD +QAPLRAAIFGEIKARTVETDRSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADW +TPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPDSTRVAYAVDHTGDERFTLRV +REIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE +ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLAD +VEPVTGADGVRRLLVVHDRTVARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPH +REDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGEAADWREPAFEEELYACHLAS +TAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS +SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVA +HVRGGGELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGA +VLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEWGNPIEDPEVYAAMRDYTPYE +NVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG +GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD +>MOLHKGIG_01798 +MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD +QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW +TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV +REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD +VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK +VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFDEELYACHLSATAAES +PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE +DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG +GELGRRWYEDGKKLAKRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLA +PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV +DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA +SGRYQGWEDTAWEYAFLLTALGATARIV +>NAFOICDF_01013 +MYETSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQA +DLRAAIYGEIKAHTVETDQSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTP +PVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPDGALAAYAVDLAGDERYTLRVRE +IATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYEES +DPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVDASPLPAPRVLVPRTARMLADVEP +FDMDGRRRLLIVHDRLADGTTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTR +THVGLAVRRDTTPRVLIAPLEGLREGSAPAWTEPSFDEELYMCRLAGVNLDSPFLRLSYA +SWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPSSLTGEQVRIPLTV +IRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWY +EDGKKAAKRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACL +AVVPFVDALTSILDPDLPLSALEWEEWGNPIEDPEVYATMKAYTPYENVRAVDYPAIAAV +TSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDGGHGGASGRYQGWE +DTAWEYAFLLTALGATARVD +>MHAAABBN_01495 +MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD +QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW +TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV +REISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD +VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK +VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFEEELYACHLSATAAQS +PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE +DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG +GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA +PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYEAMRAYTPYENVRAV +DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA +SGRYQGWEDTAWEYAFLLTALGATARID +>LFPAFLNI_01717 +MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD +QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADW +TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV +REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD +VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK +VDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQAAHWREPAFDEELYACHLSATAAES +PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE +DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG +GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA +PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV +DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDGGHGGA +SGRYQGWEDTAWEYAFLLTALGATRRVV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000714.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000714.fa new file mode 100644 index 0000000000000000000000000000000000000000..1f6d6240b690e1e2dd3d764f97ad77e9001a77b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000714.fa @@ -0,0 +1,49 @@ +>ACLBLIBL_01089 +MGQEFRGGLATFLAMSYIVVLNPLILSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWA +RHPFAVAAGLGVSAFVSITIATTPGLTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPE +ALKSGIVVGIGLFIALIGLVNAGFVRRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLL +TAVLVIRKVRGAILIGIVAATILANVLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTA +PDLHLLGSVDLFGAFTSVGGLMASLLVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPD +LNRVLAADALAVAVGGGASGSAHQIFVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLI +HLVPFEAVAPALVVVGFMMCQHVVQIDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVA +YAVIRTGQGRGREVHPLLWFVALAFVAYFGLGVVRASLGLN +>MOLHKGIG_01787 +MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI +LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG +LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPESLKSGIVVGIGLFIALIGLVNAGFV +RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVVATILAN +VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL +LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVAVGGAASGSAHQI +FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ +IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF +VAYFGLGVVRAALGLN +>NAFOICDF_01015 +MSSRTTGATPPGTAPSNPASPAGPRSGLDRFFGISALGSSVGQEVRGGIATFLAMSYIVV +LNPLILSGPDSTGAVLGIPRVAAATALVAAVATLAMGLWARHPFALASGLGVNAFLAITV +ATTPGLTWPDVMGLVVIAGLVMVVLVATGFRTAVFNAVPEALKTAIVVGIGLFIALIGLV +NAGFVRRLPDAAGTTVPVGLGTGGELAGWPVLVFIVGLLVTAILVIRNVRGAILVGIVTA +TVLANILEAVFHIGPSVGADGSHNPTGWALVAPSLPEWAAPDLSLLGSARPFGAFEAVGG +LMGALLVFAILLSVFFDAMGSTVGLAREAGSMDEHGNVPRLNRVLMVDALAVTGGGAASA +SAGQIYVESGTGIGEGARTGLASVVTGLMFVATIFLTPLIHLVPFEAVAPALVVVGFMMC +SQVVRIDWTDWGAALPAFLTFILMPFTYSIANGIGAGMIAYAVIRTGQGRAREVHPLLWV +VAAAFVLYFGMGVFRGILGLA +>MHAAABBN_01494 +MASRTASPPPSPAPSPAAARGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI +LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG +LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV +RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN +VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL +LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI +FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ +IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF +VAYFGLGVVRAALGLN +>LFPAFLNI_01716 +MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI +LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG +LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV +RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN +VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL +LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI +FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ +IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF +VAYFGLGVVRAALGLN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000715.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000715.fa new file mode 100644 index 0000000000000000000000000000000000000000..31c60c5b3f8cbff8d4bdd3c0e00ae2bb51ec52d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000715.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01093 +MPTEALDRVDRAIVRALTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD +PVKVGFGASAHVTLKLRQHNWRELRATLLAIPEVWHVSLVGGNVDVILLVRARDTADLRR +VIFDELQTLPGVVDTQTYMVFDDHASGQTLPPEDPAA +>MOLHKGIG_01785 +MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD +PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR +VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD +>NAFOICDF_01016 +MSTSSPLDRVDRAIVRELSQDGRLSVAALAERVHVSRAHCYSRLNRLQNSGVITGFSARV +DPVKTGFTASAHVMLKLRQHDWRELRAALLAIPEVWHVSLVGGNMDVVLLVRARDTADLR +HVIFEKLQSLPAVVDTQTYMIFDDHASGQTMPPEEGADAPRTPTAFG +>MHAAABBN_01492 +MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD +PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR +VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD +>LFPAFLNI_01714 +MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD +PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDPADLRR +VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000716.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000716.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a14638162346255f57fd808aab9ab448811f4ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000716.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01094 +MSDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQGAE +PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG +KQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHAVG +MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ +SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAHTN +TDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAMNA +EAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA +>MOLHKGIG_01784 +MSDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE +PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG +EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG +MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ +SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN +TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA +ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA +>NAFOICDF_01017 +MTSTRPGPATPDTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQGTAPGHEYP +LPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLGQDDWLF +PTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHAVGMAKAAR +LRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFAKQSAAPSL +AHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAHTNTDDPTR +YREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAMNADVELDP +LELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA +>MHAAABBN_01491 +MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE +PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG +EHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG +MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ +SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN +TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAMNA +ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA +>LFPAFLNI_01713 +MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE +PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVSLG +EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG +MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ +SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN +TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA +ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000717.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000717.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3282e53b28111735e186ad6443701a82462e851 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000717.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01095 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTKRFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPMTIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRAAIRLDDPVVFMEPKKMYWTK +AELDLEDLRAEFEERWGRVEEKKEHGEAWARAAVVRAGSDVTLVSYGPSVPTCLAAARAA +EEEGLSVEVVDLRTVNPLDEDTMVASVSKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>MOLHKGIG_01783 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>NAFOICDF_01018 +MANLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTQRFGDERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQVASHVAKMRNRTKGGAPMPIVIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYLMLRSAIRLDDPVVFMEPKKMYWTK +ADLDLDELRAEFDEQWARAQEKTAQGEAWARAAVVRQGADVTLVSYGPSVPTCLAAAQAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNVDRILDAIDDLNWDLDAEEARA +>MHAAABBN_01490 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITLRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>LFPAFLNI_01712 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLREEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMTASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLGAEEARA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000718.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000718.fa new file mode 100644 index 0000000000000000000000000000000000000000..eeaca3454e23ffcd5b9d0f93df0da6f1d702ff24 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000718.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01096 +MSNTFLLPDLGEGLTEADIVRWLVAEGDEVVVDQPIVEVETAKALVEVPSPYAGTVLTLH +GAEGQTMEVGRPLITVGAAGESGEGSAPVAGTEAQAVPPATGEDAAEADRPGALSYREEE +MAGVQPKPDKARGGDGDVAGSDEEASGAVLIGYGTSGHSATSRTRPSKRGRRGAGTTTAG +GSGAASGQGEQAGQARAPRVTSPIVRKLAREQGVDVAALTGTGPDGLITRADVLSAAQGG +DAPQAAAAPAAQPAATAGAASTVGAGSADARTGLAVVARTPISGVRKVIADQLSRSRREV +PEVTAWLDVDVTALLELRAALKAKDAENAPSLLGLIARFTLAGLRRYPVMNARIEAGADG +KDEIVEVDGVHLGLAVQTDRGLMVPSVEHAERLSADELTAAINETVTRAREGKAAPAELT +RGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHR +VTDGATASAFLTFVADCLNDPQSALARI +>MOLHKGIG_01782 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH +GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE +MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP +TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL +VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT +ALLELRASLKAKDSENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL +GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL +GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT +FVADCLHDPTAALARI +>NAFOICDF_01019 +MSNTFLLPDLGEGLTEADIVRWLVAEGDEVAVDQPMVEVETAKALVEVPSPFAGTVLTLH +GAEGETMEVGAPLITVGAVGESAGDAPPPSSAADAGTAPAADGAVPGALSYREEERAGVQ +PKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHTATSRSRPSKRARGGAGTTQAAAGAAP +AASGRAPRVTSPIVRKLARERGVDVATLTGTGPDGLITRADVLGAAGGASAPQDAQAPAP +VQTAPSAAAQAPAVAAGATDARTGLAVVARTPISGVRKVIADQLSRSRREVPDVTAWLDV +DVTALLELRAQLKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDG +VHLGLAVQTDRGLMVPSVEHAEKMSADELTRAINDTVSRAREGRAAPAELTRGTFTLNNY +GPLGTDGATPILNIPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASA +FLTFVADCLNDPQAALARI +>MHAAABBN_01489 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH +GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE +MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP +TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL +VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT +ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGQDEIVEVDGVHL +GLAVQTDRGLMVPSVEHAEKLSADELTAAINDTVSRARAGRAAPAELTRGTFTLNNYGPL +GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT +FVADCLHDPTAALARI +>LFPAFLNI_01711 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH +GAEGETMDVGSPLITIGAAGESGEGSAPVAGTEALAVPPSTGADAAEAARPGALSYREEE +MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGATRPTPAP +TAWAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPS +VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT +ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL +GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL +GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIMVRKVTEMTVTFDHRVTDGATASAFLT +FVADCLHDPTAALARI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000722.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000722.fa new file mode 100644 index 0000000000000000000000000000000000000000..d127bd65489351107143d6bc69baf4bb83fe2d78 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000722.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_01102 +MSTADPGFALPSGFEPLAEHGRVLEVVLTGLEQVEEQLDRAVSFEDPFSDTAAHHLLAAG +GKRVRPVLTVLASLLGDPALASGEVADVNAQVRQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSAAILAGDLIFARASQLMSELGMRPVRVQADTFERLVQGQLWETQGPAE +GADPVEHYYRVLAGKTGSLIAAAGMLGALLGGADEEAVQVMSAYGEKVGLAFQLADDLID +LTGTAEQIGKTPGTDLRERVPTLTTLLLDRAAAGEGPDAQEARRVRALVDGPLDTDEQLA +AAVAALTAHPAIDEAWAVTRAWVDDAKQALAPLPDSVVKTSLEGFADYVVERSAWPGARP +RAVHRRAAVRAPLGGADLSPGRSGPGRARRRAPGP +>MOLHKGIG_01775 +MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDTALGFDDLFSDTAAHHLLAAG +GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE +GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID +LTGDAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA +AAVAALTGHPAIDEAWAITRGWAEQAKQALDPLPDSAVKAALEAFADYVVGRSA +>NAFOICDF_01026 +MTTSAAGFALPSGFDPLAEHGRVLEAVLTALERVEEQLTASLEFDDVFSQTATRHLASAG +GKRVRPVLTVLASLLGDAGLAEGQVGEVGPETRQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSQAILAGDLIFARASQLMAELGPRPVRIQAETFERLVQGQLWETRGPDE +GQDLLEHYYRVLRGKTGSLIAAAGVLGAYLGGADETAVQVMADYGEKVGLAFQLADDLID +LTSSAEELGKTPGTDLREHVPTLSTILVARAAAGEGPEADDARRVLALVDGPLDTDEQLA +AAVAALTAHPAFAEAGALTRRWAEEAKAALAPLPESVVTEALAAFADYVVSRAS +>MHAAABBN_01482 +MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDSALGFDDLFSDTAAHHLLAAG +GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE +GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID +LTGNAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA +AAVAALTGHPAIDEAWAITRGWAEQAKQALDPLPDSAVKAALEAFADYVVGRSA +>LFPAFLNI_01704 +MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDTALGFDDLFSDTAAHHLMAAG +GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE +GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID +LTGDAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA +AAVAALTGHPAIDEAWAITRDWAEQAKQALAPLPDSAVKTALEAFADYVVGRSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000723.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000723.fa new file mode 100644 index 0000000000000000000000000000000000000000..7cd6c2c53545e6e6e094778652b9d22712129ca8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000723.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01103 +MSGPRLRSHAPEGYVCPFCGLVAGDVSDPGNRCELADTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAGHYENLYELPPRVLQRIALMAREVALAMKRAWSPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDLLYRQLRHPVSPEVRALKARELAAELDPAPTFLD +>MOLHKGIG_01774 +MTAPAPVSHAPDDYVCPFCGLVASDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD +>NAFOICDF_01028 +MSAQPLSHAPEGYVCPFCGLVAGDVSDPGNRCELEDTVYQDEDVLVLIAVDGFGEHDGHA +MVCPSGHYENLYDLPPRVLQRIALMAQQVALAMKRAWGPDGVSTRQHNEPAGNQHVWHYH +LHVFPRYEDDLLYRQLRHPVAPEVRAARARELAAALDPAPTLLD +>MHAAABBN_01481 +MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLIVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD +>LFPAFLNI_01703 +MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPEGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRALKARELAAALDPVPTRLD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000726.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000726.fa new file mode 100644 index 0000000000000000000000000000000000000000..db50ea4405532495d932ef7c93163f0a1dbd0a95 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000726.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01107 +MARLLVDLTPLKVSPAYRRLWVGNTLSFVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAVADRHDRRTVALASSAVMWLTTVGIAAHAWAGIESVPLLYALVALHSG +ASGINQPTRGAIIPALVGMKLVPAANALNMMTFSVAMMAGPVLGGVLVASVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRAEGEAAPTGRVGVRSVVEGLRFLGSRPNLRMTFLADIVA +MATAFPRALLPAVGGVVLGGGEAAVGVLLAAMAAGAFLAGLFSGPFTRLHAQGWGVYVSI +LVWGASVAAFGGVVWWAQGLPDGDPRLTGAFVAAALCLAVGGAADSISGVFRTTILQSAT +PDHLRGRLQGVFVVVVAGGPRVGELLTGGASVAVGEGLTLLLGGLACVLGVSLLMRRQPE +FLKYDARSPTP +>MOLHKGIG_01770 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGFESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQQAEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGGAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELITGGASVVLGEGPTLLAGGVLCMLGVSALMRWQPG +FLRYDARNPTP +>NAFOICDF_01033 +MPRLLVDLAPLEASPAYRRLWLGNALAFVGTQLTLVAVSLEVFALTGSSFAVGMLGLAAL +IPLVVAGLYGGAVADRHDRRTVALASGAVMWAATALIAAHAWAGVESVGVLYGLVALHSA +ASGINQPTRGAIIPALVGPALLPAANALNMLTFSTAMMAGPLLGGVLVASVGYAWTYTVD +VVTFLAALWAVWRLPSLPPDRSAAPDDAGRGGLSSVLDGFRFLGTRRNVRMTFVADIVAM +ATAFPRALLPAVGGTILGGGEAAVGVLLASMAAGTFLAGLFSGTFTRVHRQGRGVAVAIA +AWGLSVAAFGAVVLWAAPLPDGDPRLGPALAACAACLVVAGAADSVSAVFRTTILQSATP +DHLRGRLQGVFVVVVAGGPRVGEMIQGTASAALGEGATLVLGGVLCVAGIALLMRVQPGF +LHYDARRPTP +>MHAAABBN_01477 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRAETATASGTRWGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVTALMRWQPG +FLRYDARNPTP +>LFPAFLNI_01699 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRGEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVSALMRWQPG +FLRYDARNPTP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000727.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000727.fa new file mode 100644 index 0000000000000000000000000000000000000000..d7608eaf02f861e545eb02a1dd10d0569df2d706 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000727.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01108 +MLYLIDPRGAVWSADATIGQARARARVDGRPIDDLKFARAAMLLTLDDYVDLALRHGVEA +PRGILLDHGFVAQALAPANLKAQRANQDAMAEQLLPVERRTEDAGSLRGHRHDAAYEGAH +QDLDRRIKKAEETARETLQKTPDEDLIRHWRRLGGDVPATIEADRKD +>MOLHKGIG_01769 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFAKAAMLLTFDDHVDLALRHGVAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QSLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQAGRDR +>NAFOICDF_01034 +MLYLIDPRGAVWQSDVTLGRALARQKVDGRPVDDVPLKKAVLPIDEADVLDLGLRHGVAA +PRGILLDGGWVTQVLQPSQLKRQRANQDATADQLEPVELRTETDSLRSSRHAAVVEGAHR +DLDTRIEKAEKAAREALQAAPRRELVTHWRGMGGGLPATIQADLADAD +>MHAAABBN_01476 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR +>LFPAFLNI_01698 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000729.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000729.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a0c7d7239cae4d99e85a007359ee351719b7b71 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000729.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01112 +MTTAFEPRPHTGLAPREPEPHGPGTPGPLRPGVRGSVLIVSEHADPDTAMRHAMAWITAF +EDDCGLVLDADGTELYAVGLAGELGASLRRSPGVAEDGTPTDTSEFVDAILTGGVWRLRE +PDARAWSTAYRAAILGAAPHAVCTVWDVLPLPAA +>MOLHKGIG_01765 +MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLADGTWRLRD +ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA +>NAFOICDF_01037 +MTAQHAEPTRTDRAEPHGPGTPATLRPGERGSVLVLSPAGPPEAAMGHAVAWITAFEDDC +GLVLDRDATSLYAVSPADGLRREGDVPSDGGIAEHLDFVLAGDVWHHRGTCPPAPAGSDV +DGWALLVHRLQREAPRGALGTVWDVFPLPAAG +>MHAAABBN_01472 +MTTAFEPRPHAAAAPREPDPHGPGTAGSLRPGARGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD +ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA +>LFPAFLNI_01694 +MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD +ADPREWSTTYRAAILGAAPEAVCTIWDVFPLPAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000730.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000730.fa new file mode 100644 index 0000000000000000000000000000000000000000..a326e0c72a74aaa09a5426f6a259e83bb52e3119 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000730.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01113 +MSAPDAVRRVRVPVPVDVPLTLRPLQRGAADPTVRAVPEGVWLTLRVPDQGAPAGSPGRP +TSLLVSGAREAAGPGTVVTARAWGPGARAAVASVERLLGVDDAGWDAFDALLHRDSSAPA +LPRHVREARRTRAGLRLPAAGALSGQLITVVLEQKVTHDQARHGWRTLVRLAARIDDDGP +APGPVPSGMLPPPSPAAVLRIPSWDWHARAWVQPAQSHTVLEVARRAASIDRLGAAVAPG +DTAGIAALARRLESLPGIGPWTTAEALQRSHGAADLVAVGDYHLAQFVGQVLTGRRTDDA +GMLRLLEPWAGHRQRVVRMIGISGARKQAFGPKLAPADHRAY +>MOLHKGIG_01764 +MIAPDAERCVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDAASGGPGRP +TSLLVSGVRETAGGGTAVTARAWGAGARTAVADVERLLGLHDDGWAAFDALLRPDSGAPA +LPRHVREARRTRAGLRLPAAGALSRQLLTAVLEQKITHDQARHGWRTLVRLAARIDGDGP +APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTVLEVARRAASIDRLGDAVAPG +DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA +GMLRLLAPWAGHRQRVVRMIGLSGERKQAFGPKLAPADHRAH +>NAFOICDF_01038 +MVPPLSVPPDAVVRLAPGVPVDVAATLRPLQRGAADPTVRAAPTGVWLTRRERVDGATLP +ATLLVSPQVRGEVTARAWGPGAAAALAGLPALLGLHDTGWDAFDALLAPDPRRPSLPHAL +REARRTREGLRLPAAGHLSTQLMTVVLEQKVTHDQARHGWRTLVRLAHGIDDATPPGPAP +AGMLLPPTPRAVLAIPSWDWHARAWVQPAQSRTVLEVARRASAVDRLGAAVAPGDVAGTA +ALAARLQAIPGVGPWSAAEALQRSHGSADLVSVGDFHLAHLVGQVLAGRRTDDAGMLRLL +QPWEGHRQRVVRMIGASGASKERFGPRLAPADHRAY +>MHAAABBN_01471 +MTAPDAERRVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDVASGGPGRP +TSLLVSGVREAAGGGTAVTARAWGAGASAAVAGVERLLGLHDDGWDAFDALLRPDSGAPA +LPPHVREARRMRAGLRLPAAGALSRQLLTAVLEQKVTHDQARHGWRTLVRLAARIDDDGP +APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTMLEVARRAASIDRLGDAVTPG +DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA +GMLRLLAPWAGHRQRVVRMIGLSGERKQGFGPKLAPADHRAH +>LFPAFLNI_01693 +MTAPDAERRVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDAASGGPGRP +TSLLVSGVREAAGGGTAVTARAWGAGASAAVAGVERLLGLHDDGWGAFDALLRADSGAPA +LPRHVREARRTRTGLRLPAAGALSRQLLTVVLEQKVTHDQARHGWRTLVRLAARIDDDGP +APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTMLEVARRAASIDRLGDAVAPG +DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA +GMLRLLAPWAGHRQRVVRMIGLSGERKQAFGPKLAPADHRAH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000731.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000731.fa new file mode 100644 index 0000000000000000000000000000000000000000..944ec652c02fa64b3ea7960fdf6e65b0d4497847 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000731.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01114 +MQYAENVLELIGHTPLVKLNSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEDAEKAGK +LAPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLTAYGAEIVVTPTSV +APESEESYYGVANRLERDIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAHRVTHVVIGA +GTGGTITGTGRYLKEVSADRESGPVRVIGADPSGSVYSGGTGRPYFVEGVGEDMWVDNYD +PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARDLGPKDVMVIVLPD +SGRGYLAKIFNDPWMDERGFDYDVQDTVLPEWARGRTRSAAPEADDDGAQGAAGGAGTPV +EALEQADAAAGADAGQVADAPAEADRWAATAGELLAEKADLFPGSVPTLVTASPTTSVAD +AVATMNRYGVDALPVVAEPRHDLRIGEVRGTVSAAALGEALAAGRVHPGTPVAEAMGPVL +PCIGARTPLRAVARRLAQDPTLLVLSAGRVAGVVTLHDVLAHVTA +>MOLHKGIG_01763 +MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL +LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV +DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA +GTGGTITGTGRYLKEVSADRPSGAVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD +PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD +SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV +EALEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT +MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG +ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA +>NAFOICDF_01039 +MGAVNEINPAPAHGQPRWAENVLDLIGRTPLVKLNRVTEGVEATVLVKVEYLNPGGSVKD +RIALRMLEEAERDGKLAPGGTVVEPTSGNTGVGLALVAQQKGYRAVFVTPDKVGQEKRDV +LTAYGAEIVVTPTSVEPSSDESYYGVANRLEKEIPGAFQPNQFFNPAAPASHYETTGPEI +WEDTAGTVTHVVIGAGTGGTITGTGRYLKEVSADRASSPVRVIGADPEGSVYSGGTGRPY +FVEGVGEDMWPGNYDPSVPDEVIAVSDDAAFEMTRRLAAEEGLLVGGSSGMAVVAGLQAA +RELGPDDVMVIVLPDSGRGYLAKIFNDDWMDERGFHYAQEETVLPAWAQGRTRSAVATAP +SDSREGARGGVGTPVEAPGEGSPQDGAATATPAPGSRWDASLADVLADKEDLFPGSVPTL +VTASPDTTVADAVATLARYGVDALPVIAEPRHDLRINEVRGTVSAPALAAALAAGRVQPG +SAVSDVMEPALPSVGAAMTLRAAARRLQEDPILLVMDAGIVQGVVTLHDVLVYATA +>MHAAABBN_01470 +MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL +LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV +DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA +GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD +PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD +SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQMDDDGATGAAGGAGTPV +EVLEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT +MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG +ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA +>LFPAFLNI_01692 +MQYAENVLELIGRTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL +LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV +DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA +GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD +PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD +SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV +EVLEHADAELATRAGAPAETDRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT +MNRYGVDALPVILEPRHDLRIGEVRGTVSTAALADALAEGRATAQTPVADVMGPVLPCLG +ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000734.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000734.fa new file mode 100644 index 0000000000000000000000000000000000000000..173dbeb91c6d61e86d1a2d49baa4f345ccf22898 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000734.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_01117 +MPQNSEDRPLARGLGRAAGRAARSFQESQRADDARLRAERARLAAEDEERLSRRREDRER +GLAERDAAESDAGLVHPLLRIARMYWLALTVVLAVVAGAFVWNGMRARESGEPVVDPLTG +IESVGVLGGATGQFTMGVTVALFAAAALWGWIGLLRRRRSAIGTLTFIALLLAAPAFLRA +NGLLIVLAVIMLVGAALLWLPPVRSRLRR +>MOLHKGIG_01760 +MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER +DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG +MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA +NGLLIILAVVMLLGAALVWLPPVRSRVRR +>NAFOICDF_01042 +MADNSAENSSDRIARAAGRAARAFREGQDAERIRREQARAEAPRTADADGSRATGLRERA +VRAAAQAAERAEPLKERVGHAAGEAGRSFKENQAQDAARLRGVREQVRADDDAARAERQA +ERERALDARDETEAGRVHPLLRLTRLWWLAVSLLLLGLATAFVYNGVRADRDGGEVIDPV +TGLQSIGPLGGATGQYTVGGVLAALALVTLWGWVGLLRRRRASLGTLTTVAVLLAIPAVL +RPNPLFIVLGAAMAIGAVLLWLPPVRSRVRR +>MHAAABBN_01467 +MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER +DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG +MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA +NGLLIILAVVMLLGAALVWLPPVRSRVRR +>LFPAFLNI_01689 +MPQNSEDRPLARGLGRAAGRATQSFRENQRADDARLRAERARLTAEDEERLERRRADRER +DLAARDAAESDAGLVHPLLKVARLYWLAVTVVLVGIAGAFIWNGARAQDSGEPVIDPLTG +MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA +NGLLIILAVVMLLGAALVWLPPVRSRVRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000735.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000735.fa new file mode 100644 index 0000000000000000000000000000000000000000..35a930117f565f3bab453da8523248a5ab11e19f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000735.fa @@ -0,0 +1,66 @@ +>ACLBLIBL_01118 +MSDALDPQTTPEAQVDAAELAEARQEAAEAAAPKAETPETAAAATETDSAPEAETAEEPE +APAEPAGPTFLDLGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTG +AFALPALARLAETADVNGRADTPQVLVLAPTRELALQVADAFDSYAKHLEDVSVLAVYGG +SPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDR +ILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWK +LEAFTRILETEDHDGVIAFVRTRAGTEELAQKLNRAGFKAVAISGDIAQKQREKTVEDLK +AGRVDILVATDVAARGLDVERISLVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPR +ERFLLKQIERTTRQQVEEMAVPAVKDVNAARKRRFADGITRTLERASEEELAVFGEIVAA +YVEEHDAEPSRVAAALGMMAQGGRPLLAKEQEIPTGPRGRKERDGGRDGGREHGTADGRG +SRGPAREPAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELP +ADLTPAQLEAAANIEISGRRLGLRKDTGRPTRAERDGDERRGGFRKDRGERGGHGGHRGG +FRKDRDERGFRGDREERGGFRGDRDDRGDRGGFRKDREDRGGFRKDREDRGDRGGFRKDR +EDRGGFRKDRDERGGFRGGKAGGRKPRWGAQERSDRGPRR +>MOLHKGIG_01759 +MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL +DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD +VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ +VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS +ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG +VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR +GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ +VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA +LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA +GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA +AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG +GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR +>NAFOICDF_01043 +MTPHETIPADDQAPVDLTEFDPELAETTAEAPAAEQDADDAEADAEPAGPTFLSLGLDAR +VLAAVEDLGYQRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETQDVNG +RSQAPQILALAPTRELALQVAEAFESYAKHLDDVSVLAVYGGAPYGPQLAGLRRGAQVVV +GTPGRVIDHLERGNLDLSQLQTLVLDEADEMLRMGFAEEVDRILAETPDSKQTALFSATM +PPAIRRISAQYLNDPEEVAVARQSTTGTNIRQRYLQIAHQWKFEAMTRILETEDHEGVIA +FVRTRAGTDELAQRLNQAGFSAVAISGDVAQKQREKTVDDLKAGRVDILVATDVAARGLD +VERISLVVNYDIPQDAESYVHRIGRTGRAGRSGDAVLFMTPRERFLLKQIERTTRQEVEE +MQVPTVAQVNEARTRGVVAGIGRTLETASEADLDTYARMVAEYVEANDVDPARAAAALAL +MAQGGRPLLTEADEVPAGGRVRRDRDRDDRRERGDRSERGDRDGRGSRGPRREPAAGNAT +YWIGVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHALVELPADLTAAQLDAAANT +EINGRRLNLRKDTGRPTRAERDGDGERGHRGPREDRGGFRRDRGDRGGFRRDRGERPERG +GFRKDRDDRGPREDRGGFRHDRDDRGGRPGARKPRWGSDDRRDRGPRR +>MHAAABBN_01466 +MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL +DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD +VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ +VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS +ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG +VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR +GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ +VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA +LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA +GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA +AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG +GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR +>LFPAFLNI_01688 +MSDILDPQTTAEAAPELAEAEQEATGTVPQVDAAEPAAPEAPAGPAGPTFLDLGLDARVL +AAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRA +DTPQVLALAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGT +PGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFSATMPP +AIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDGVIAFV +RTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVE +RISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMA +VPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAALGMMA +QGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAAGNATY +WIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAE +INGRRLGLRKDTGRPTRAERDGEDRGGFRKDRGERGERGGFRGDRDGGQRGGYRKDRDDR +GSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000736.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000736.fa new file mode 100644 index 0000000000000000000000000000000000000000..a8ebf7633c82b3cfef455ac5b80e74b069d21bae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000736.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01121 +MSSHRPSSQRRPDRGPSTGPQRAGFVSPWENGSALYRALVLTGSALFLVGIVLAVVGATT +SQLTVSWFALGVLGLGVVVHLSAQMVRFRQAARRQGQRPPGR +>MOLHKGIG_01756 +MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV +SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR +>NAFOICDF_01046 +MPTSARRPEPSARSGGFVSPWEHGSRLYRGMVLTGSALFLIGIVLSVVGATAHVLALSWT +ALGVLGAGVLVHLSAQLVRLREAGRRESAARSARRKGRGSGR +>MHAAABBN_01463 +MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV +SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR +>LFPAFLNI_01685 +MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV +SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000738.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000738.fa new file mode 100644 index 0000000000000000000000000000000000000000..f463434932f8fc9c6b9e70f8b7816a78919053a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000738.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01123 +MSTAPRLSELSKGETIGTRTVPLTRADLVAYAGASGDHNPIHWSPSFAERVGLPGVIAHG +MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGQTGDDGAPVPGATLQVVGKVG +AVDEAAGTVRIDLDVTNPDAEKPRVLTKAQAVVRLAEPAPAAGESA +>MOLHKGIG_01754 +MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG +MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG +AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA +>NAFOICDF_01048 +MRAQSARPVLAELAKGQSIGSRTVPLTRAGLVAYAAASGDHNPIHWNQAFAASVGLPGVI +AHGMLTMGAAVQLVTDWAGDPGAVVDYQTRFTAMVPVADTTGQTDDAGAPVPGAVLEVSG +AVGAIDAEAGTVRIDLTVNDPAQAKPRVLTKAQALVRLTRAVETPEETA +>MHAAABBN_01461 +MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG +MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG +AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA +>LFPAFLNI_01683 +MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPTFAEHVGLPGVIAHG +MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTVRTDDDGAPVPGATLEVVGTVG +AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000740.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000740.fa new file mode 100644 index 0000000000000000000000000000000000000000..6def85b862cd374040c9b5583469fcf70f9c8603 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000740.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01125 +MTSAAPPPSPPPDAAAVPTVGLIGWRGMVGSVLMQRMAEEGDFARIRPVFFSTSNAGGPA +PTFEGLPGDAGPLQDAYDLNVLASLPVIVTAQGGDYTKDVYPRLRAAGWDGIWIDAASTL +RMEDTSVIALDPVNRSVIDAALASGVKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY +QAASGGGARHMRELLTQYADLGGVVRDELADPASAILEIDRKVLELQRDGLDATQFGVPL +GGSLIPWIDSDLGNGVSREEQKAFDETNKVLGLRGEDRIAFDSLCVRIGAMRSHSQALTL +KLTRDVPLDEVEQIIAEDNEWVRLVANTKEASVAELTPIAATGTLQIPVGRLRKLNMGPE +YLSAFTVGDQLLWGAAEPVRRMLMIATGNL +>MOLHKGIG_01752 +MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF +FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD +GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG +LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG +LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA +MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG +RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL +>NAFOICDF_01050 +MTSAAPAPVSPAAPAAVPTVGIVGWRGMVGSVLMQRMAEEGDFARIHPVFFSTSNAGRPA +PVFEGMDGDAGTLQDAHDVEALKALPIIVTAQGGDYTKAVYPALRAAGWDGIWIDAASTL +RMEDSSVIVLDPVNRSVIDAALASGTKDFIGGNCTVSCMLMGLGGLFREGLVEWGTAMTY +QAASGGGARHMRELLTQYAALGGVVAEELADPSSAILEIDRKVLELQRGGLDASQFGVPL +GGSLIPWIDSDLGNGVSREEQKAYDETNKVLGLTGDDRIPFDSLCVRIGAMRSHSQALTL +KLTRDVPLDEITEIVADGTEWAQVVPNEKEASLRDLTPIAASGTLQIPVGRLRKLNMGPE +YLSAFTVGDQLLWGAAEPIRRMLMIATGNL +>MHAAABBN_01459 +MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF +FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD +GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG +LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG +LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA +MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG +RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL +>LFPAFLNI_01681 +MTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARIHPVFFSTSNAGGPA +PVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWDGIWIDAASTL +RMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY +QAASGGGARHMRELLIQYAELGGAVRAELADPASAILEIDRKVIELQRDGLDSTQFGVPL +GGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGAMRSHSQALTL +KLTRDVPLDEVEQIIAADNEWVQVVPNTKEATVTDLTPIAATGTLQIPVGRLRKLNMGPE +YLSAFTVGDQLLWGAAEPVRRMLMIATGNL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000741.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000741.fa new file mode 100644 index 0000000000000000000000000000000000000000..04fa3c72dab8bd38c29ddfddf55e512e5d1caa29 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000741.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01126 +MAPTDPQDRLFTPQAVTFLALVACPVLAFVCAVMGLILVLQGKTIAGLVFLIVLTQVFAV +GGLIAWNKRKRAQQGR +>MOLHKGIG_01751 +MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV +GGLIAWNRRKRAQQGR +>NAFOICDF_01051 +MADLPSDEKAPLLDAQAVTFLTLIAFPVLAFVCAVMGLILVLQGKVVAGVVFLVVLTQVF +AAGGLITWNRRRRDRSGR +>MHAAABBN_01458 +MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV +GGLIAWNRRKRAQQGR +>LFPAFLNI_01680 +MAPTDSDQRLLSPQAVSFLALVVLPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV +GGFIAWNKRKRAQQGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000742.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000742.fa new file mode 100644 index 0000000000000000000000000000000000000000..a5d22fa5bd4cb365504d1d3225563e2f494c0cda --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000742.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01127 +MRSDPMSRATRPTEPAIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTASEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPVLDPRWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>MOLHKGIG_01750 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>NAFOICDF_01052 +MARHHDDGARPRQTIAMIWAQTPDGVIGADGTMPWHLPEDLARFKALTLGHPVIMGRRTW +DSFPARVRPLPGRTNIVVSRTLTATPEAGEAVRAAGAVVVPDFGAALTAADEADGLDLVW +VIGGATLYEQALDVATRAEITVVDVDAPGDTHAPALDSRWRLVAADPSPDGWLDSAAGPR +RRDERWERD +>MHAAABBN_01457 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>LFPAFLNI_01679 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPLLDARWRRTAVEPAPDAWLDSASG +PRHRFERWERD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000743.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000743.fa new file mode 100644 index 0000000000000000000000000000000000000000..861ea171abf28a2f5cea755511475a065c09494c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000743.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01128 +MSIPTPYEDLLADVMANGAVKSDRTGTGTRSVFGRQMRFDLSRSFPLITTKRVHFKSVAL +ELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAKVVE +QIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSADLF +LGVPFNIASYALLTVIVAQQTGLAPGEFVWTGGDVHIYANHEEQVREQLSREPYPYPRLW +LRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>MOLHKGIG_01749 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>NAFOICDF_01053 +MSIPTPYEDLLADVLAHGAVKADRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKSVAL +ELLWFLRGDSNVRWLQERGVTIWDEWADEGGELGPVYGVQWRSWPTPDGGSIDQIAKVVE +QIRTSPDSRRHLVTAWNPAEVDEMALPPCHAMFQFYVAPDVDGAPGVLSCQLYQRSADLF +LGVPFNIASYALLTLMVAQQTGLTPGEFVWTGGDCHIYANHEEQVREQLSREPYPYPTLR +IRRTPESIFDYEYDDFELVDYRHHPAIKAPVAV +>MHAAABBN_01456 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>LFPAFLNI_01678 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000744.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000744.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6e064db808babcb9f0eae5d15401b6779411531 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000744.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01129 +MENTAAKSQPEKIVHERLKVTRDPDRERFELRQDGTFIGFLGYAQETVPGPDGEDRTVVR +LQHTIIDEAHGRKGYARALVTMVLDRLRAEGDSIVAECSYVEDYLRRYPEYQDMVFNG +>MOLHKGIG_01748 +MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR +LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG +>NAFOICDF_01057 +METTANQHPEKIVHERLQVTRDPDRQRFEMRQDGVFIGFLGYDVEELPAADGGEDETVVR +LQHTIIDEAHGRKGYARALVTIVLDRLRAEGEKISPECSYVQDYLRRYPEYQDMVREV +>MHAAABBN_01455 +MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR +LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG +>LFPAFLNI_01677 +MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR +LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000745.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000745.fa new file mode 100644 index 0000000000000000000000000000000000000000..f18f01b71ddbd65978be7cbef3fa11e9d9802f97 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000745.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01130 +MPSTPTERVARWSTEDRAADGPRAEVLAAGVVPWRRTPGGRLEVLVIHRPRYDDWSWPKG +KLDPGETLPQCAVRELREEVGLALRPGIPLCVTEYEVSGKRGARLTKEVWYWAADAGAQR +AVPDGDEVDEVRWVRPEEAEALLTNETDREPLELLVRADSRGRLRTLPLLVLRHAKAKPR +SSWSRAEQERPLAATGRRQALAVEGLVAAWAPDRLVSSPWRRCVETLAPLVKSSRLPLKT +KGAFTETAAKEKPKKTRKAMHELLGRQRAQVVCTHRPVLPVLFEVVEDAARRQERVLRAM +PREDPWLRPGAVLVVHRSLDGDVVAVEAYDPWDD +>MOLHKGIG_01747 +MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK +LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA +LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS +SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK +GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL +PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD +>NAFOICDF_01058 +MTRPLSWDGIPDPIPPEDPRTMSAHPDDRAAAWSTPDGAVTAPGAEVLAAGMIPWRPGAE +GLEVLVIHRPRYDDWSWPKGKVDDGETLPEAAARELAEEVALTLRPGLPLAVTRYDVPDR +KGKGMLSKEVWYWAGEATGQRPTPDGDEVDEARWVSSARAREMLSNATDLEPLDRLERAD +ARGHLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQAHSVARLIAVWRPERVVSSP +WRRCVETLAPFVKATRLPLKTKSAFTETTAREKPKKTRRAFRDLLARRRPQVLCLHRPVI +PSILEEVDDAAARPASDVLAALPRRDPHLRPGGVLVLHQGLDAKGAVVAAEVYDPWSD +>MHAAABBN_01454 +MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK +LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA +LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS +SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK +GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL +PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD +>LFPAFLNI_01676 +MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK +LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA +LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS +SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLPLKTK +GAFTETTAREKPKKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGQADRVLRAL +PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000746.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000746.fa new file mode 100644 index 0000000000000000000000000000000000000000..eac49058bf23ed1cd6766256bfe0aacf5c9c42eb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000746.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01131 +MAENPVPATPTDPAAPRVSEPRPDEVDAVLALADRAQAADGHPPLSDQTRVVLARGRQRW +WGVVREADGSVSGAAVLAPEGGEDSGSVLELVVDPEARRAGRGAALADAAAAAVRERGLE +STTSVWAHGMLPGSDALARRHGLEPVRELRRMRLPHEALADLPQPQLADGVALRGFVPGR +DEQAWLDANAAAFADHPEQGGLTRADLEDRMAEDWFEAEGLLLAVREEDDALLGFHWTKV +EPQAGPGPRVGEVYAVGVTPATQGLGLGRALTLAGLHRMAGQGVDVVDLYVDADNAAAVR +LYESLGFGLFAADAQHRRP +>MOLHKGIG_01746 +MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW +WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT +SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ +AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD +AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY +ASLGFELFAADAQYRRP +>NAFOICDF_01059 +MSEQPASPALPPTPGVVSPGTPSDVDAALALADRAHRSDGHPPLNDQTRAVLARDAQRWW +GLTRDEAGAVTGVAVLAPEGEAAGPGVVELAVDPAHRGAGLGAALAEAAADAVRERGEAR +RTSAWAHGALPGALALARRHGLEPVRELRRMRLDPAGLGALPPTRLPEGVTLRGFVPGRD +EDAWLALNAAAFADHPEQGSLTRADLDAREAEDWFEAAGLLLAEDAEGTPVGYHWTKVTP +AEAGAPSEGEVYAVGISPAAQGRGLGRALTLAGLHHMAGRGVDAVDLYVDADNVPAVRLY +ESLGFALAAADVQLRPAR +>MHAAABBN_01453 +MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW +WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT +SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ +AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD +AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY +ASLGFELFAADAQYRRP +>LFPAFLNI_01675 +MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW +WGATRGTDGAIDGAAVLVPEGAAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREATT +SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ +AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD +AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVALY +ASLGFELFAADAQYRRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000751.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000751.fa new file mode 100644 index 0000000000000000000000000000000000000000..c3e9bdcb5f47942c71d2297c94cdeebb4fdd4e1e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000751.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01136 +MSGAPSFAGVLALGLARRLGLPDTALLPDDDGATKPRRLEAVREDAAEAEVLALPWATVV +AGPAWFAAACRNVPAEVLGVESALLRTAAGAAPGAGSGGGAAVRSRGEFTLYAAEEPPVL +EPSRSVAVSEDPAHALAVAAQAPADDLAEAAAQAWTSSASLVPDDGAGHGLEAPVAAAGH +RVSGGILAELGVLTVPRLRGHGLGRYAAAVAMDRATLEGLLPVAHLRAGHTAAHHVAIAV +GLEPVGSRTVLALG +>MOLHKGIG_01741 +MRPDHPAVGVLALGLARRLGLPDTALLPDDAPAAGAEPRRIEVARQGVAEAEVLALPWAT +VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR +TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG +GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA +AGTRTVLALD +>NAFOICDF_01065 +MTAAEPLPEHVRELVALAWGRALGVPDDVAALARATGRRVALPRPAGPETDILLLEAAGL +EVLAGPEPLLAAAADRATEELALESTLLRLASGWGPRSRGEHTLLHLDEPPEVAPSGRVA +VSDDPADAAALARECPADDARAAGLDELHALRTLVPDDGAGRATGTPLAAAGHATRAGLL +ADVRVLVRPELRGRGLGAYAAAVAAGAAWDEGLVPQARVPAAQDGALRLALGVGFVPTGR +LTRVELTRAG +>MHAAABBN_01448 +MRPDHPAVGVLALGLARRLGLPDTALLPGDAPAAGAEPRRIEVARQDVAEAEVLALPWAT +VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR +TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG +GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA +AGTRTVLALD +>LFPAFLNI_01670 +MRPDHPAVGVLALGLARRLGLPDTALLPGDAPAAGAEPRRIEVARQGVAEAEVLALPWAT +VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR +TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG +GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA +AGTRTVLALD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000752.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000752.fa new file mode 100644 index 0000000000000000000000000000000000000000..1faba259624fbd2d6f1cd775640fe15170f1d33c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000752.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01137 +MRVGMLTSGGDCPGLNAVIRSAVLHGIKTYDMEMVGIRNGWSGLIEKDVEELPRTRVRGL +ARNGGTILGTSRTHPYDTEGGGPENMRRNMRELGLDAVIAIGGEGTLAGANRLAADGLPI +VGVPKTIDNDLRGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMEQVAEWVKQVHDRGRSPLVVVAEGFIPEGHDDPLSEAGVED +SGRPRLGGIGEWVTREIEAMTGVETRNTVLGHIQRGGAPTATDRVLSTRFGMGAVDLAAQ +KRWGQMVAANGTDIISIPMSAALKGLKEVPVERYEEAKVLFGR +>MOLHKGIG_01740 +MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL +ARTGGTILGTSRTHPYNAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI +VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFIPEGHDDPLAEAGVEA +SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ +RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR +>NAFOICDF_01066 +MRVGLLTSGGDCPGLNAVIRAAVLHGIKTYDMEMVGIRNGWAGIIEQDVEDLPRTRVRGL +ARTGGTILGTSRTHPYDADGGGPENMARNLRELGIDAVVAIGGEGTLAGANRLAQDGLPV +VGVPKTIDNDLQGTDYTFGFDTAVEIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMSQVAEWVTQVHEKGRSPLVVVAEGFIPEGHDDPLADAGMEA +SGRPRLGGIGEWVTREIEEMTGIETRNTVLGHIQRGGAPTARDRVLSTRFGMGAIDLAAQ +HRWGSMVAARGTDIITIPMSAALKGLKEVPRERYDEAKVLFGR +>MHAAABBN_01447 +MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL +ARTGGTILGTSRTHPYDAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI +VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA +SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ +RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR +>LFPAFLNI_01669 +MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL +ARTGGTILGTSRTHPYNAEGGGPKNMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI +VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA +SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ +RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000753.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000753.fa new file mode 100644 index 0000000000000000000000000000000000000000..50a042719546a0825a54ca63222464413b8c5bc4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000753.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_01139 +MRRSDSSWVGGVLAGVAERYRVDPLLARGVFVALCVVSAGFGLLAYAVAWALLPDGDGTV +HYGRLRRGEWQDATVAIAVIGGIGVLNVVLGAGFTLLAPVVGGPGSLLGLAAVAVLVWWL +VTRWDGSTQSRVGPAPASEPEASGRAAARPAWYLRRDDARAAASRQDAHGFRADWLDPET +GTWRSPVHSRELRAAARLAEEEQAAPAGPSGRGSAVVAAPRRLSPAVQAVTYAVAALAAA +AAVGASLLVGVGSLTLLAVPAIVAALAVIAPVMLAALLTGRRPGSLAPASGILVGAAALQ +VAVAVAVL +>MOLHKGIG_01739 +MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG +VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDPDGRVQFGRLRRGEWQDATV +AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG +RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA +TRLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP +TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG +>NAFOICDF_01068 +MDTAHDPFPAPRSSPATRPLPPGPASDARSRSAGTDGPAPDGLEVLPVWLRRPVEGWGVR +RSRSSWVGGVLAGVAERYRIDPLLSRGVFVALCVVSAGIGLLGYALAWAVLPDADGRVHY +GRLRRGEWSDAPVAIAAIAAIGALNVVLGAGFTLIAPVLGGPGSLIGLTALAVLVWWLVT +RWDGEGERRMAPAQPARDAAARPAAEPSWYLRRHRPESATVDAHGFRSDWIDPETGSWRE +QPHSREHRAAARLAEAQVRAAGQAAGRRPAGTGRGSHSAVKPLLGRGTRIATCVVAAGVA +LAVSLAMVLGNVSTSATLFPVWPALAALGVMAAVMTAGLLRGRRPGLLAPLSGILVGVVA +LQVCAHLLFTPLP +>MHAAABBN_01446 +MTSTHDPFTGPGPHVAPDGAASGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG +VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDADGRVQFGRLRRREWQDATV +AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLLGLGALAVLVWWLVTRWDGRAQARVAPG +RAPDADQPSHAVPRPAWYVGGGPRERAAEVTDPHGFHPEWIDPATGTWRDHVHSRERRAA +ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP +TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG +>LFPAFLNI_01668 +MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG +VAERYRIDPLLARGVFVAVCMISAGLGLLAYAAAWAVLPDADGRVQFGRLRRGEWQDATV +AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG +RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA +ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP +TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000754.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000754.fa new file mode 100644 index 0000000000000000000000000000000000000000..6156c5db83c5107157aff1bde1a2b4e6bbee88ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000754.fa @@ -0,0 +1,42 @@ +>ACLBLIBL_01140 +MPASAVPPSAPSGRAGPRRAAADDARTRPIGADPRTSEARASGTRAPLMRHRADRPVSGV +AAGAARHLGLSPRTARAGFAVLALAGGAGLALYVWLWLLMPEEGADGAPTGEAPSLRGRA +PEVLERVREGGWPVLLAAVVLGVGVITIADGLGLAVDWALVGPVAVLVIGLGLAWMQLDL +AGGPPAGRVGRVVRLALGTALVLLAVLAIVLGGVTSGDLWLGLLVAVALIAGVAMVAMPY +ALSWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAHDPEAVARAARAQEREL +RRFLALDDRGGHDSLAATLREHAAAVEDAHGRRVEVVAVGEASGAWLEPLTAAAREAMLN +AARHAGDAQVFAEVAEDDDGRTVAEVFVRDRGPGFDPGAVPADRLGVRESVVGRMERAGG +AARIRSGPGGTEVHLTLTRPDRVPPHAAQERP +>MOLHKGIG_01738 +MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY +VWLWLLVPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG +LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA +VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL +QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR +VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDRGRTVAEVFVRDRGP +GFDLPTVPADRLGVRESILGRMGRAGGTARIRSGPGGTEVHLTLAEPEGARARTGQEHP +>NAFOICDF_01069 +MPAPAIPPPADLSARPALLRHAADRPVSGVAGGVARHLGLDPRLARAGFAVLALAGGAGI +ALYAWLWLLMPEEGPDGAPAGPAPTLRGRAPEVLERLREGGWPILLAVVVLGVGVLTVAD +GLGVPVDWALVGPVAVLVIGLGLAWMQLGAADGPEGGRWARRARLGLGTALVLLGVLAIV +VGAVTAGDLWLGLLVAVALLAGGALVAMPFVLARRRRRDEERTGAAVRAQRDEIAAHLHD +SVLQSLALIQRRADDPETVARVARAQERELRQFLALDSARAHGTLAEAVEDHAAAVEDAF +GRRVEVVSVGEASGPWLEPLASAAREAMVNAARHAGDVQVFVEVSEDDGGRTLAEVFIRD +RGTGFDLADVPADRLGVRESILGRMRRAGGTARIRSGPSGTEVQLSLADPGAPGVGLREG +RGRA +>MHAAABBN_01445 +MPTPSAPAQAPRPPLMRHGADRPVSGVAAGLARHLGVPVGRVRAALALLSLMGGAGLALY +VWLWLLMPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG +LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA +VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQVQRAEIAAHLHDSVL +QSLALIQRRAHDADAVARVARAQERELRQFLALDSRGGPRSLAEALEEHAAAVEDAHGSR +VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDHGRTVAEVFVRDRGP +GFDLHTVPADRLGVRESILGRMERAGGAARIRSGPGGTEVHLTLTEPEGARARAGQEHP +>LFPAFLNI_01667 +MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY +VWLWLLMPEERPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG +LAVDWALVGPVAVLVIGLGLAWMQLDLAGGSRAGRSGRLVRLVLGTALVLLAVLAIVLGA +VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL +QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR +VEVVAVGRAAGAWLEPLAAAAREAMQNAVRHAGDAQVFAEAGEDERGRTVAEVFVRDRGP +GFDLHTVPADRLGVRESIVGRMERAGGTARIRSGPGGTEVHLTLTEPEGARARTGQEHP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000757.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000757.fa new file mode 100644 index 0000000000000000000000000000000000000000..42f15dc5ad1ccc03520067233ef70cd9c31cbd80 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000757.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01144 +MTDIAANGGGSTPAPDRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVA +FMILLVMGLDWVFGTVAGLLFGGGGGL +>MOLHKGIG_01734 +MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI +LLVMGLDWVFGTVAGLLFGAGGL +>NAFOICDF_01073 +MTANHGSSASGPESRRRGPFGRIALFLRQVLDELRKVVTPTGDELLKMTGVVLAFVAVMI +LLVMGLDWVFGTLAGLLFGAGPA +>MHAAABBN_01441 +MAANGGGPTPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI +LLVMGLDWVFGTVAGLLFGAGGL +>LFPAFLNI_01663 +MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI +LLVMGLDWVFGTVAGLLFGAGGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000759.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000759.fa new file mode 100644 index 0000000000000000000000000000000000000000..6dd8f20f2d4577404c265a10de1776fd5f26901d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000759.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01146 +MAPKKKVSGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFITKTPPAAELIKKAAGVAKGSATPHTAKVGKLTQAQCEEIAQTKMEDLNA +NDVKAAAKIIAGTARSMGITVEG +>MOLHKGIG_01732 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG +>NAFOICDF_01075 +MAPKKKVAGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATEAQRGNVIPVEI +TVYEDRSFTFITKTPPAVELIKKAAGVQKGSSTPHTAKVGTLTQAQCEEIAQSKMEDLNA +NDVKAAAKIIAGTARSMGITVEG +>MHAAABBN_01439 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG +>LFPAFLNI_01661 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000760.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000760.fa new file mode 100644 index 0000000000000000000000000000000000000000..079152793aa1c36d817b38d8115875e774894bef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000760.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01147 +MAQRSKAYKAAKAAIGEDVYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGERAEAARAAGADVVGDDDLIAKISEGWVDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVTDIKGGKIDFRVDKHSNLHFIIGKTSFE +AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVSMDPNVTSVDSSEL +>MOLHKGIG_01731 +MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE +AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL +>NAFOICDF_01076 +MAQRSKAYKAAKAAIGDTVYAPAEAIALAKETNPSKTDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGERAEAARAAGADHVGDDDLIAKIADGWTDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE +ANQLVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVQMDPNAAPPKDEAQA +>MHAAABBN_01438 +MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKIDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE +AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL +>LFPAFLNI_01660 +MAQRSKAYKAAKAAIGEDLYSPAEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE +AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000761.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000761.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c17ffa4fc262781c310726c2730d88abdeaf322 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000761.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01148 +MATSAKESAVAELTDLFRESNAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKEAGVEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKIADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAQQGEAA +>MOLHKGIG_01730 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KQLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA +>NAFOICDF_01077 +MATSAKESAVAELTDLFRSSSAAVLTEYRGLTVSELKQLRDSIRQDATYSVAKNTLTEIA +AKEAGVEGLDAHLAGPTAIAFVTGDPVTVAKALRDFAKDHDKLVLKGGYMDGQPLDEAGI +EKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTARTVEALRAQQDQAA +>MHAAABBN_01437 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA +>LFPAFLNI_01659 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000762.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000762.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b95b3524cb371d268b1d689334f71545dfa6ea3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000762.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01149 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAAGAAGGDAAAAEEKD +EFDVVLESAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG +AGATVTLK +>MOLHKGIG_01729 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRAITSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK +>NAFOICDF_01078 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAMAAAGAPAGGDAAAAEEKD +EFDVILEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG +AGATVTLK +>MHAAABBN_01436 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK +>LFPAFLNI_01658 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000764.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000764.fa new file mode 100644 index 0000000000000000000000000000000000000000..05626cd42870c1f4483e4817531cbfda17a8bb88 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000764.fa @@ -0,0 +1,115 @@ +>ACLBLIBL_01151 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEGRHRDLANLQAEYDQETRVLADQRDADIAAVAADLEKD +LAKLESEGAKAAEKKKARDAADKTMSQIRKRADAELDRKEQVWDRFKNLKVADLEGDEGL +YRTMRDKYGQYFEGSMGAEAIQRRLQTFDLAAESEMLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDAVGAGN +AYATVGEAVMAFDGGDLHLNAPVKIGVDGFVPSTAVPAPEGWSEGELAVIETTLGKVLFN +ELLPADYPWLDTQATKGSLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQALRVQQQYEKGLIADDERRSELIDIWNKATDEVAAAMKDGLP +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREEDCGTERGLSVTIAVPNADGELVAHE +QVENSAFARTLAQDVTGEDGSVLASGGADVGDVLIDQLVGAGVSEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTDASVRLLLTPDDGSEEIAYPVLRRARILVADGEH +VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGETDLLPGELTDRARFVAANRSAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA +SPAGFADFDYPGLDQQLGESDFHAVSLDDYGRGGDFRS +>MOLHKGIG_01727 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD +LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN +LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN +ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE +QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH +VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA +SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA +>NAFOICDF_01080 +MTTENPFGLMRIGLATADDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEARHRDLPNLQAEHDQETRVLEDQRDADIAAVAADLEKD +LAKLEAEGAKAAEKKKARDAADKTMAQIRKRADAELDRKAQVWDRFKNLKVADLEGDEGL +YRAMRDKFGAYFEGSMGAEAIQRRLQTFDLAAESELLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNVKSAKRMVERFR +PQVWDVLEEVISEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRAEGKGAGR +QFATVGEAVMAFDNGELHLNAPATIGVEGFVPSAAVAAPEGWTEGEVALIETTLGKVIFN +DLLPADYPWLDTQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKASIMQGYEDQAQRVQAQYDKGLIADDERRSELIDIWNKATDEVAAAMKAGLS +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTGRGLSVTIAEPNHDGELVVRE +QVENSAFARTLAQAVTAEDGTVLAEAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTDASVRLILTPDDGSEEIAYPVLRRARLLVADGEH +VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVQEVQDVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGETDLLPGELTDRSRFVAANRAAVAEGKQPAAGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKEDPLLGLKENVIIGKLIPAGTGLDRYTQTTVEPTEEAKANLFA +APVGFADFDYPGLDQPLGEAEFHAVSLDDYGRGGDFRA +>MHAAABBN_01434 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD +LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN +LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN +ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE +QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTEASVRLLLTPDDGSEEIAYPVLRRARILVADGEH +VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA +SPAGFADFDYPGLDQSLGENDFHAVSLDDYDRGGDFRA +>LFPAFLNI_01656 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD +LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN +LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN +ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE +QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH +VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA +SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000765.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000765.fa new file mode 100644 index 0000000000000000000000000000000000000000..36db97e44fc1bf036e44fb4758f2b9d4a09b1e2b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000765.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01152 +MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK +>MOLHKGIG_01726 +MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK +>NAFOICDF_01082 +MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +VEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK +>MHAAABBN_01433 +MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK +>LFPAFLNI_01655 +MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000767.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000767.fa new file mode 100644 index 0000000000000000000000000000000000000000..091b9510a7688b09a994e1fa0a8168909077be35 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000767.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_01154 +MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE +RGITITSAAVTCFWNDNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVNRLGARPLVMQLPIGAENDFVGVVDL +LSMKAFVWPGDAKGDVTMGAEYETREIPAELQEKAEEYRAQLVEAVADTSEELMEKYLEG +EELTTEEIQAGVRHLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHDV +KDEEVELEREASKDAPFSALAFKIASHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDAAHPIILESMTFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTADGEIYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVKALVPLS +EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE +>MOLHKGIG_01724 +MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE +RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL +LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG +EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV +NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS +EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE +>NAFOICDF_01084 +MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE +RGITITSAAVTCFWKNNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGAKPLVMQLPIGSESDFIGVVDL +LTMKAFVWPGDAKGDVTMGAEYETQEIPADLQEKAEEYRTQLLEAVADTSEELMEKYLEG +EEISEEEIVAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHAV +GDEEQVLEREPSKEAPFSALAFKIASHPFFGTLTFIRVYSGRLEGGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPQNPIILESMTFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNDETGQTEIGGMGELHLDVFVDRMRREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPVLLEPLMAVEVRTPEEFMGDVVGDLNSRRGQIQSMEDATGVKVVNALVPLS +EMFGYIGDLRSRTQGRAVYSMTFHSYSEVPKNVADEIIQKSQGE +>MHAAABBN_01431 +MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE +RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL +LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG +EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV +NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESITFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS +EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE +>LFPAFLNI_01653 +MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE +RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL +LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG +EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV +NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS +EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000768.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000768.fa new file mode 100644 index 0000000000000000000000000000000000000000..4dd88ad707f14628046212ed2578a36105e83c54 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000768.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01155 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDDAPVIRTSGLKA +LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVAPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MTVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>MOLHKGIG_01723 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>NAFOICDF_01085 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEKRDFASIDSAPEERQ +RGITINISHVEYQTDKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA +INSEVEIVGIRPVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVQPGS +ITPHTDFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKINK +>MHAAABBN_01430 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDPQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>LFPAFLNI_01652 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000769.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000769.fa new file mode 100644 index 0000000000000000000000000000000000000000..49514fc026099442eff1f6bb5e0afb3e7aefaf49 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000769.fa @@ -0,0 +1,10 @@ +>ACLBLIBL_01156 +MPELLITLLVLAAAVVAVVWALRTFRPEIDRARRIRRANRNGELRR +>MOLHKGIG_01722 +MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER +>NAFOICDF_01086 +MEWLIALVVIAAVVAGGLWARRAFAPEIERARRIRRAERGGRLER +>MHAAABBN_01429 +MSDDGAAAAARLGSMPELLILIVVLAVAVVAVRWALRTFRPEIDRARRIRRANRGGELER +>LFPAFLNI_01651 +MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000770.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000770.fa new file mode 100644 index 0000000000000000000000000000000000000000..90d3a35b90a3db9d3b3e76368cb684276047fffc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000770.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01157 +MSLPSPRSLFRVTAAAEMVTWAGLLTAMALKYTGVTDAVMPIAGGIHGFVFLCYFVVTVA +VWIDGRWPAARGLLGLGSAVVPFMTVPFERAQLRRGEPARHWRVLEGEPGERTGAQRVLA +AVLGRPLVSALVALIAVVVVFTLLLNAGPPTEWGR +>MOLHKGIG_01721 +MSLPSPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA +VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERRPLERLLV +VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR +>NAFOICDF_01087 +MRVPGPRSLYRATAVAEMATWTLLLLAMALKYGGVTAALMPAAGGVHGFVFLCYAAVVVA +VWIDGRWGVGRGLLALGSAVVPYMTVPMERALLRRGEPAPRWRVLEEAGRTSATDRLLRT +VLRRPRVSALAVLVAVVVVFSLLLRAGPPTEWFSR +>MHAAABBN_01428 +MSLPGPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA +VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERGPLERLLV +VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR +>LFPAFLNI_01650 +MSLPSPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA +VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERRPLERLLV +VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000771.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000771.fa new file mode 100644 index 0000000000000000000000000000000000000000..550aaccbd2ec181bae721251977e10860861d652 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000771.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01158 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>MOLHKGIG_01720 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>NAFOICDF_01088 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>MHAAABBN_01427 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>LFPAFLNI_01649 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000775.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000775.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ace828ca3cf6d9140a4cb9b86c6435c81e0ac8f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000775.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01162 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG +PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG +EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR +>MOLHKGIG_01716 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG +PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG +EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR +>NAFOICDF_01092 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLIDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLQQGDVVEAG +PNADIKPGNNLPLRNIPVGTTIHAVELRPGGGAKMARSAGASIQLVAREGKYAQLRLPSG +EIRNVDVRCRATVGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNPNGKPEGRTRRPNKESDKLIVRRRRTGKNKR +>MHAAABBN_01423 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG +PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG +EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR +>LFPAFLNI_01645 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG +PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG +EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000777.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000777.fa new file mode 100644 index 0000000000000000000000000000000000000000..398dce7c5aa93b4649edf30443dd0ca9754f2ce9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000777.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01164 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG +N +>MOLHKGIG_01714 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG +N +>NAFOICDF_01094 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGVAFNEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASQDEKGG +N +>MHAAABBN_01421 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG +N +>LFPAFLNI_01643 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG +N diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000779.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000779.fa new file mode 100644 index 0000000000000000000000000000000000000000..63528e06de4bb8df03957c41e02f041c4889870f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000779.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01166 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL +AIHKLPLKARVIRREGGE +>MOLHKGIG_01712 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE +>NAFOICDF_01096 +MLIPRRVKHRKQHHPKRSGMAKGGTTVTFGEWGIQALSPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL +AIHKLPLKARIIRREGGE +>MHAAABBN_01419 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE +>LFPAFLNI_01641 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000781.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000781.fa new file mode 100644 index 0000000000000000000000000000000000000000..631a9c66a0d0c928f3e18b0b807efb66e8f737fc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000781.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01168 +MTEQTPAVSEERGYRKALRGVVVSDKMDKTIVVEVEDRKKHSLYGKVMKTSKRVKAHDED +NTAGIGDRVRIAETRPLSASKRWRLVEIVERAK +>MOLHKGIG_01710 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK +>NAFOICDF_01098 +MTEQTAAPVEERNYRKSLRGVVVSDKMDKTIVVEVEDRKKHALYGKVMKTSKRVKAHDED +NTAGVGDRVLIVETRPLSADKHFRLVEIVERAK +>MHAAABBN_01417 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK +>LFPAFLNI_01639 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000784.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000784.fa new file mode 100644 index 0000000000000000000000000000000000000000..62d9335e5dac729166ebfa8d8b41a9491bbd3bb3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000784.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01171 +MTEVQQTEKVAPRLKTKYREEIRATLQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII +DGAVTDLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDQ +>MOLHKGIG_01707 +MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII +DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDQ +>NAFOICDF_01101 +MTEVQQTEKVTPRLKTKYREEIRASLQEQFEYANVMQVPGLVKVVVNMGVGEAAKDSKII +DGAIADLTAITGQKPMVTKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDK +>MHAAABBN_01414 +MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII +DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDQ +>LFPAFLNI_01636 +MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII +DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000785.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000785.fa new file mode 100644 index 0000000000000000000000000000000000000000..23a2f0d8dcc84236c961e82385af191d2d6567c7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000785.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01172 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKSEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>MOLHKGIG_01706 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>NAFOICDF_01102 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKVRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTDRQASQ +KGVGGEVLAYVW +>MHAAABBN_01413 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>LFPAFLNI_01635 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000786.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000786.fa new file mode 100644 index 0000000000000000000000000000000000000000..53668ccd2d43a8f99ec87052a5e8d73138c38bfd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000786.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01173 +MSRIGRLPITIPSGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTTGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>MOLHKGIG_01705 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>NAFOICDF_01103 +MSRIGRLPITVPSGVDVTIDGARISVKGPKGQLEHTLPSPITATLEEGQVIVARPDDERE +SRSLHGLSRTLINNMVLGVTEGFTKALEVVGTGYRVQAKGQDLEFALGYSHPVPVKCPEG +ISFTVEGNKVTVAGIDKQKVGETAANIRKLRKPDPYKGKGVRYAGEQIRRKAGKAGK +>MHAAABBN_01412 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>LFPAFLNI_01634 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000788.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000788.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a1f3d5d50dce26afa018d240373d84cae4c96da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000788.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01175 +MTENNNQKDTQVTESTETTVSETASGSSSQTTERSAGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVAINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSAKAGA +>MOLHKGIG_01703 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSAKAGA +>NAFOICDF_01105 +MTETNDQKDTQVSETTETTVSETSAGSAGQSTERSGGRGGRDGGRGGRDGDRRGGRRDDR +NRRGAQEDEKDAFLERVVAINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVPA +AIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLECA +GIHDVLSKSMGSANAINIVRGTVDALKRLEEPQAVAARRGKALDEVAPHAMLRTMENDRA +SKGAQKAGV +>MHAAABBN_01410 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSAKAGA +>LFPAFLNI_01632 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSAKAGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000789.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000789.fa new file mode 100644 index 0000000000000000000000000000000000000000..339ab96491d101ca6f7061ad774e25c68390709e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000789.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01176 +MTEPTRKNIQPSDATLVITQTRGVTGTKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>MOLHKGIG_01702 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>NAFOICDF_01106 +MLQTTRKNIQPSDATLVITQTRGVTGTKQNQRDTLRSLGLKRIGHQVTRKADAATVGMVN +TVPHLVSVEEVNHG +>MHAAABBN_01409 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>LFPAFLNI_01631 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000791.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000791.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd9ce45f5e2693693f54c00f2f0295d9e021d1ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000791.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01178 +MFKAIARIVRTPDLLRKIAFTLGIIAVYRMGAFVPSPGVDYPAVQQCLAAGNAQGGLYSF +VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQSTLTQYTRYL +TLALSLLQATTMASLARTGALLGCQLPLLRNDSILTVLLVVVVLTAGCIIVMWLGERVTE +NGVGNGMSLLIFASIAAGFPAGLGQVVQTQGWRVFAIVMLIGLLTMLAIVFVEESQRRIP +VQYAKRQIGSRTVGGSSTFIPIKVNMANVIPVIFASSVLMLPGILIQFNTPQDGTAPAPW +IAWLSRYFGNGDHPVYMAVYFLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITLAGALYLGIVAMIPLIAFVVIGASQNFPFGGTSILIMVGVGLQTVKQ +VNAQMEQRHYEGLLR +>MOLHKGIG_01700 +MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF +VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL +TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE +NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP +VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW +ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ +VSAQMEQRHYEGLLR +>NAFOICDF_01108 +MFKAIARIVRTQDLRRKILFTLALVAVYRLGAFIPAPGVDYAAVRQCLAAGSAQGGLYSF +VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL +TIALAVLQGTTMASLARTGALLGCRVPLLHDQSIATVLLVVVVLTTGCVIVMWLGERITE +NGIGNGMSLLIFASIAAGFPAGIGQVLQTQGWRTFAIVMVVGLLTMLAVVFVEESQRRIP +VQYAKRQIGTRTVGGTSTFIPIKVNMANVIPVIFASSVLMLPGILAQFNTPQDGSAPPAW +VSFLSTYFVGGDHPLYMALYLLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITLPGALYLGIVAMIPLIAFVLIGANQNFPFGGTSILIMVGVGLQTVKQ +ISAQMEQRHYEGLLR +>MHAAABBN_01407 +MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF +VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL +TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE +NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP +VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW +ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ +VSAQMEQRHYEGLLR +>LFPAFLNI_01629 +MLKAIARIVRTPDLLRKIAFTLGLIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF +VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL +TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE +NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP +VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPGILIQFNTPQDGSAPAPW +ITWLSRYFGSGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITFVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ +VSAQMEQRHYEGLLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000792.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000792.fa new file mode 100644 index 0000000000000000000000000000000000000000..5ea761037d17ff5e06a4fe70abd0daa218c8951f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000792.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01179 +MTRMLLMGPPGSGKGTQATRIADKLGIVAISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDDVTNRMVADRIAQPDAEHGFLLDGYPRTKGQVEALDAMLTEAGLALSAVVELEVPDAE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETEAVIQEYVERGIVARVDGTGQIDDVTE +RLLQSVYAVRAATGSLPVIAPDTES +>MOLHKGIG_01699 +MTRMLLMGPPGSGKGTQATRIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGLSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES +>NAFOICDF_01109 +MTRMLLMGPPGSGKGTQATRIADKLGIVAVSTGDIFRHNVKNMTELGKEAKRYMDAGDFV +PDEVTNRMVADRLSQSDAETGFLLDGYPRTAGQVDALDAMLKDTGQALSAVVELEVPDAE +LVARLLKRAEIEGRADDTEEVIQHRLDLYHRETESVIESYAERGIVARVDGTGQIDDVTE +RVLQSVYSVRAATGTLPIITPDTQA +>MHAAABBN_01406 +MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAESGQSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES +>LFPAFLNI_01628 +MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKRYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGQSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000793.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000793.fa new file mode 100644 index 0000000000000000000000000000000000000000..696b4ed923171234f387c57603de4d4552f1879c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000793.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01180 +MVGRRSLELKTTPQLQTMRRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAEHGATS +NFLGYYDFPATICASVNEEVVHGIPGDRVLQAGDVLKVDGGAIVDGWHADSARTLVLGSS +EAGTADEGDERLSAITREALWVGIAAFATAKHVGDIGDAIDDFVSAQPGEPLGILEEYVG +HGIGSSMHMPPDVFNYRTGHRGPKVRPGLALAVEPMLVRGGIETRVLEDDWTVVTVDGAR +ASQWEHSVCRHAGGLWVLTAPDGGASELERFGVVPVPPGE +>MOLHKGIG_01698 +MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +EAGTAGPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE +>NAFOICDF_01110 +MFSRRSIELKTTPQLQTMQRAGVVLSEALDAAVAAAAPGVTTAEVDAVFADVLAQHGATS +NFLGYYGYPATVCASVNEEVVHGIPGERVLQQGDVLKIDGGAIVDGWHSDSARTLILGSS +EAGTADPEDERLSEITRQALWVGIAAFAQARHVGEIGDAVDDFVTSQPGAPLGILEDYVG +HGIGSAMHLAPDVFNYRTGHRGPKVQHGMALAIEPMLVRGGIETRTLEDEWTVVTTDGAR +ASQWEHTVCRHPGGVWVLTAPDGGAAELAAHGVVPVPPGE +>MHAAABBN_01405 +MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE +>LFPAFLNI_01627 +MIGRRSLELKTAPQLQAMQHAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVTAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000794.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000794.fa new file mode 100644 index 0000000000000000000000000000000000000000..4729b2883186b584163f8f680fa5ea9ac3e6c061 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000794.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01181 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>MOLHKGIG_01697 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>NAFOICDF_01111 +MAKKEGVIEVEGTVTEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRVVVELSP +YDLNRGRIVYRYK +>MHAAABBN_01404 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>LFPAFLNI_01626 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000796.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000796.fa new file mode 100644 index 0000000000000000000000000000000000000000..2d7a7c3f43ac9f2dabb090d5b2bff634209dea4d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000796.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01183 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK +>MOLHKGIG_01695 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK +>NAFOICDF_01113 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDRDIRVKDLTDDQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK +>MHAAABBN_01402 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK +>LFPAFLNI_01624 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000797.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000797.fa new file mode 100644 index 0000000000000000000000000000000000000000..83586b0888f108314412f45b8ce04496a3700009 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000797.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01184 +MPPKTRASAARKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>MOLHKGIG_01694 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>NAFOICDF_01114 +MPPKTRSAVRKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGSR +KSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTPQ +AHNGARPAKRRRV +>MHAAABBN_01401 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>LFPAFLNI_01623 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000798.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000798.fa new file mode 100644 index 0000000000000000000000000000000000000000..f92d6a622d435a731fc4d74c69c81fbe0111e39b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000798.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01185 +MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN +PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLARSLNVEAEGVDLGDEPQT +AEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK +LYELGLSLKDSPAGYDPQAHARQMDDDPFSDF +>MOLHKGIG_01693 +MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN +PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPDV +VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK +LQELGLSLKDSPAGYDPQAHARQMDDDPFSDF +>NAFOICDF_01115 +MLIAQRPTLTEEVVSDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGSGVVTAADITAPAGVEIHN +PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADQEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLAKGLNVEAEGIDLGEAPAE +ADGSADLAQPIEDLELTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKEK +LYELGLSLKDSPAGFDPQAHASQDDDPFSDF +>MHAAABBN_01400 +MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN +PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV +VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK +LQELGLSFKDSPAGYDPQAHARQMDDDPFSDF +>LFPAFLNI_01622 +MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN +PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV +VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK +LQELGLSLKDSPAGYDPQAHARQMDDDPFSDY diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000799.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000799.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bd42c89ffde43c9296315de01d481efdeebb315 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000799.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01186 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKSIVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +IMEPISGKQAVVREAEQAAASAPAAETAPVQETAPVEAVDPAAAEDVTVAESQEAAAEID +GAVATTEDGSAPEGASIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE +AAQKMAD +>MOLHKGIG_01692 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP +TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK +MA +>NAFOICDF_01116 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPHAERLITIAKKGDL +PARRKVQGIIAAKSRTNKSIVHELFTVIAPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +VMEPVSGKQAVVREAEQAAASAPAAAPVEETPVEVVDPAATEEVTVAESEETAAEIDGAV +ATTEDGSAPEGATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQ +KMA +>MHAAABBN_01399 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP +TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK +MA +>LFPAFLNI_01621 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP +TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK +MA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000800.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000800.fa new file mode 100644 index 0000000000000000000000000000000000000000..b48df7f113692259c580f98101a51f91c0c404ec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000800.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_01187 +MTEQPAPSAPRPSAAGEEPVRVRLDLAYDGGAFRGWARQPGLDSVQGALEDGLERILRRP +VRTVVAGRTDAGVHARGQVVHLDLAEGEWAGLTRGRPDLEPGASLARRLGGVLSGWDGAV +VVHGARRAPAGFDARFSALWREYEYRIDDAPDRRDPRTRAFTHWHGAALDERLMALEADA +VLGLHDFLSFCRPREGATTIREVQDLRVARDEDGSVRVRIRADAFCHNMVRAVVGALLQV +GEGSREPGWLGLRVATPARDSQVRLAPPRGLTLLAVGYPEDGEGLRRRAEGTRARRTL +>MOLHKGIG_01691 +MSEQHRPDAPTAPGEPPSVRVRLGLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV +RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV +VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV +LGLHDFLSFCRPRAGATTIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG +EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL +>NAFOICDF_01117 +MVGMPDDALPAAPVEPRPEPTTGLPREGEVRLRLDLAYDGSDFRGWAAQPGLATVQGALE +GALETIVRRPVRTVVAGRTDAGVHARGQVVHCDLTEAEWSALARGRADVDPADALVRRLQ +GVLRPWQGAVVVRGARRAPDGFDARFSALWRAYEYRISDRPETRDPLARHGVLWHGARVD +ERLMAVEAGALLGLHDFLSFCRPREGATTVREVQDAEVVRTPDGLVRVRLRADAFCHSMV +RTIVGALLEVGEGRRTPGWTAARVAGPVRDSAARLAPAHGLTLLEVGYPETGEELRARAE +GTRARRAPLADLG +>MHAAABBN_01398 +MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV +RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVV +VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV +LGLHDFLSFCRPRAGATTIREVTHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG +ERAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL +>LFPAFLNI_01620 +MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV +RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV +VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV +LGLHDFLSFCRPRAGATTIREVKHLEVRRDEDGVVRIRIRADAFCHNMVRAIVGALLQVG +EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELRRRAEGTRAKRTL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000804.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000804.fa new file mode 100644 index 0000000000000000000000000000000000000000..48425ad0f2800fc8331dad3bbc8bc81e24b4438e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000804.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01192 +MSRLFGTDGVRGLANETLTVELSVQLAQAAAPVLGAEALEAGRRPVAVVARDPRISGEFI +AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLGADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVEPRRPQGADVGRVKVFSDAEDRYVVHLLQALPHRLEGLKVVL +DCAHGAAAGCSPEAFRDAGAEVVVIGASPDGLNINEGYGSTHLEKLQAAVLEHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVAMKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLAARVAETGRP +LSALAAVMDRLPQVLVNVRGVDKSRAAEDVAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAEALADVVQRELRLHV +>MOLHKGIG_01686 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD +>NAFOICDF_01122 +MSRLFGTDGVRGLANDVLTVELSVQLAQAAAPVLGADALAAGRRPVAVVARDPRISGQFI +AAAVIAGLASSGVDVHDAGVVPTPAAAFLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDEQEDEIIQHLESEHPLRPTGAEVGRVRTFSDAEDRYVVHLLQTLPHRLDGLTVVL +DCAHGAASGCSPDAFRDAGAQVIVIGAEPDGLNINEGVGSTHLEKLQAAVKEHGADLGIA +HDGDADRCLAVDELGEVVDGDQIMGIMALALKDRGQLKEDTLVVTVMSNLGLKLAMRGAG +IELVETQVGDRYVLAGMRLGEYSLGGEQSGHVIFADHATTGDGVLTGLQIAARVAETGTP +LSQLAAVMTRLPQVLVNVRGVDKSRAAEDAAVQSAVREAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETARREAEALAEVVQRELRLHD +>MHAAABBN_01390 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDEHGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD +>LFPAFLNI_01615 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000805.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000805.fa new file mode 100644 index 0000000000000000000000000000000000000000..314afdc20e4fbaf28d35d01b5aed06a1b15e1907 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000805.fa @@ -0,0 +1,14 @@ +>ACLBLIBL_01193 +MSSEAVPRPPRWSPFGALLAGLAVLWGAAFLAVDAPVCERHGAPVEWLPCLDRDRGDPDV +APQR +>MOLHKGIG_01685 +MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV +APDAGSSADRTTSRP +>NAFOICDF_01123 +MSPRRDPGRLRPLAGPAALLAALWVAAWLAVSVPVCDRGGPADWLPCVDPGRSVPAPGAP +>MHAAABBN_01389 +MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV +APDAGSSADRTTSRP +>LFPAFLNI_01614 +MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV +APDAGSSADRTTSRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000806.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000806.fa new file mode 100644 index 0000000000000000000000000000000000000000..95bcdafd6a074a1466c18ec89246fc903b934123 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000806.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01194 +MKGNVIDLAVAVVIGAAFGAVINAVVDSVLMPLIAALFAAPSFDDWLVLDINGVLVKFGV +VLTAVVNFLLIAAAIYFAIVLPMNKMIERRNRRLGIDPAEEEVPEDVALLTEIRDLLSAQ +RGGAAGTTHTTL +>MOLHKGIG_01684 +MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV +NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVPADVAVLT +EIRDLLAERRGGPTSGTTTL +>NAFOICDF_01124 +MKGNVVDLAVAVVIGAAFGKVVTALVDSVLMPLIAALFKAPSFDSWLVLNLNGVDVKFGV +VLTAIVNFLLIAAAVYFCIVLPMNTMIERRNRRLGITPAEDEVAPDVAVLTEIRDLLARQ +NGAPRV +>MHAAABBN_01388 +MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV +NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVAADVAVLT +EIRDLLAERRGGPTSGTTTL +>LFPAFLNI_01613 +MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV +NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMVEARNRRLGIDPAEEEVPADVAVLT +EIRDLLAERRGGPTSGTTTL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000807.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000807.fa new file mode 100644 index 0000000000000000000000000000000000000000..3322222fa541df08aafe755091d374c556a579c8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000807.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_01196 +MKDSTQPAPSVPEDLEDDLVSDHHRSPFVELERQTWARLATEMAQPFDQGDVERLRGLGE +HLSLREVAEVYLPLSRLLSINVEASGALRSATNAFLGERTGRTPYVIGVAGSVAVGKSTT +ARVLQEMLRRWPTTPRVELITTDGFLHPNAVLQERGIMARKGFPESYDRRALLRFMVDVK +SGAQEVRAPVYSHITYDIVPGEEQVVRRPDVLIVEGLNVLAPPVTRADGTAGLSVSDFFD +FSVYVDARADWIRSWYIERFMGLRSGAFADPRSYFHRYATLSDAEAQGTAESIWDSINGP +NLQQNVQPTRGRARLVLTKNAQHEVTRVLLRKV +>MOLHKGIG_01682 +MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER +LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA +VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR +FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS +VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW +DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV +>NAFOICDF_01125 +MRADAPPPPPPPCAVVLAGRRDAVAGRRPRACHDGPVKDTRDGGGGAPTAPADAPGPASA +GDPHLSPFVELERQTWARLADQLDQPFDQDDVERLRGLGETLSLREVAEVYLPLSRLLGI +HVEAAGALRRATNEFLGERTGRTPYVIGVAGSVAVGKSTTARVLQEMLRRWPSTPRVELI +TTDGFLHPNAVLQERGIMDRKGFPESYDRRALLRFMADVKSGAAEVSAPVYSHVTYDIVP +ERRQVVHRPDVLIVEGLNVLAPPLLRADGTPGLSVSDFFDFSVYVDARADWIRDWYVERF +MGLRSSAFRDPDAFFHRYASLSDEEARETARSIWDRINGPNLAQNVQPTRGRARLVLTKN +RQHEVTRVLMRKV +>MHAAABBN_01386 +MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER +LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA +VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR +FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS +VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW +DSINGPNLEQNVRPTRGRARLVLTKNAHHEVTRVLLRKV +>LFPAFLNI_01611 +MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER +LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA +VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR +FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS +VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW +DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000808.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000808.fa new file mode 100644 index 0000000000000000000000000000000000000000..576a8c4ac119bc8bd30daf06b64b6b9b3123850b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000808.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01198 +MCGIVGYIGQPSSTREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGELYHRKKAGKLANL +AQELEEHPVPTGLVGIGHTRWATHGGPTDVNAHPHVADEGRLAMIHNGIIENYAELREEL +LAKGAEFLSETDTEVAAHLLTDVYRNAGGQDLTRSLQLASQRLEGAFTLLAVHVDHPDRV +VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITAEGVEITDFAGSPA +EGKRFTVDWDASAAEKGGYETFMEKEIHDQPQAVQDTLLGRMDAAGTLVLDELRIDPEEL +KAVNKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPNTLVVSISQS +GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT +AAYLLGLYLAQLNKKLFSGQIKDILADLHAIPGKIQEILDDKEQVKELARSMADTSSVLF +LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQAVFVVMPSPMDRHSL +HAKVVSNIQEVRARGARTFVVAERGDQAVRSHAEVVIEVPETQPMLMPLLTTVPLQIFAL +ELASAKGYDVDQPRNLAKSVTVE +>MOLHKGIG_01680 +MRRSRARSGILVRMCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQ +LYHRKKAGKLANLAEELAEHPVPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLAFIHN +GIIENYAELREELLAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAF +TLLAVHVDHPDRVVASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITA +DAVEISDFRGGPAEGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGA +LMLDELRIDPEELKAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPI +IDPHTLVVSISQSGETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEI +AVASTKAFLAQITAAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAGKDQVKE +LARSMADATSVLFLGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPV +FVVMPSPLDRHSLHAKVVSNIQEVRARGARTFAVAERGDAAVRAQAEVVFEVPETQPMLM +PLLTTVPLQIFALELATAKGYDVDQPRNLAKSVTVE +>NAFOICDF_01127 +MRMCGIVGYIGQPSSTREHDALEVLMEGLRRLEYRGYDSAGVAVVADGELYHRKKAGKLA +NLAAELEAEPVPSAQVGIGHTRWATHGGPTDVNAHPHVADEGRLALIHNGIIENYAELRA +ELLEKGVTFLSETDTEVAAHLLADVYRGAGEGDLTRTMQLASQRLEGAFTLLAVHVDHPD +RVVASRRNSPLVVGVGEGENFLGSDVSGFIDFTKEAIELEQDQVVTITADAVEITDFQGA +PAQGKAFTVDWDASAAEKGGFDTFMEKEIHDQPQAVQDTLLGRTDATGALVLDELRIDPE +ELKAVRKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDDHTLVVSIS +QSGETMDTLMAVRYAKEQGARTLSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQ +ITAAYLLGLYLAQLNKKLFTGQIKDILADLAEIPGKIQEILDSSTPVRELARSMADTSSV +LFLGRNVGFPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDEGQAVFVVMPSPLDRH +SLHAKVVSNIQEVRARGARTFVVAERGDEAVRDHAEVVFEVPETQPVLMPLLTTVPLQIF +ALELASAKGYDVDQPRNLAKSVTVE +>MHAAABBN_01384 +MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL +AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL +LAKGVEFLSETDTEVAAHLLADVYRHAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV +VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA +DGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL +KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS +GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT +AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF +LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPLDRHSL +HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL +ELATAKGYDVDQPRNLAKSVTVE +>LFPAFLNI_01609 +MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL +AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL +LAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV +VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA +EGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL +KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS +GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT +AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF +LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPMDRHSL +HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL +ELATAKGYDVDQPRNLAKSVTVE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000809.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000809.fa new file mode 100644 index 0000000000000000000000000000000000000000..efcf05c60b6a05bf92d3c42843e838e81248708f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000809.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_01200 +MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHV +HVAGVGHGQRYGYRVTGPWDPSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPD +RMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYETHVKGMTMRHPAVPEELRGT +YAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA +SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEA +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG +ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNV +YCQDNEISWIDWSAVDDSLVAFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVW +LEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPYRDFYVLMNAWWEPVPYTLPG +PLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQVPEGA +>MOLHKGIG_01678 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA +HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD +RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT +YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV +YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW +LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG +PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA +>NAFOICDF_01128 +MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHV +HVAGIGGGQRYGWRVHGPWDPARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPD +RMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYETHVKGLTALHPDVPEELRGT +YAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS +ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEG +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG +DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNV +YCQDNELSWIDWSTRDDALIAFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVW +LEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAFRDFYVLMNAWWEPVPYTLPG +PLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG +>MHAAABBN_01383 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA +HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD +RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT +YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV +YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW +LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG +PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA +>LFPAFLNI_01608 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA +HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD +RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT +YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDTVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV +YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVW +LEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG +PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000810.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000810.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa085815dc25135d48e803965d805f4e7be02928 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000810.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01201 +MSEGSDRARARRGARGVPRGVRALLSAAAGTATLALAFGVGWAAHAVTSPRPDDPERVDA +LLVLYSQPRVYDAAIELAADGVADRLFVSAHLGPDGHERLCGPEERRDPRLAGVSVECFA +PDPLTTQGEAMHAAARMRELGLEHLGVLTFHQHLERSRLLVERCWTPQEGRVSMFAFDAG +LDRWGRVRHGAYGVLAYGKAMATPGCDQELPGVLQWPLDLAKRLRGQPVGAEAGAAGPAG +AVSAAPAAATPAAPARGEGPA +>MOLHKGIG_01677 +MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV +LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP +VTTQGEVIHAGERMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR +LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA +GAA +>NAFOICDF_01129 +MSRPAGSAPAVDGDAQAAPRGPQAGRRVQADRGRGRRRRRILGAVLAAAALVLAAAFGPG +LMRAADMTLHPRPDDPPRVDALLVLYSQPAVYDAALELLDRGVADRVFVSAHLGPDGFEK +FCGTPAQRDPRTRGVEVECFSPDPVTTQGEVMFAADRMRALGLRRLGVLTFDQHLERARL +LAERCLPAADGSVSMYRFDGGYTGAEKVRQDVYGTAAFAKVALTTDCSGELPDVLQWPLD +LVKRTAGMPVGAVAESAAGVGRAGAGVRP +>MHAAABBN_01382 +MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV +LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP +VTTQGEVIHAGDRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR +LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA +GAT +>LFPAFLNI_01607 +MSAQADRGRVRRGLPRWARALCATVATLAALGLAFGAGWATHAVTEPHPDDAPRVDALLV +LYSQPRVYDAAIELAASGVTDRLFVSAYLGPDGHEKLCGGPGERDPRLAGVSVECFAPDP +VTTQGEVIHAADRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR +LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA +GAV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000811.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000811.fa new file mode 100644 index 0000000000000000000000000000000000000000..1d7bda59c8e55b5387c069f79944c16806cee7f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000811.fa @@ -0,0 +1,19 @@ +>ACLBLIBL_01202 +MIVGVGMDVVDVPRFRAQLERTPALRERLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEAQGITHWHLSLSHDGDVAAAYVVAERRA +GEDGA +>MOLHKGIG_01676 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA +>NAFOICDF_01130 +MIVGIGVDVVDVPRFERQLARTPALRERLFTEEERDLSLRSLAARFAAKEAIAKALGAPP +GMMWHHCSIPRPAHGDGRPEVRLTDSVRDRADELGVTHWHLSLSHDGDVAVAYVVAERHD +>MHAAABBN_01381 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA +>LFPAFLNI_01606 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAVAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000813.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000813.fa new file mode 100644 index 0000000000000000000000000000000000000000..205ad41c6b58eb850ef731d5eb971fdebd8c0b51 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000813.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01204 +MTQQDRSAGPAERTARIDLAAVRHNVAAVRARTVRQDGTRPLLTAVVKADGYGHGAVAVA +RAAQAAGADRLGVAHVREALELRGAGLRLPILAWLHTVGTDFAAALEADVTLGVSGWDLD +AVAAAVRALRPAPGTADSGPVRARVHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVR +VEGVFSHLGVADDPERAEETTAQLRRFEEAAAAAAAALGRPLLRHLANTPATLSRPDTHL +DMVRVGLGLYGLSPFEGVDAAGLGLRPAMSLGTTLANVKPVPAGQGVSYGFRHVAPAPTT +LGLVPLGYADGVPRIAEGARVHVGGRTVPVVGRIAMDQFVVDLGPDARDRPGDAVELFGP +ASGIPADEWAAAAGTINYELVTRIGARVDRAHEGGEAPDAQEARA +>MOLHKGIG_01674 +MSRADVAPADTERAVRIDLAAVRHNVGVLQERIRRPDGSRPLLTAVVKADAYGHGAVAVA +RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD +AVADAVRGLRARGGAGPEARADLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE +GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM +VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG +LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS +GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP +>NAFOICDF_01132 +MDDAPDLTPSAAEAAPAERRALVDLAAVRSNVAALRARLGRPDGASTALMAVVKADAYGH +GAVPVARAALEAGADRLGVAHVTEALALRAAGVTAPILAWLHTRDTPFRAAVETDVALGV +SGMWDLEAVAQAARAAGRRATVHVKADTGLGRNGCLLADLPALAARAAALQDEGVVDVEG +LFSHLAVADELDRAAETDAQAAAFGEATVALDAAGLRPRVRHLANTPAALTRPDLHHDMV +RVGLGLYGLSPFPDRAPAEFGLRPAMSLQTTLAAVKAVPAGQGVSYGFRHRTAEPTVLGL +VPLGYADGVPRIAEGAPVAVAGRRVPHVGRVAMDQLVVDLGPGAAERVGDPVELFGPASG +IPADAWAEAAGTINYELVTRISPRVPRVHVDGAAAGEVAA +>MHAAABBN_01379 +MSRADVNPADTERAARIDLAAVRHNVGVLRERIRRPDGGRPLLTAVVKADAYGHGAVAVA +RAAAAAGADRLGVAHVREALALRAAGVPLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD +AVADAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE +GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM +VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG +LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS +GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP +>LFPAFLNI_01604 +MSLADVNPADTERAVRIDLAAVRHNVGVLRERIRRPDGSRPLLTAVVKADAYGHGAVAVA +RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD +AVAAAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVRVE +GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM +VRVGLGLYGLSPFADVTAAELGLRPAMSLVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG +LVPLGYADGVPRVAEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS +GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000814.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000814.fa new file mode 100644 index 0000000000000000000000000000000000000000..dec6b44b3b01252ba195159eb229c6f0c643015d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000814.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01205 +MSRHEPPAPDPALPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF +TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAT +VDRSVTVVEWGRGLAESLAGFPEDPDASWLDVEIVRARGGEDPAPAGPGADDGGIVTDFS +DEDGEQAEELRSAVVTGYGPRWAGVRLP +>MOLHKGIG_01673 +MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF +TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS +VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAASAGEGEDGIVTDFS +DEDGGQAEELRSAVVTGRGPRWAGVVLP +>NAFOICDF_01133 +MIAGRRAEQPLPAPVWERRVPLDGAAGTREFGAALAGVLRAGDVLILTGELGAGKTTLTQ +GLGAGLGVREGVISPTFVLSRIHPSLADGPDLVHVDAYRLRSAGELTDLDLEATADRSVT +VVEWGRGMAESLAGFPEDPEASWLDVEVLRARGGADLPDGPAGGDAAPDAPVIVTDFSDE +EGEAAEEVRTAVVRAHGPRWAAVALP +>MHAAABBN_01378 +MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF +TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS +VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAAPAGEGEDGIVTDFS +DEDGGQAEELRSAVVTGRGPRWVGVVLP +>LFPAFLNI_01603 +MSDHEFPAPGPTLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF +TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS +VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDGPAASAGEEDGIVTDFSD +EDGGQAEELRTAVVTGRGPRWAGVVLP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000815.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000815.fa new file mode 100644 index 0000000000000000000000000000000000000000..c694bc2bf53998d09ab20369d543c98b9e3ec011 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000815.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01206 +MALLLALDSSAAASVAVLRDGEALARWATEDTHAHAEVLAPAVRAVLAEAGVAGAGLDAV +AVGVGPGPFTGLRAGLATAAALGLAWDVPVRGVRSLDALAHDAAVDAFRHGAEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPAYGAGAGLYPEALRAVPGWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA +>MOLHKGIG_01672 +MALLLAIDSSAAASVAVLRDGEELARWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWESATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA +>NAFOICDF_01134 +MPLLLALDSSSAASVALLRDGEPLAAWSTADTTSHAEVLAPAVRQVLAEAGVAGGDLDGI +AAGVGPGPFTGLRAGLATAEALGFAWDVPVHGIRSLDALAHRAGTDAFAHAVEEFVVVTD +ARRREVYWAHYAQVGGQPTLLHGPFVTPAAEVTPLPAYGAGAGLYPEALHAVDGWEGAVP +DAVSLGRVDELALRRGRGVLPPTPLYLRESDATVPAPRTPARPAGA +>MHAAABBN_01377 +MALLLAIDSSAAASVAVLRDGEELAHWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHAAGVDAFRHGIEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA +>LFPAFLNI_01602 +MALLIAIDSSAAASVAVLQDGEELARWATDDTHAHAEVLAPAVQAVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVIATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000816.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000816.fa new file mode 100644 index 0000000000000000000000000000000000000000..01d6f18cc426ed7ec00ed58f194c1268a3ba02ba --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000816.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01207 +MSPVEPAPGGDERPAEDEHGLPPGYLLRPMTVWDIPEVLAQEATLFPLDAWPARFYEEEL +AQTGPAGGRDAHGRPPTRDYRVVVRDVPAPVAPDEDGPAPGEIVGYGGIMVVGDVADVQT +VGTVAAAQGRGIGAAQLRWMAAEAAARGASALMLEVRASNAAARRLYARHGFEELHVRRR +YYPGGEDAVIMRKAL +>MOLHKGIG_01671 +MSPAEPDPAGDGRPAEDAHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL +AQTGPAGGRDAHGRPPTRDYRVVVRDVAAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT +VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR +YYPGGEDAVIMRKVL +>NAFOICDF_01135 +MSLPDATDPGDDAAPAHGLPAGFLLRPMTVWDVPEVLEHEETLFPLDAWPGHFYAEELAQ +AGPAGALDAHGRPTTRDYRVVVRQDTGEIVGYGGIMAVGDTADVQTIGTAAAVQGRGIGA +AQLRWMVAAARERGAESLLLEVRESNAAARRLYARHGFEPIAVRRGYYPGGEDAVVMRRA +L +>MHAAABBN_01376 +MSPAEPAPTDDGRPAEDEHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL +AQTGPAGGRDAHDRPPTRDYRVVVRDVPAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT +VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR +YYPGGEDAVIMRKAL +>LFPAFLNI_01601 +MSPAEPAPAGDGRPAEDGHGLPPGYLLRPMTVWDVPEVLAHEATLFPLDAWPAHFYEEEL +AQTGPAGGRDAHGRPPTRDYRVVVRDAAAPSSADDDGPAPGEIVGYGGIMVVGDVADVQT +VGTVAAAQGRGIGAAQLRWMAAEAAARGAGFLMLEVRASNAVARRLYARHGFEELHVRRR +YYPGGEDAVIMRKTL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000820.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000820.fa new file mode 100644 index 0000000000000000000000000000000000000000..3814724fbd275ba87aaf2716402ff957a560a667 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000820.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01227 +MTITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA +EPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHASLT +RDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR +>MOLHKGIG_01667 +MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV +SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA +SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR +>NAFOICDF_01138 +MQTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDAAGA +EPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDAGLT +RPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA +>MHAAABBN_01372 +MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA +EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT +RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR +>LFPAFLNI_01597 +MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA +EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT +RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000821.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000821.fa new file mode 100644 index 0000000000000000000000000000000000000000..810c0e769b6b2fa7e437d967f0252d0182968cd2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000821.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01228 +MRIVVLGATGNVGTALLERLHAADEVTSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA +GRLSEIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEARVPHLVYASSVGA +YGPGPKGRAVPESHPATGVPTSHYAAQKAEVESILDRVQAEHPEMLVTRLRPGLIFQAGA +GPEIKDYFLGDLVPARLVARLRAPVLPFPRGLRFQALTAQDMADAYWRVIAHRAGGAFNV +AAEPVLDAHTMGTVLGARRILELPVGLFRAAASLTYRARLQPTDPGWVDMAAAVPIMDTT +ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE +>MOLHKGIG_01666 +MRIVVLGATGNVGTAVLHRLQAADEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA +GRLHDIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEAGVPHLVYASSVGA +YGPGPKGRAVAESHPTTGVPTSHYAAQKAEVESILDRVQAEHPEMLVTRLRPGLIFQSAA +GPEIKDYFLGDLVPARLVARLRAPVLPFPRGLRFQALTAQDVADAYWRVIAHRAGGAFNV +AAEPVLDAHTMGTVLGARRILELPVGLFRAAAALTYRARLQPTDPGWVDMAAAVPIMDTT +ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE +>NAFOICDF_01139 +MRIVVLGATGNVGTALLERLHRAPEATELVGVSRRGPDRAGAPYDGVEWHRMDIADAASA +PRLTEVLRGADAVVDLVWVIRPNRDRAHLRAVNVDGNERVFRAAAAAGVPHLVYASSVGA +YGPGPKDVRVDESHPTTGVPTSHYAAQKAEVETILDRVAAEHPRMLVSRLRPGLIFQSGA +GPEIKDYFLGDLVPARLAARLRTPVLPFPTGLRFQALTAQDVAEAYWQVVAHRAGGAFNV +AAEPVLDAHTMGTVLGARRILELPVAVFRAAAAVSYRARLQPTDPGWVDMAAAVPVMDTS +ALRRATDWRPRTDARDAVRLVLDHLDGREGLGNAGHRSHSPLE +>MHAAABBN_01371 +MRIVVLGATGNVGTAVLHRLQAAAEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA +GRLREIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEAGVPHLVYASSVGA +YGPGPKGRAVPESHPTTGVPTSHYAAQKAEVESILDRVQAEHPELLVTRLRPGLIFQSAA +GPEIKDYFLGDLVPARLVARLRTPVLPFPRGLRFQALTAQDVADAYWRVIVHRAGGAFNV +AADPVLDAHTMGTVLGARRILELPVGLFRAAAALSYRARLQPTDPGWVDMAAAVPIMDTT +ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE +>LFPAFLNI_01596 +MRIVVLGATGNVGTAVLHRLQAADEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA +GRLREIVAGADAVVDLVWVIRPNRDRDHLRAVNVVGNERVFRAVAEAGVPHLVYASSVGA +YGPGPKGRAVAESHPTTGVPTSHYAAQKAEVESILDRVQAEHPELLVTRLRPGLIFQSAA +GPEIKDYFLGDLVPARLVARLRTPVLPFPRGLRFQALTAQDVADAYWRVIAHRAGGAFNV +AADPVLDAHTMGTVLGARRILELPVGLFRAAAALSYRARLQPTDPGWVDMAAAVPIMDTT +ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000822.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000822.fa new file mode 100644 index 0000000000000000000000000000000000000000..e63ec5be37a72d3a728c4c2451f98c9ed48c7323 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000822.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01229 +MRALTWQGKRNVAVEDVPDPRIQEPTDAIVEITSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGAEVTHIKPGDRVVVPFNIACGRCWMCERGLQSQCETTQVREQGSGAALLG +YSRLYGSVPGGQAEYLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYAQVPRGG +TLAVIGLGPIGQLAARIGVHQGLRVIGVDPVPERRAMAARHGVEVLDSSDGGVAELLREC +TQGRGPDGVVDAVGMEAHGSPVAKAAHTVVGLLPDALGRAAMKTAGVDRLDALHTAIDAV +RRGGTVSLSGVYGGMQSPMPLLTMFDKQVTLAMGQCNVRRWVDDLLPLLDDPSDPLGVLD +LTTHTAPLEDAPALYETFQKKEDGCIKVVLKP +>MOLHKGIG_01665 +MRALTWQGKRNVVVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGCGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT +GGRGPDAVLDAVGMEAHASPVGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR +RGGTVSISGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL +TTHTAPLEDAPALYETFQKKEDGCVKVVLKP +>NAFOICDF_01140 +MRALTWQGKRSVSVEDVPDPRIQEPTDAIIKVTSTGICGSDLHLYEVLGPFMDKGDVIGH +EPMGIVEEVGSAVTNLSPGDRVVIPFNISCGHCWMCQHGLQSQCETTQVKEQGSGAALLG +YSRLYGSVPGGQAEYLRVPHADYGPIKVPHTGPDTQWLFLSDVVPTAWQAVQYANVSKGD +TLAVLGLGPIGQMSARIGVHLGCRVIAVDPVPERRHMAARHGVEVLDMEGSGTGVPDLLR +QATGGRGPDGVVDAVGMEAHGAPVAAAAQTAAGMLPGPLARAAVKTSGIDRLTALHTAIE +SVRRGGTVSLSGVYGGMQDPMPLLTMFDKQIQFTMGQCNVRRWVDDLLPLMDDPSDPLGV +LDLVTHTAPLEDAPAMYEKFQKKQDGCIKVVLTP +>MHAAABBN_01370 +MRALTWQGKRNVAVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT +GGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR +RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL +ATHTAPLEDAPALYETFQKKEDGCIKVVLKP +>LFPAFLNI_01595 +MRALTWQGKRNVTVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT +SGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR +RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL +TTHTAPLEDAPALYETFQKKEDGCIKVVLKP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000823.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000823.fa new file mode 100644 index 0000000000000000000000000000000000000000..f9d2c31e66b70224d10314586a1a5ee7216e8e9d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000823.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01230 +MNLPFADSTQSTLGIEWEVALVDAATGDLRSEAPAILHELHKEAGLAEGEDHPHVTGELL +QNTVELVTGVHEAVPTAVAELGTIAARVARAAADRGLALYCQGTHPFGEAMTQPITPKER +YGRMVDLTQYWGRQMLIFGVHVHVGLDDPAKAMPAVNRLISRFPHLLALSASSPFWVGAD +TGYQSQRTQLFQQLPTAGLPFQFETWAEFEACVQQMTDVGMVEDVTECRWDVRAVPRLGT +VEMRACDGMATLEEIAAVAAYTQCLVHELSADVERGRHMEILPPWYTQENKWRASRYGMD +ATVIVDAAGTQVPLAEHLGADLERLAPIAEELGCAAELAHARVLMEHSPADRQRAVEAEA +LAGPPAEGESAHDAAAPLRAVVLDAAARTRESLERVGG +>MOLHKGIG_01664 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFADAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDADDAVAPLRAVVLDAAARTRASLDGRAG +>NAFOICDF_01141 +MSLPFADSAQSTLGIEWELALVDPLTGDLRSEAPGILEELRAEAGLDADADHPHVTGELL +QNTVELVTGVHGSVPDAVADLGGIAARVQRAAADRGLALFCQGTHPFGEAMTQPITPKAR +YGRMVDLTQYWGRQMLIFGVHVHIGLDDRAKAMPAVNRLISRLPHLLALSASSPFWVGAD +TGYQSQRTQLFQQLPTAGLPFQFETWEGFEHCVEQMTGVGMVEDVTECRWDVRAVPRLGT +VEMRVCDGMATLEEIGAVAAYAQCLVHELSAQVEDDEPVAILPPWYTQENKWRAARYGLE +ATVITDDAGTQVPLAEHLAADLERLAPVAEELGCAAELAHARVLMEHSPADRQRRVAAEA +AAGPPRTGEDPADPVAPLRAVVRDAADRTRESLRAFQG +>MHAAABBN_01369 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRTLHATEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAARGISLFCQGTHPFADAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDTDDAVAPLRAVVLDAAARTRASLDGRTG +>LFPAFLNI_01594 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFAEAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEDFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDADDAVAPLRAVVLDAAARTRTSLDGRTG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000825.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000825.fa new file mode 100644 index 0000000000000000000000000000000000000000..54437cab45158f8e3c0e9c6429bf2221506c67d9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000825.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_01232 +MQRSPRTPRLKALALASVAALALVGCSAGGAAEGPASGSADTGSAAGSGSASAPAGDGVA +AGATVTDMSGAEITLPEEIDSVITTDNRTFRTLDEWGVELSAAPKQLMFKGEGGPGYLQD +DEVADIGNHREPDMEVFVTAEPDVVFNGQRFNERKAEIDELTGDAAVIDTDFDPKQKPMD +EGLKELTTLLGEATGHQDDAAALNKEFDDAVAKAKGAYDSEQTVMGLISTGGELSYVAPG +TGRSIGPMFDILGLTPALEQAGSDNHQGDDISVEAIAQSNPDWLIVMDRDAATGEANATA +AELIERSEALKDVTAVKEGNIVYLPQDFYVAEDIQNYTTVMDDLAKAFEGAR +>MOLHKGIG_01662 +MPRSVSAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASAAGGSSAASGG +IAAGVTVTDMSGAEVTLPEEVDSVIATDNRAFRTLDDWGVELSAAPKQIMYKGEGGPSYL +QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTDFDVTQTP +MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA +PSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA +TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ +>NAFOICDF_01143 +MRTARLSTAAALASLAALTLAGCGAGGPAAEGSSPASSAASSSPASSAASSSATAGGVAA +GVTVTDMSGTEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYLQDD +SVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTPMDE +GLKKLTTLLGEATGHEADAEKLIADFDAATQLAKDAYDPEQTVMGLIASGGELSYAAPST +GRSIGPFFDMLDLTPALDQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAVGEENATAA +ELIERSEALQDVTAVKEGNIVYLPADFYVSEDIQNHTTVMEDLAKAFEGAQ +>MHAAABBN_01367 +MPSSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGESSASASA +AGGSSAASGGIATGVTVTDMSGAEVTLPEEVDSVIATDNRTFRTLDDWGVELSAAPKQIM +YKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVV +DTDFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLI +ASGGELSYVAPSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMD +RDAAVGEENATAAELIERSEALQDVTAVKEGNIVYLPTDFYVAEDIQNHTTVMEDLAKAF +EGAQ +>LFPAFLNI_01592 +MPRSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGGSSAASGG +IATGVTVTDMSGAEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYL +QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTP +MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA +PSTGRAVGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA +TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000826.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000826.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0f5e95fdc9512f8a5a8f3c2298ab60dcc385b33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000826.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01233 +MTDLHPGVADARTRLPEPGPGERVCWVPPTVLRPQRSRWQRTWPLLAGVAVTVLLAVVSL +FVGVYDVGAEGGREMFAITRVPRTVALVLAGAAMAMCGLIMQLMTQNRFVEPSTTGTTEW +AGLGLLVTMILIPGASIVTRMTGAVLFAFVGTMVFFLFLRRVRLQSSLIVPIVGIMLGAV +VGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLVVCVAVFVIADRFTVAGLG +KDVATNVGLNYNAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNIVSMVRGDNLRTNLP +WVVMVGIWVVIVCDLIGRTVIAPFEVPISLILGLVGAVVFLGLLIRQAKHG +>MOLHKGIG_01661 +MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRMNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>NAFOICDF_01144 +MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVLVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGSGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>MHAAABBN_01366 +MILDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLAGIVVTAVLVVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>LFPAFLNI_01591 +MILDVRHHVADAPPRLEELGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFLIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000827.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000827.fa new file mode 100644 index 0000000000000000000000000000000000000000..82429bd19f7bd0fd189cf11f8397e6f80776b0ba --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000827.fa @@ -0,0 +1,39 @@ +>ACLBLIBL_01234 +MVAVLAVVAVLSTAGILLWGNEAEPGSRAFWMIAGMRLDSLGVIAIVALCHSFATVSFHT +VTGNRIITPSIMGFEALYTAVQTGAVYVLGAAGIGVVTGTGPFLAQAALMVVLATVLYSW +LLSRPYGSIHLMLLVGVVLGGGLAALSTFMQRLLDPNSFDVLSARLFGNISNARSEYVAI +AAPIVVVVCLVLWLRSRRMNVLALGADSATNLGLHHRRELMVTLLLVSVLMAMTTALVGP +MTFLGFLVATLAYSLVDTHDHRMVLPVAALGAYAVLTLAYFVLRHVFYAGGAVTVIIELV +GGITFLIVVMRKGRL +>MOLHKGIG_01660 +MAEPLATAPGRLPAPLGGATAAGPVDADAPRRSGAFVTAAERRRYAVVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG +FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALTTALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL +>NAFOICDF_01145 +MAEPLATAPGRIPAPSGGATAAGPVDADAPRRSGAFVTAADRRRYALVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG +FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLIVVMRKG +RL +>MHAAABBN_01365 +MAEPLATAPGRIPAPPGGATAAGPVEADAPRRSGAFVTAADRRRYAVVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG +FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL +>LFPAFLNI_01590 +MVEPLATAPGRIPAPPGGATAAGPVDADAPRRSGAFVTAADRRRYAVVVAVLAVVAVLST +AGVLLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG +FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000828.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000828.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec3ec9a53b0b1440d47abd7004f4d92784bde028 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000828.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01235 +MIELRGVVKRHSDEVCIGPVDLDIEAGGITALVGPNGAGKSTVLTMIGRLQDVDAGTIAV +GGQDITSTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERYVSEAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADMLGRTVVIVLHDINFAARYADHIVAMGDGQVVETGTPGEILRPEVLERIFRTPCSVV +DGPHGPLAVYY +>MOLHKGIG_01659 +MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV +GGHDITTTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV +DGPHGPLAVYY +>NAFOICDF_01146 +MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV +GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV +DGPHGPLAVYW +>MHAAABBN_01364 +MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV +GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILCPEVLERIFKTPCSVV +DGPHGPLAVYY +>LFPAFLNI_01589 +MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV +GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTCGRLTLEDERHVSDAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV +DGPHGPLAVYY diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000829.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000829.fa new file mode 100644 index 0000000000000000000000000000000000000000..1854dfd994ebda8fc2be022d57e15f14d03cc379 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000829.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01237 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>MOLHKGIG_01657 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVAK +>NAFOICDF_01148 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGTRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>MHAAABBN_01362 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>LFPAFLNI_01587 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000830.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000830.fa new file mode 100644 index 0000000000000000000000000000000000000000..e01e1a401fcd275966766b2e910deff4e121ec7d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000830.fa @@ -0,0 +1,46 @@ +>ACLBLIBL_01239 +MSTTQSSPEPAPRRRLPAWTGNFGWQIVAALVLGLVLGLVARSMGHTPDSPTWLGETLAT +IGSVYISILKATVIPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG +VVMQPGVGTGQSAPESYQARDVGWLDFLTSMVPANFLGLTVKSTVGEDGAVASSPTFNVL +QILVIAIVVGIAALKVGEKAAPFLTFSRSVLAVIQKLLWWIIRLAPIGTVGLLGNAVASY +GWSTMGTLAKFVVAIYVGLAIVMFVVYPVLARLHGLCVKQFFTGVWPAVQLGFVSRSSLG +TLPVTQRVAERNFGVPTGYAAFAVPLGSTTKMDGCAAIYPAIAAVFVAQFYGIEMSLGQY +ALVVLVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGLALLLAVDPIVDMGRTATNVAGQ +ALVPALVAKQEGILDQARYDAERVDIMGEDEEEIVEARAQDRDDDQDQMVGAAARPARD +>MOLHKGIG_01654 +MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTAEHPTWLGETLAT +VGSIYISLLKAAVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG +VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL +QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY +GWSTMGTLAKFVVAVYVGLALVMLVVYPLLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG +TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIEMSLSQY +ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ +ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAELVGTPEPRA +>NAFOICDF_01150 +MTSHPSSPASGASTPARRRRLPAWTGNFGWQIAAALVLGLLLGLAARAMGHTPDSPTWLG +ETLALIGSIYVQLLKATVVPLVFFAVVASVANLAQVTNAARLAAKTLLWFAITSFIAVLI +GLAVGVVMQPGVGTGQSAPEGYQARTVTWLDFLTSMVPVNMLGLTVKTTAGDDGALTSTP +SFQVLQILVIAIAVGVAALKVGEKAEPFLAFSRSVLAVIQKVLWWIIRLAPLGTVGLLGN +AVASYGWSTMGTLVKFVVAVYVGLALVMLVVYPLLARVHGLSVKQFFTGVWPAFQMGFVS +RSSLGTLPVTQRVAERSFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFVAQFYGIDM +TLGQYALVVLVSVLGSAATAGTTGATVMLTLTLSTTGLPLEGMALLLAVDPIVDMGRTAV +NVSGQALIPALVAQQEGILDRTRYDAERGDVMADEDETIVEARHDDARGASRADLTEAGS +AR +>MHAAABBN_01359 +MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT +VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG +VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL +QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY +GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG +TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY +ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ +ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTSEPRA +>LFPAFLNI_01584 +MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT +VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG +VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL +QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY +GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG +TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY +ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ +ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTPEPRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000831.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000831.fa new file mode 100644 index 0000000000000000000000000000000000000000..9476f9e772d9a2aa9e8aa24d1cf0438325c7ba72 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000831.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01240 +MARTRVAGLTPGHRIAETPVPKGAFVTTTSTGPSSEPVHSSADPFGFFGLTYDDVLLLPS +ATDVIPAEADTSTQLTRNIRLNIPVVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ +ARHVDTVKRSESGMIKDPVTIGPKATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT +RFIPHEEWETRTVDTAMTRMPLITAREGISREETIRLFSQNRVEKLPLVDEAGRLTGLIT +IKDFDKAEKYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV +LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV +PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGAESVMLGSLLAGTAESPGDLV +FYQGKQFKAYRGMGSLGAMQTRNGKRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA +SVVHQLVGGLRQTMFYTGASTVDELKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>MOLHKGIG_01653 +MARTRVAGLTPGHRIAETPVPKGVFVTTTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN +ATDVIPADADPGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ +ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT +RFIPREEWATRTVDTAMTRMPLVTAQEGVSRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV +LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV +PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV +FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA +SVVHQLVGGLRQTMFYTGASTVTDLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>NAFOICDF_01151 +MSTSTGPSSDPVYASEDPFGFFGLTYDDVLLLPNATDVIPADADTSTQLTRNIRLNIPVV +SAAMDTVTEAPLAIAIARQGGMGIIHRNLSIEDQAKHVDTVKRSESGMISDPVTIGPKAT +LAELDELCAQYRVSGLPVVAEDMTLLGIITNRDTRFIPHEEWDTRTVDTAMTRMPLITAQ +DGISREEVLHLFSQNRVEKLPLVDDAGRLTGLITIKDFDKAEKYPDAAKDDEGRLRVGGA +VGFFGDGWERAMTLVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIGGQAATY +AGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGL +QHSGDIGKALVAGADSVMLGSLLAGTAESPGDLVFYQGKQFKAYRGMGSLGAMQTRNGTR +SFSKDRYFQADVPDEDKLIPEGIEGQVPYRGPIASVVHQLVGGLRQTMFYTGAPTIVDLK +ENGRFVRITTAGLKESHPHDIMMTVEAPNYRSK +>MHAAABBN_01358 +MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN +ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ +ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT +RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV +LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV +PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV +FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA +SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>LFPAFLNI_01583 +MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN +ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ +ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT +RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV +LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV +PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV +FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA +SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000832.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000832.fa new file mode 100644 index 0000000000000000000000000000000000000000..b74031d80bea4155b9ef401980c071b66856b6b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000832.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01241 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPKDVSLTWRIDAYTFEMPVIGAPMDSVM +SPETAIALGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPDGTEATRRLQEAYAAPI +RAELITERLAQIREAGVVVAGSLTPQNTQEFYKTVLAAGVDLFVIRGTTVSAEHVSSSHE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGSSTTTRRAMGIRVPMA +TAIADIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKALAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTHVGQVAPLEEVLWGPGHHADGTSNLMGGLKRAMATSGYT +ELKEFQKVEVLVTPTQTV +>MOLHKGIG_01652 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPEAAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALQAGPAGTEATRKLQEAYAAPI +RPDLITERLAQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTQVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV +>NAFOICDF_01152 +MTNQIEIGRGKRGRQAFSFDDVSVVPSRRTRDPKDVNLSWRIDAYTFDMPVMGAPMDSVM +SPETAIALGRLGGLGVLNLEGLWTRHEDPEPLLEEIAAMEAEAGSPEVTRRLQEIYSAPI +RADLITERLAQIRESGVVVAGSLTPQNTQQFSQTVLAAGVDLFVIRGTTVSAEHVSSTHE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAIADIAEARRDYMDESGGRYVHVIADGGVGTSGEIVKAIAMGADAVTLGTALARATEAP +GRGWHWGLEAAHPELPRGHRTRVGQVAPLEEVLWGPGHTTDGTSNLMGALKRAMATSGYT +ELKDFQKVEVLVTGARTH +>MHAAABBN_01357 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPETAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPAGTEATRMLQEAYAAPI +RPDLITERLAQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAVHPELPRGHRTHVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV +>LFPAFLNI_01582 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPETAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPAGTEATRKLQEAYAAPI +RPDLITERLEQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTHVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000834.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000834.fa new file mode 100644 index 0000000000000000000000000000000000000000..bad8a08c2eea6b4be49b79b28d0a5f805f2625d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000834.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_01243 +MSHTEPVDPAALPDPEDITEADLPEAPPRPGRERRRFAGTQQQIRSATRFYVVCSWITGV +MLLLLVAEMVFKYAWGQELFAGGTTVDGEQNILGLHPEDSVTGGVNLSLFILIAHGWMYV +VYLLACFRLWSLMRWQPMRLLAMAGGGVVPFLSFVVEKKVTKVVRDDVHRFPDAARRY +>MOLHKGIG_01650 +MSTQHPGPEPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW +ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG +WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR +RY +>NAFOICDF_01154 +MSQPHHDAGREAARAGEAPVDPATLPDPEDITEADLPAPPPRPGRAVRRFAGTRQQIVSA +DRIYKVCAYITGVMLLLLVAEMVFKYGLHQELFAGGTTVDGEPHGFGLAPEKSVTGGVNL +SLAILIAHGWMYVVYLLACFRLWSLMRWAPGRLLAMAGGGVVPFLSFVVERKVSGQVREE +LAQFPDAARRY +>MHAAABBN_01355 +MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFSGTQQQIRSATRLYVVCAW +ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG +WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFMVEKRMTRVVRDELHRFPDAAR +RY +>LFPAFLNI_01580 +MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW +ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG +WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR +RY diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000835.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000835.fa new file mode 100644 index 0000000000000000000000000000000000000000..60d43593fdd3914811b74b077f654828ff7b07c9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000835.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01244 +MTENAPHSDAPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER +RPAALILSGGPSSVYEPGAPTLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG +STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDAERRIY +GVQWHPEVGHSSHGQQVLEHFLHQGAGLGSDWTASNVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESAEIEQAFGEAHGGARLVMVDAREDFL +SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPEATEVRFLVQGTLYPDVVESG +GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRSADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPIVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>MOLHKGIG_01649 +MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER +KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG +STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY +GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTVSNVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL +SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG +GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>NAFOICDF_01155 +MTQNEPTRDQPAPLHDVLPTVLVMDFGAQYAQLIARRVREANVYSEVVPSSTPAQEILDR +RPAALILSGGPSSVYEAGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVARTGTREYG +STRLESADGGSVLLAGQDAAQVVWMSHGDAVTEAPEGFAVTAVTAGAPVAAFEDRERRIF +GVQWHPEVGHSERGQEILANFLTEGAGLSQDWTAENVIEEQVARIREQIGDARAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESDEIERAFGEAHGGAKLVMVDAREDFL +AALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESAHDPNAPEVRFLVQGTLYPDVVESG +GGDGTANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRQADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPSEVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE +>MHAAABBN_01354 +MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER +KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG +STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIF +GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL +SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG +GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVISEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>LFPAFLNI_01579 +MTQNAPHPDTPTPLSDVMPTVLVLDYGAQYAQLIARRVREANVYSEVVPASTPAAQILER +EPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG +STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY +GVQWHPEVGHSSRGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL +SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG +GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000837.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000837.fa new file mode 100644 index 0000000000000000000000000000000000000000..0b2145536fa3869eb4b7af9471303782de6d5559 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000837.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01246 +MGAEVPDPAPRRRGPRRADAPGTGPASADAPEPRLPGVGAGTDGARGAEGVRGAGGVRGA +VGVRGAAGEPTADERDRWLLEQRPPHWG +>MOLHKGIG_01647 +MPADGAPRRRGPRRADAPGTGPASADGREPRLPGMPRLIGQAGTSPATAPTGDVAGVESG +PAEAERDRWLREQRPPHWG +>NAFOICDF_01157 +MRTTPTASPEPGRRRGHRRADAAGTGPASADGPEPTLPEPTLPGPALPGAQTAGDATPSR +PAVSRGRAVTSAAGADRPQPADELGRWLLEQRPPHWG +>MHAAABBN_01352 +MSADGAPRRRGPRRADAPGTGPAAADGREPRLPGMPRLAGQAGTSPVTAPTGDVAGVESG +AAEAERDRWLREQRPPHWG +>LFPAFLNI_01577 +MSADGAPRRRGPRRADAPGIGPAAADGREPRLPGMPRLAGTSPATAPTGDAAGVESGPAE +AERDRWLREQRPPHWG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000839.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000839.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f7e48b788c1af3f6cdd83774116617400e21617 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000839.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01248 +MRTPPPAPEPASTGPVAGVDDVVAAKAALRARLRAARRERSPERRAAESAAAVEHLWAWL +GPRVAQAARDGEAVVATVLPMPTEPDTGPLRERLVAAGARVLVPVIEPQRRLNWTAWHPG +VATARAAAAPVDEPVGERHGVEALAEAVAVVMPALAVAEDGMRLGQGGGYYDRFLARLPR +SVPTVALVFEDELLPAGSVPAEPTDRPVDALVTAAGLRHV +>MOLHKGIG_01645 +MRTPPPVPEPAATGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL +GPRVAAATADGTAPVVATVLPMATEPDTGGLRTRLLAAGARVLVPVIEPERRLSWASWHP +GVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP +RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV +>NAFOICDF_01159 +MPAAAPAPHPDDAAAALASTEAKAALRTRLRAARRGLDPAVRARQAEAAAEHLWTWLGPH +LEERTADGPPVVATVLPMPTEPDTGPVRERALAAGARVLVPVIEPGRHLSWTAWRPGVAV +ARAANAPLDEPVGPREPGSVLDGAALVLMPGLAVDLTGARLGQGGGYYDRFLATLPSSVT +TVAFVHPSEVLEPGVIPLEPTDRPVDGVLTADGLLWCEPASAGPQ +>MHAAABBN_01350 +MRTPPPVPEPASTGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL +GPRVAAATADGTAPVVATVLPMATEPDTGVLRTRLLAAGARVLVPVIEPERRLSWAPWHP +DVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP +RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV +>LFPAFLNI_01575 +MRTPPPVPEPAATGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL +GPRVAAATADGTAPVVATVLPMATEPDTGGLRTRLLAAGARVLVPVIEPERRLSWAPWHP +DVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP +RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000841.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000841.fa new file mode 100644 index 0000000000000000000000000000000000000000..3fc7c5858c360a50a7e093b999de633939048bbc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000841.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_01250 +MEDTTAPASAGRAALDALADARVSASFVILALVAYFAWRLVVRRRRVESAPARPTMLRST +MHRLQSSPAVRALTERLSGRVSGLADSARAAGRRTAGLQVRWGRTALFLAALAALAVALV +AGVAAAFGAGTAGLAGACLLFAVAAVAGLRALAVRDRARRAPAAVVEAPAEAAPHAAPEA +PRVDPERDRRVFETVLGLEDEAARVSAAAPAAPAAAPTVVAASAVRAPEATDTVTLPVVP +RPTYLDAPEMLRPAPAPLTAPEAAGSDVRLKDAARAAEHEEALSATAEQDVAALDLDHVL +ARRRAS +>MOLHKGIG_01643 +MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLSAAADAARAARGRTGLHIRWGRTALFLAALVALLVFLVA +GLAAAFGAGTLALAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPAAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAAPRVEPVVVTASAAAPAADRVVTIPAVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLTDAARTADDQISAAAEQDIAALDLDNVLARR +RAC +>NAFOICDF_01161 +MTETPSPREDARLDAEPGHADSGFHVHWDRASLFLVGVGALAVALVTALCALAGLPTAGL +AGWSLLVTVGAVVGLRVLAARDQREHHDDLADDADEPNLAEEDLDTHELPVVPDPERDRR +VLAAALSLTDEAEDEEPAAEPVPVVVDALQRRRAPRIPLGGIVIPEVPRPTYLDAPEAPA +AEAQAEYPAEDDAVATRPEAEEQAASAEVVEIPEPAARAVVLDLDGVLARRRAS +>MHAAABBN_01348 +MDETTPPTTAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLGAAADAARAARGQTGLHIRWGRTALFLAALAALFVFLVA +GLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAADVVPARPAAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAASRVEPVVVTASAAAPAADRAVTIPAVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLQDAASTADDRISAAAEQDIAALDLDNVLARR +RAC +>LFPAFLNI_01573 +MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLSAAADAARTARGRTGLHIRWGRTALFLAALVALLVFLVA +GLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPTAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAAPRVEPVVVTASAAAPAADRAVTIPTVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLTDAARTADDQISAAAEQDIAALDLDNVLARR +RAC diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000842.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000842.fa new file mode 100644 index 0000000000000000000000000000000000000000..a561202c0c53c5f3a9c4cd325f41f9979d3cf91c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000842.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01251 +MSIGRASAPLAVRASGLRWLRTRADALHLQRGRRLARVLDVDVMEGRAGDARVRTRTLVL +ARDPRTGPDAAPPGSARTSERGVLEDGTLWWWAAADPALPGLALTENDAGLAALLGTAPG +RVRLTWRGYRPRERAVIALDAADAGLAGSRAYLKVLAPAAAEAVAARLSAARAAGVPVPD +LLAAPERGTLLLGNVPGLPWGALLGDARADALDPARVAEVLDRMPAPPGEAGPAPDAAAA +LLEHAAWAAVVLDPERQAESAARADRLRAALAAGDPGPPVPVHGDLHPGNLHVDASGGRV +TGLVDCDGLGLGHRVDDWATLLAHLEAAAADLGPGGGAVRAVAERVRAHARTETDEVALA +ARAAVVLAALGADPSVPRAARTARRAAADAALARVSR +>MOLHKGIG_01642 +MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL +ARDPRHPDVPAAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG +RARLTWRGYRPRDRAVLAVEATGDDGVAARTFLKVLPPARAARVARRQAAAGAAGVPVPA +VLATPEHGVLPLASVPGLPWRALLAGPEAAGLDPARVAALLDRLPPVPEEPPGPAGPTAG +AAGCADTDDGGPAILLEHATWAAVVLDPEAQDEVAARADRLRAALAAGDPGPRVPVHGDL +HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF +RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL +>NAFOICDF_01162 +MVLLEGPPGAGVARERVLVLRGPVEPAVAVPGPPGPPVPASGPAPRRRGRGRLPDGTRWW +LLPHDPALPGLDLALDHERLDAWLPGLGRAGEPAWVAYRPGERAVLRVPLDAVPARPDEP +GSSLHLKVLPPARLHGMHGRLLAARAAGLPVPPPLAPPDLGVLALGTLPGEPWRARLGAD +APQPAPAAVAALLDALPDALAAHDDGPSRTPAWSALLAHAVRAGTLLDPGAAEELRERAR +RLEESLAAADPGPRVPVHGDLHPDNLLLAPGTDRIVGVLDPDSLGPGHRVDDWAVLVGHL +AVAAADAAVPGPSHDPERARRTAALAAEFTGHACGVVDEEALRARADVTALALAAAPDLP +AAVRAARRSAR +>MHAAABBN_01347 +MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL +ARDPRHPDVPAAACPPVPGERGFLEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG +RARLTWRGYRPRDRAVLAVEATGDDGVVGRTFLKVLPPARAARVARRMAAAGAAGVPVPA +VRAAPEHGVLPLASVPGLPWRALLAGPEAAALDPARVAALLDRLPPVPEEPPGPAGPPAV +AAGGADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRIRAALAAGDPGPRVPVHGDL +HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF +RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRAARRAAADAALARVGL +>LFPAFLNI_01572 +MSIDRAAARQAVRASGERWLRTRADALHLQRGRWLARVLDLDVMTGRAGDARVRSRTLVL +ARDPRHPAAPGAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALVALLGTAPG +RARLTWRGYRPRDRAVLAVEATGDDGVVARTFLKVLPPSRAARVARRMAAAGAAGVPVPA +VRAAPEHGVLPLASVPGLPWRALLAGSEAAALDPARVAALLDRLPPVPEEPPGPAGPTAG +VAADADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRLRAALAAGDPGPRVPVHGDL +HPGNLHVDAAGERITGVLDADDLGTGHRVDDWAVLIAHLEAGAADLGAGGAALRAVAARF +RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000843.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000843.fa new file mode 100644 index 0000000000000000000000000000000000000000..1dafbfb146a2062e394fb0cf802cb9f051e62665 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000843.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01254 +MDAPQQTPAPADVGPTAVLARVRTLLAEARTSGAPEDAVDAAPVDHDARQWWELSLEAAL +RDEPRESARCAESGLAALGPGEDGVRLSLLRALAVAADRLGDETGLTRWVEARAALLRTL +GRPRQAALETQLGASLVREPDGFEAAVLAGVVEEEPGVPGEDPGDTVLPEAALALAVHRV +HASDLDGALAAARRAVESLRGLRAAGAVLPVGSWSSAHLLLSRLHLWRGEHAEADEAAAV +VTSLPAARAVLASATTVRAIAAHEQDRPTAALALALDAADRMARVGLRRGAASAAALAGR +VAGDLEGHEEAAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRPDEAEPLLARLVR +REAAQGHDVEQARALVDLGHAHHDQDRSENALPLWREAAGLFEAHGRWEDAARTLLAAGA +LVNRERDELTRPSALDLFERAVAAARRAVDEDPAVLPAALHAHGYLLCESGRPEGLELLD +EAVALVREAEAPWQVADYTDTRARALWSLEQGAEAVSTALHAADLFTAAQDPEGAAQAEL +FAASVVAEDGSPEQAATLFRLVSESTQSTLVRLGALTGLHQCLSAVGDHDGAARVRDDLD +AVREQLGAD +>MOLHKGIG_01641 +MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA +ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR +HLGRPRQAELESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH +RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA +AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA +GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL +VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA +GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL +LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA +ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE +LDALREGLGAD +>NAFOICDF_01163 +MAEDAPALLAGRDPLAAVEALLAAARDDAALPLPAGSDAPSLRERALEALLREDPASAAR +AAEDGLDAPGGQDPALRLALLRLRATAAAHAGDEPALEEWTARRADLLRRLGRPRQADLE +VQLGASLLREPDAFEATVLAGVAEDERGRITADPAALEDTVLPDALLALCAQRVQAHDLD +AALEAAEEALAVIRAQETAGVVLGEAAEPHALLMLARLHLWREEHRASDDAARAVLARPC +AAVVRASATLVRALAAHGQDRPEAALDFALRAAEAMSRAGLRRGAASAAALVGRVAGARA +DRQDLAVAAWELSCVHAEKAEAPEAPSLAYWWAHQLLIAGRAEEAEPVLTALVRREAAAG +DEAAQARALVDLGHACHELDRPSEALPLWREAAELFTRRGHHADAAHTLLAAGALCHRDP +HDAAHAGALDLFEQAVDAARRSEGDSAVLASALHALGYLRCETGRGDGLELIDEAIALAE +GSGAAWQKADYLDTRARSLWALHRGDDAVSAALTSADLFTDAGDPSGAAQAELFAAHVVA +EDGRPEQAATLFRLVSESTHSDLVRLGALTGLQQCLAALGEHAEADRVRADADAVRRALG +GRD +>MHAAABBN_01346 +MDTPQDPPRRDDPSGGPVEPAVDAALDRVHALLRQARVIAAPDAPTALDARGWWELSLEA +ALRDEPRESARLADSGLAALVPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR +HLGRPRQAGLESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH +RVHTGDLDTALELTRRVIAVLGGLRAAGALLPIGSWSSAHLLLARLHLWRGEHAEADAAA +AVVTVLPAARAVLASATTVRAIAAHELDRPTAALDLAFEAAERMASVGLRRGAASAAALA +GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL +VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA +GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL +LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA +ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE +LDALREGLGAD +>LFPAFLNI_01571 +MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA +ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR +HLGRPRQAGLESQLGGALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH +RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA +AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA +GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL +VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA +GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL +LEEALALVRYAGADWQVANYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA +ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE +LDALREGLGAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000844.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000844.fa new file mode 100644 index 0000000000000000000000000000000000000000..7bd70a9393826e7d838e819d503c796859f31ea7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000844.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01255 +MSPTPVPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIELG +ESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGGV +LRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA +>MOLHKGIG_01640 +MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES +PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGGVLR +PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT +>NAFOICDF_01164 +MSAASPTAASTAPGPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIELGESPEE +ACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGGVLRPEA +DGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR +>MHAAABBN_01345 +MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES +PEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGGVLR +PEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT +>LFPAFLNI_01569 +MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES +PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGGVLR +PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000846.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000846.fa new file mode 100644 index 0000000000000000000000000000000000000000..71edbd941d22d6141e70cf475890958cf266b0fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000846.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01257 +MPTPRPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL +QAMYRHLPHAQGYSDSQGIYSARTAVSQYYESRGIRDIGVEDVFIGNGVSEMISMVLQAL +VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWAPDLEHIESLVTERTKGIVLI +NPNNPTGAVYSRQILQGIIDVARRHGLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF +SGLSKAYRVAGFRSGWVAVSGPKHRARDFLEGLTLLANMRMCANVPAQHAIQVALGGYQS +IDDLVLPGGRLLEQRNLAQKRLNDIPGVSVQPAQGALYLFPRLDPEVYAIEDDQEFVIDL +LRAKKILVSHGGAFNYPHTDHFRLVTLPSVEDLDVALDRLEDFLEDWRERRG +>MOLHKGIG_01638 +MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL +AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL +VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI +NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF +SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS +INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL +LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG +>NAFOICDF_01166 +MAPSTPREFRQSSKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL +QAMYQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDISVDDVFIGNGVSEMITMVLQAL +VDDGDEILVPSPDYPLWTGATTLSGGRAVHYRCVEEEGWAPDLEHLESLITERTKGLVII +NPNNPTGAVYSREVLNGVVDIARRHNLVLLADEIYEKITYDGARHINAAGLSDDVLTLTF +SGLSKAYRVAGYRSGWVAVSGPKHRAKDFLEGLTLLSNMRMCANVPAQHAIQVALGGYQS +IEDLILPGGRLLEQRNLAQKRLNDIPGVSVQPAHGALYLFPRLDPEVYAIDDDEKFVIEL +LQAKKILVSHGGAFNYPQPDHFRLVTLPSVKDLDIALDRLEDFLEDWRERRG +>MHAAABBN_01343 +MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL +AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL +VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI +NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF +SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS +INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL +LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG +>LFPAFLNI_01567 +MGGMPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPD +AVLAAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVL +QALVDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGI +VLINPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLT +LTFSGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGG +YQSINDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFV +IELLRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000849.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000849.fa new file mode 100644 index 0000000000000000000000000000000000000000..cd6b7c7a2dfdbeb5416244529bc4e607e9420797 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000849.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01261 +MDPSSTAHVEADALLDAGVPATASQTSAERPWPLRRLSENLKLHIERAPATWIEGQLIEY +KTNRGNVYMTMRDLEEEYSLPVTAWRNVAVTFEGTVQQGSRVVARVKPNFWTKAGRLSMV +VQEMRPVGLGDLLARVELLRRRLGEEGLLDPARKRPLPLLPGLVGLITGRDSDAKKDVLR +NAQLRWPAVRFEVREVAVQGPEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS +DEALVRAVAAARTPVVSAIGHEADRPVLDDVADVRASTPTDAAKRIVPDAAQEAAGIAEA +RRRLAAAVERRVQREGEGLAQLRSRPVLADPVVMVDGREQDLHAWRERARRATAHRLTRE +RDAVEHLVARVRALSPQQTLDRGYAVVQQEGRLIRDAAQVAPGEDVDILVASGRISAEVT +AVRPGRVGGVGTVQDEDEQAGTKEQA +>MOLHKGIG_01634 +MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF +KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN +VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPRRIGLITGRDSDAKKDVLR +NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS +DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA +RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE +EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAAGRIAADVV +ATHRTTPTPSHERTRQA +>NAFOICDF_01170 +MEESAAREEGTVVVPATASETSPERPWPLHRLSENLKLHIERAPATWIEGQLIEHKNNRG +NLYMTMRDLEEEVSLPLTAWRAVAAGIDPSVQQGSRVVARVKPNFWVKGGRLSMVVQEMR +PVGLGDLLARVELLRRRLAEEGLTSPARKRQLPVLPGVIGLITGRDSDALKDVVRNTHLR +WPAAVFEVREVAVQGPDAPRQVAAALAELDARPEVEVIVIARGGGALEEVVLPFSDEALV +RAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQESVGIREARLRLA +GAVERRVRGEADALAALRSRPVLAHPHVMVDTRTEDLGRWQERGRVALGHRLAREADAVS +ALRAQVRALSPQQTLDRGYAVVQHAGHVVRRAEDVTPGDDLDVLVAAGRIEAYVTDVTPV +ETPSPTQEDA +>MHAAABBN_01339 +MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF +KNNRGNVYMTMRDLEEEVSLPLTAWRNVATTLDGTVQQGSRVVARVKPNFWLKAGRLSMN +VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR +NTLLRWPAAEFETREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS +DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA +RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDIRQEETDRWRERGRSALGHRLVRE +EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAVGRIAADVV +ATHRPTPTPSHERTRQA +>LFPAFLNI_01563 +MDQPVTEGASAAPDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF +KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN +VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR +NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS +DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA +RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE +EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVREADQVATDDRLDILVAAGRIAADVV +ATHRTTPTPSHERTRQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000850.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000850.fa new file mode 100644 index 0000000000000000000000000000000000000000..6575cd2e4e2001cee3e9d9329b4357c0587ebb75 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000850.fa @@ -0,0 +1,38 @@ +>ACLBLIBL_01262 +MRQLTAVLLALVAGVLAVLATAGALVDEAAHRPALVRQAAEQVASDDDVRAAIPGAVADA +VGDAVPEGVPGPLRGLAQDLVRPMAESAAQDEGVVRGWSDTADEARRAWLHDLREASDAT +GPVPGGDFTIPFGPVAQSGVAAALGDLETDLREDRLNLPGQQLVERLLGVDFGDWAVDTL +VGPLHERAAELRDRTDLTMTVTVDALRDVDRSEVARWVSASVHWRWAAGGAVVLLAAAVL +IAPLRWRGVAVLLSAATALVGGYLLANATRAEAFAVAAPEGAPAGIARLVERVEQALRPA +VDAALAPYADGLTTAGWIALAVGAALLVAELVLSAARAGRTTPPRARGGSRAAADPASR +>MOLHKGIG_01633 +MRTTLSLLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV +VHDAVPEQVPDPLAQAAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD +EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIAGADVGDWAADTL +LAPLYDRAADLRDSTALRMDARIDALAGTDRATVHRWVDASAHWRWAAAASVLALVGALL +LAPRGRRGLAVAVAGAVALAGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAARPA +FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARADGPPAVGRSHTAADVT +SR +>NAFOICDF_01171 +MRSLLSLLSAVLAALLAVLATAGALVDRTAHQPDTVRQVAERIAADDAVRAAVPRAVTDS +IEGAVPESVPAPLTQLAQDIVRPIAEDVAKDPDVATGFADTADEARRAWLMDLERARDGG +EHAPGGEFRIPFGPVAQSGVASAVGDLETRLRSDQLNLPGQSIVEAIVGVDVGTWAADTL +VKPLYDRAAELRDSTDLTMTVRVDALAGTDRATVARWVDASAHWRWAAGGSVLALVASLL +LARRGRRGLALAVAGVTVLLAVLLASSAVDSSRWSLAAPDGATGGVAALARAAEAAFRPA +VADVLAPWLGGLTTWGTVALLAGLVLMAIEVLAGPVRRRLARTRPSGTGSHTGR +>MHAAABBN_01338 +MRTTLSFLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV +VHDAVPEQVPGPLAQVAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD +EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIAGADVGDWAADTL +LAPLYDRAAELRDSTALRMDARIDALAGTDRATVHRWVDASAHWRWAAAASVLALVGALL +LAPRGRRGLAVAVAGAVALAGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAARPA +FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARADGPPAVGRSHTAADVT +SR +>LFPAFLNI_01562 +MRTTLSFLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV +VHDAIPEQVPGPLAQTAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD +EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIVGADVGDWAADTL +LAPLYDRAAELRDSTALRMDARIDALDGTDRATVHRWVDASAHWRWAAAASVLALVGALL +LAPRRRRGPAVAVAGAVALVGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAAGPA +FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARVDGPPAVGRSHTAADVT +SR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000851.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000851.fa new file mode 100644 index 0000000000000000000000000000000000000000..28114d34a88dad47939836539c2af43ef022d4e7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000851.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01263 +MGGMSAPSVSARPSAVGLGMPQVPRVRRTREDVEAAAPVSGDKRVLLAAPRGYCAGVDRA +VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVEELDEIPEGALTVFSAHGVSP +AVVQDAERRSLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTYGEAPEHT +TVINDVAEARAVQVADPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATS +NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFASQVDESWFEGVS +TVGLSSGASVPEVLIQDVLALLAEYGYGQVDEVVTAEEDIMFSLPKELRAELKRVGDDSR +GLGGRRQTEG +>MOLHKGIG_01632 +MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA +VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP +AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKRILLIGHDGHEEVEGTFGEAPEHT +TVINDVAEARTVQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS +NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVA +TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGR +ALGGRRRAAEA +>NAFOICDF_01172 +MDGMSVPTASAPSTVGLGMPQVPRTRRSREEVEAAAPVAGDKRVLLAAPRGYCAGVDRAV +VAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGAVFVQELDEVPAGALTVFSAHGVSPA +VVAEAAERDLQTIDATCPLVTKVHREAVRFARQDKRILLIGHTGHEEVEGTYGEAPEHTT +VINDVEEARTVQVDDPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATSN +RQAAIKRISPQCDLVIIVGSANSSNSVRLKEVALEYGAARAERVDFASQVDESWFEGVAT +VGLSSGASVPEVLVQDVLALLADYGYGQVEEVVTAEEDIIFSLPKELRAQLKQAGDEERS +LGGRRRPAE +>MHAAABBN_01337 +MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA +VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP +AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHT +TVINDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS +NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFTNQVDESWFEGVA +TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAELKRVGDESR +SLGGRRRDAEA +>LFPAFLNI_01561 +MSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRAVVA +VEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSPAVV +EEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHTTVI +NDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATSNRQ +AAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVATVG +LSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGRALG +GRRRDAEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000853.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000853.fa new file mode 100644 index 0000000000000000000000000000000000000000..4107b7b797506284e6f8f531e1b97a780dd30975 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000853.fa @@ -0,0 +1,19 @@ +>ACLBLIBL_01267 +MEHVFDTLGRRPVFHPTILAVTADGQRGMWEHPDLEPEQAAAEVAKISPRPARAVAVFEG +EAATEDGPRPAVAVEAFDAAALASVRLVFTYLPGVPGAGIAAQVDGDPQVVANGPNPLFG +>MOLHKGIG_01629 +MSTPTPTGPTPTPPGGELLPLISLAVEHVFNTLGRQPVFAPTILAVTADGQRGMWEHPDL +QPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV +AAAGIAARVDGDPQVVANGPNPLFG +>NAFOICDF_01175 +MTPPTHEILPLVSLAVDHVFDTLTRQAVFDPTILAVTADGARGMWTLPDLAPEQAAAEVG +RIQPLPQRAVAVFDGEVQTPQGPRPAVAVEAFDAGAVQSVRLVFEYVPGIPGTEITGRIE +GEPHIVANGHNPLFGQIS +>MHAAABBN_01334 +MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQPVFAPTILAVAADGQRGMWEHPDL +EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV +AAAGIAARVDGDPQVVANGPNPLFG +>LFPAFLNI_01558 +MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQSVFAPTILAVTADGQRGMWEHPDL +EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV +AAAGIAARVDGDPQVVANGPNPLFG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000854.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000854.fa new file mode 100644 index 0000000000000000000000000000000000000000..772bc39f8303d4bd6be23a04dbe7b7f000ec0a3c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000854.fa @@ -0,0 +1,23 @@ +>ACLBLIBL_01268 +MELLIAPGDITATTADVVVNAANSTLLGGGGVDGAIHRRGGPEILAACRRLRETELPDGL +PVGQAVATTAGRLPARWVVHTVGPVWAKTIDKSATLASCYRESLRVAAELGARSVAFPAI +SAGVYGWPMDDAARIAVTTCREVAAQGAGSVERVLFVPFGERAEAAFRAALDAPDETGAP +AAS +>MOLHKGIG_01628 +MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGDTVDEVLFVPYGETAEAAFRAALGHLEAPQTT +DDEGDTGR +>NAFOICDF_01176 +MKLSIAPGDITATHADAIVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPDGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLRVARELGARTVAFPAI +SAGVYGWPMDDAARIAVETSHAMADEVGDVVEEVLFVPFGDRAEAAFRAALEHLT +>MHAAABBN_01333 +MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGGTVEEVLFVPYGDTAEAAFRTALDRVERG +>LFPAFLNI_01557 +MQLTIAPGDITATRADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAETIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGGTVDEVLFVPYGETAEAAFRAALGHLEDPQAT +DDEGDTGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000855.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000855.fa new file mode 100644 index 0000000000000000000000000000000000000000..2ac486175a15ccb8e9a970453fa2f738e1bb0e4e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000855.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01271 +MARPIDPFREMERPFREMERLVNGLTRTSGTASMPMNLFREGDRFVAEVELPGVDPASID +VDVEERTLTVRAERKESPAGEDRRWLTRERSAGTFARQLTLGEGLALDRIEADYEDGVLT +LTIPVAEQAKPRKISVKHSGAGAGAGQTVPGETAEVEERSAEQEAAQNGGAPQA +>MOLHKGIG_01626 +MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER +TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA +EQAKPRKISVTHGGAAPVAGQTVEGETAETTGE +>NAFOICDF_01181 +MARPIDPFREMERPFREMERLVNGLTTRATGTASMPMNLYREGDAFVAEVELPGVDPASI +DVDVEERTLTIRAERKEAAASEGRQWLTRERSSGTFARQLTLGQGLALDRIEADYRDGVL +VLSIPVAEQAKPRKIQVKHSAADQVEGQEVAGQESVQDSAAVEAPQQPSGE +>MHAAABBN_01332 +MARPIDPFREMERLMTGFARTSGAASMPMNLYREGDVFVAEVELPGVDPSSIDVDVEERT +LTVRAERKEAPAGEDRRWLTKERPAGTFARQLNLGQGLALDKIEADYSDGVLLLTIPVAE +QAKPRKIQVKHTGSAAQVEGEAVEGEAVEGSAAEASGE +>LFPAFLNI_01555 +MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER +TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA +EQAKPRKISVTHGGTAPVAGQTVEGETAETTGE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000856.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000856.fa new file mode 100644 index 0000000000000000000000000000000000000000..72d1ce5f463e294aa29e26367621bf9dabe1232b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000856.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01286 +MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTSVVYKPVAGEAPLWDFPAGTLAR +REVAAYLVSEALGWDIVPRTWLREGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +ILEGEDEGGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRYGVDHGLTFH +VADKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGRGLVQLLSAEEVEALAERCAQLL +DDGVFPAPSGLTPAVPWPLF +>MOLHKGIG_01612 +MSAADVPAGELMSGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAATLAR +REVAASLVSEALGWDIVPRTWLRDGPFGKGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +VLEGEDEGGNRLVLAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH +VQDKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGQGLAELLGAEEVEALAARCAQLL +DDGIFPAPSGLTPAVPWPLF +>NAFOICDF_01191 +MSAADVPAGELVDGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAAHLVSEALGWEIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPAAGWLT +ILEGEDEEGRRLALAHENSAALRRMAVFDVIVNNADRKGAHILAMPGGHRYGVDHGLTFH +VAGKLRTVLWGWLGEALSEEERDGVGRVLDGLDGELGRGLAELLSAEEVEALAERGARLL +DDGIFPAPSGRTPAVPWPLF +>MHAAABBN_01323 +MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAASLVSEALGWDIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPAGQVPASGWLT +ILEGEDADGNRLVLAHEDSAALRRMAVFDVIVNNADRKGAHILAMPGGHRHGVDHGLTFH +VADKLRTVLWGWLGEELSEEERDGVGRVLDGLDGELGRGLAELLSAEEVQALAERSAGLL +DDGRFPAPSGLTPAVPWPLF +>LFPAFLNI_01538 +MSAADVPAGELVSGELTLTGRITTASNATFLGAVGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAAHLVSEALGWDVVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +ILEGEDEDGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH +VEDKLRTVLWGWLGEALSDEERDGVARVLDGLDGELGRGLAELLSAVEIGALAERSAGLL +DDGTFPAPSGLTPAVPWPLF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000857.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000857.fa new file mode 100644 index 0000000000000000000000000000000000000000..fe8e2e8901caea425d5f3111410be8040b0c0203 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000857.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01287 +MTESPAHVHEFDWPDRVVIGTIGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMLDEI +LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD +DDADPALEVDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS +>MOLHKGIG_01611 +MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI +LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLVDAHPLTD +DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPVCSDCGQPIDPDGHDCTFPDS +>NAFOICDF_01192 +MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI +LDDLMALDGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLTD +DDADPVLETDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS +>MHAAABBN_01322 +MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI +LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGGIGLGWDPTTAQVLIDAHPLSD +DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPFCSDCGQPIDPDGHDCTLPDS +>LFPAFLNI_01537 +MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI +LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD +DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000858.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000858.fa new file mode 100644 index 0000000000000000000000000000000000000000..6699fd4a26258ed2eadcf5bd4776ef12cf7fd8fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000858.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01288 +MATVLLVRHGRTTANASGLLAGRTPGVSLDEHGREQAARTADRIAAVPVTAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQSRPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGMHLDMFQRLDV +GPASVSIVSYGSSRPRVLTVNTDAGDLSWLATKGPSGDAPVGGGAGTDPVADSANGRTPR +IDA +>MOLHKGIG_01610 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTGGRIAAVPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGAGAVDERTPRIV +A +>NAFOICDF_01193 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRVAAVPVAAVVASPLERC +AQTARALLDRQSGAVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPSRPRVWATNTDAGDLSWLSSLGPSDDAPVGGGAGTGPGAVDEQTPRIV +T +>MHAAABBN_01321 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRIAAVPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDERTPRIV +A +>LFPAFLNI_01536 +MATVLLVRHGRTTANASGLLAGRTPGVSLDDHGREQAARTADRIATLPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDEQTPRIV +T diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000861.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000861.fa new file mode 100644 index 0000000000000000000000000000000000000000..60fab720967af03fd9583fa450d3c8a1cf578085 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000861.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01293 +MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRIGLTYPQYLVMLTLWQVEGDASAE +TEAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG +RALRASARTVPADALTRIPLDATERQVLMCLLNRITEAVGPR +>MOLHKGIG_01600 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAEGDASAE +TEASTPDAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG +RALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR +>NAFOICDF_01202 +MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRLGLTYPQYLVMLTLWQVEGDASAE +TDAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG +RALRESARTVPADALTRIPLDATERQVLMGLLNRITEAAGPR +>MHAAABBN_01312 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAESDASAE +TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR +>LFPAFLNI_01527 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQVESDASAE +TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000862.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000862.fa new file mode 100644 index 0000000000000000000000000000000000000000..46667e8fa4170e99e00ce0e3e9b0b745e3182205 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000862.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01294 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGANPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA +>MOLHKGIG_01599 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA +>NAFOICDF_01203 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGSNPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA +>MHAAABBN_01311 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVIPNVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA +>LFPAFLNI_01526 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGVRVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000863.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000863.fa new file mode 100644 index 0000000000000000000000000000000000000000..c5d09630691c11740a864e6c77e039658f179c30 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000863.fa @@ -0,0 +1,18 @@ +>ACLBLIBL_01295 +MTKRRQSVPLSQTAARLGLGAALWAAGIPEREHGGRG +>MOLHKGIG_01598 +MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRG +>NAFOICDF_01204 +MTKRRQSVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRRTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREHGGRG +>MHAAABBN_01310 +MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRG +>LFPAFLNI_01525 +MTKRRQSAPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000866.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000866.fa new file mode 100644 index 0000000000000000000000000000000000000000..a163483bde5e2ffb6daf50f6bcbfc06537b53548 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000866.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01301 +MPRTRPPAQDFLAELPDGTVKQRNPFSGTEVWTVPGRGHRPLGIARPAAQPLDPDDDGRH +CAFCSARLLETPPEKSRVVRTEDGEHAILRDVPAEALFDTVPEFRRVPNLFEILSYEYWR +LNHGFVPAPGVADRRAAYLATETGRAHVLAVVGNKLRAAGRSAEEVEAMPEEERIEAASG +FFGGGHDVIIARRHFADGAQDDHALAGSGTLSPEEHRRFIALTVDSMRDLYAANPHARYV +SVFQNWLKPAGASFDHLHKQLVAIDEVGVQNEAAIARVRRNPDAFAQDALGYAAKQGLMI +ARNEHAAMFAGFGHRYPTVEIHSLSPTCEPWEQTDAERDAMADLIHAAHAATGADVPSNE +EWHTRPTGVAEPLPWRVCLKWRVSTLAGFEGATKIYLNTVSPGSVRERVATRLQELQAAG +AIADGIRIDDDGHGAV +>MOLHKGIG_01595 +MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF +CEHRMLETPPEKSRIVSTRADDGAPAWQILRHPAAERLEETIPAFRRVPNLFEILSYDYW +RLNHGYELPPDACRRRDEYLATEAGRAHVRAVVTAKLRASGRSAEEAAAMSEAELIGASA +AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFMALTADAMRDLYATTPAVRY +VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNQAALDVAVAHDLM +IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN +EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELWAA +GALADGMRIGADARVRPGMLRYAD +>NAFOICDF_01214 +MSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAFCEHR +MLETPPEKARIVPTRADDDAPAWQILRHPAAERLGETTPAFRRVPNLFEILSYDYWRLNH +GYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIAASAAFFG +GTHDVVIARRHFVDGAVDDHQLASSGTLTLDEHHAFLALTADAMRDLYATTPAVRYVSVF +QNWLKPAGASFDHLHKQLVAIDEVGAQNAAALDRLREDPQVFNHAALDVAVAHDLVIAAN +EHAVMFAGFGHRYPTVEVYSTSPVGQPWRQSAAELRAVSDLLHAAHAATGPDVPSNEEWH +TRPPGFASPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAAGALA +DGMRIGADARVRPGALRYAD +>MHAAABBN_01307 +MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF +CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW +RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIGASA +AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY +VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNHAALDVAVAHDLM +IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN +EEWHTRPPGVASPMPWRVMLKWRVSTLAGFEGATKINVNTISPWDVRDRVLARLRELRAA +GALADGMRIGADARVRPGALRYADGAARLTPPRGR +>LFPAFLNI_01522 +MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF +CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW +RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSTEEAAAMSEAELIAASA +AFFGGTHDVVIARRHFVDDAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY +VSVFQNWLKPAGASFDHLHKQLVAIDEIGAQNAAALDRLREDPQVFNHAALDVAVAHDLV +IAENEHAVMFAGFGHRYPTVEVYSTSPVGEPWRQDPAELRGMSDLLHAAHAATGPDVPSN +EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAA +GALADGMRIGADARVRPGMLRYAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000868.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000868.fa new file mode 100644 index 0000000000000000000000000000000000000000..123e65d23e72568a9e9fe54e5810cf5fe7cd506d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000868.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01333 +MRDMFVVLGPAPASVGSPGAWWAVDGDDATPLGSCPAGSVAGLVAGLPARLGVDPSTVRW +VLADVGTEYAAWLAAGVRVDRCWDVALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPE +RPARVPAGQESFFDLPDGTGSAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGAL +VAAEIRAAGLPWDRGVHEALLTEQLGPRPAQGERPARLQALAERIADVLGSPGLSPDSQP +SLLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWL +DQWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQIPAGVRDAVRADPGWALTVADASQVEP +RILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKVALLGAMYGSTTGDSAA +LMPHLRRLYPRAIGLLERAASVGEAGGQVATWLGRWSPAPEQAWLDSVADVGTQAAESAA +RRRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRAAGLGTELVFFVHDEVVLHGPAPE +AEAVRGVVAEAASAAGRLLFGAAPVDFPLTVASLDSYADAK +>MOLHKGIG_01589 +MFVVLGPAPASVGSPGAWWALDGEGDGASPLGSCAAGSVAGLVAGLPARLGVDPSTVRWV +LADVGTEYAAWLVAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPVR +PARVPAGQESFFDLPDEAGPAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGALV +AAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQTLAERIADVLGSPGLSPDSQPS +LLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWLD +QWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQVPAGVRDAVRADPGWTLTVADASQVEPR +ILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDSAAL +MPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGRKWQESVSDVGTQAAESAAR +RRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRSAGMRTELVFFVHDEVVLHGPATEV +EAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK +>NAFOICDF_01231 +MVIVLGPDPAPGTPPGRWCALVLPDDAAPSPADASPGQGDGGPVARFARDELADVVRALP +GRLGVDPAVVRWTVADAAEVYPALLAAGVRWDRCRDLSLGQRILRGAAAAGLAYAPTVDL +PVHEPEAEDPATARRAPGQGAMFELAGPEPAPDAAALARELAAQQAAVAASAHPHRLRLL +LAAESQGALVAAEMHHAGLPWRADVHEALLAEQLGPRPPEGARPARLQALGERVAAALGS +PGLNPDSPPALLRALQTAGVTVDSTRKWELTAWADQGGAQRQAREALIAPLLEYKALYRL +WTAHGWHWLDTWARDGRFRPTYLVGGVVTGRWAAHGGGAMQVPSGVRDAVRADPGHVLTV +ADASQVEPRILAAMSRDAALAAAGATPDLYREVAEQGRSAGTALDDRSRAKVALLGAMYG +ATTGDSAALLPHLRRLYPAALAMLEAAAADGEAGRPVHTWLGRTSPAPAERWLERVADRS +TREAEARARSLRRSAGRFTRNFVVQGTAAEWALCWMGQIRGGLHRAGLSTALVFFVHDEV +VLHGPAEEAGAVARIVTEAASQAGRLLFGAAPVDFPLTVAQVESYAQAK +>MHAAABBN_01300 +MRAMFVVLGPAPASVGSPGTWWALDGEGDDAVPLGSCAAGSVAGLVAGLPARLGVDPSTV +RWVLADVGTEYAAWLAAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTE +PERPARVPAGQESFFDLPDEADPAPDVTVLAAELAAQRAAVEGSAHPQRLRLLAAAESQG +ALVAAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQALAERIADVLGSPGLSPDS +QPSLLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWH +WLDQWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQIPAGVRDAVRADSGWTLTVADASQV +EPRILAAMAADQALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDS +AALMPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGPTWQESVSDVGTQAAES +AARRRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRMRSAGMRTELVFFVHDEVVLHGPA +TEAEAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK +>LFPAFLNI_01516 +MFVVLGPAPASVGSPGAWWALDGEGDGASPLGSCAAGSVAGLVAGLPARLGVDPSTVRWV +LADVGTEYAAWLVAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPVR +PARVPAGQESFFDLPDEAGPAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGALV +AAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQTLAERIADVLGSPGLSPDSQPS +LLRALQTTGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWLD +QWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQVPAGVRDAVRADPGWTLTVADASQVEPR +ILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDSAAL +MPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGRKWQESVSDVGTQAAESAAR +RRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRSAGMRTELVFFVHDEVVLHGPATEA +EAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000870.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000870.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a268c5332d3d91a8ee1b09bf885b2046b2f1e30 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000870.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01343 +MSAGTRGAWGPTPAPIADVERIVAAALAEDAPWGDVSSEAFVPADARITARVVAREAGVL +SGTAALEAAFRLVDPATEVTLHLPDGTALAPGAVVAAVAGPARSVLRAERVALNLAQRMS +GIATATAAHVAAVRAGGGHTRVADTRKTTPGLRVLERQAVRDGGGHNHRHGLSDAVMLKD +NHLAALGFGGEDAPGEELTRALRAGKARLPHTVHVEVEVDRLDQLPAVLAAGVGTVMLDN +FSLADLRAGVELVAGRAVVEASGGVSLETIGEIAATGVDVVSVGALTHSVRALDLGLDAV +VDAADAPAPGRR +>MOLHKGIG_01580 +MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREPGVLSG +TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI +ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH +LAALGFGSAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS +PAELRAGVERVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE +EVSPRR +>NAFOICDF_01236 +MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG +TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI +ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRSSLSDAVMLKDNH +LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVGTIMLDNFS +PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVRSLDLGLDAVVE +EVSPRR +>MHAAABBN_01290 +MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG +TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI +ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH +LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS +PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE +EGSPRR +>LFPAFLNI_01507 +MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG +PNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI +ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH +LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS +PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE +EGSPRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000871.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000871.fa new file mode 100644 index 0000000000000000000000000000000000000000..4fe249dfd6bf6efeaa988f961699dbbbd2449236 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000871.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01344 +MTATPETTASVARTLTLVARDPARGSACSSDLTTGPWAFDAGLPAYGPGASQDDAIPADA +PVQGRIPEEYQQASDEELHARIAAAKAALGDRAVVLGHFYQRDEVVRHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPEQAVILPNLAAGCSMADMADLDSVQDAWEQL +EEVYGTEPDADGRVPLLPVTYMNCSAALKGFVGERGGIVCTSSNASAVLEWAFERAQRVL +FFPDQHLGRNTGRAMGIELERMPMWNPRLPLGGNTEETLRDARVLLWHGFCSVHRRFTVA +QIEQARAEHPDVRVIVHPECPLPVVEAADESGSTDHIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPDAVADPARA +ALERMLAVAPRQSVAQGAGA +>MOLHKGIG_01579 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVAEPART +ALERMLAVAPKQSAAQSAGAGT +>NAFOICDF_01237 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPAAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRMPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALREAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPVSVADPART +ALERMLAVAPKQSAAQSAAQSAGAGT +>MHAAABBN_01289 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART +ALERMLAVAPKQSAAQSAGAGT +>LFPAFLNI_01506 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART +ALERMLAVAPKQSAAQSAGAGT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000872.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000872.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2a1aa59babe75bbbc7541db655999d76896d6eb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000872.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01345 +MPAPEARVTVAVSTAVFGVRPDPSGAPRLHVALVPRMREPFLDRWALPGTWLAADEELAD +AAARVAAETVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPSHGGGLD +VAGLPAGVHVRWQRADAPPAMAFDHAEILTAAVARLRADLPRAGVAHALLGPSFTLAELR +AVHEAVLGRTLDAANFRRATLATGVLEETGEVRAGTRHRPPKLYRYRPADGAPPPAAPDD +PGDLS +>MOLHKGIG_01578 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPVLDDDGAAPASRPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DARR +>NAFOICDF_01238 +MPVAEARVSVAVSTAVFGVRPDAHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPTLDDDGAAPASRPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRDGTPHRPPKLYRYRPAGPGTDPNPAGP +DASR +>MHAAABBN_01288 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGALEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DARR +>LFPAFLNI_01505 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DARR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000873.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000873.fa new file mode 100644 index 0000000000000000000000000000000000000000..c1a511e0612e9df980e53022bc00efa4cc0655bf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000873.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01346 +MTISDQGSPRRLPDSLERVSTPDPSASAAPSDAALASDVIGDGPHRVAFLHGLMGRGRNF +TGPAKALADDFTVELLDLPDHGRSPWTDRVDYQEIADRVAEHLRAGLAADGPVHVLGHSM +GGKVAMVLALRHPDLVDRLIVEDISPRLLPQATDEFVHLLGTMLRMDLDSYESRAEADAV +MAKHVHDARVRGFLLQNLRREGGRFAWQPNVAMLFEHLEAVGSFPDPAAPEDPDRVFDRP +VLWLAGANSDYVRDEDVPRMKDLFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>MOLHKGIG_01577 +MNTTAAASDPSDAPLASTRIGEGPRGVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPD +HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLI +VEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR +TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM +KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>NAFOICDF_01239 +MPTWSRASLSRVNTTAASAPSDAPLASTRIGEGSRRVAFLHGLMGRGRNFTGVATALADD +FTVELIDLPDHGQSPWTDAVDYQDMADRVADHLRAGLAADGPVHLLGHSMGGKVAMVLAL +RHPELVERLVVVDISPRMSPSATGEFVHLLGTMLRMDLASYTSRAEADAAMAEHVHDARV +RGFLLQNLRREDGHFAWQPNVRMLFEHLDEIGAFPDPVVPEDPDRVFDRPVLWLGGADSD +YIRDGDAPEMKALFPRVVRVTVRGASHWVHADQPEAFVSAVRTFLTAD +>MHAAABBN_01287 +MNTTAAASDPSDAPLASTRIGEGPRRVAFLHGLLGRGRNFTGPAKELGDDFTVELIDLPD +HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPDLVDRLI +VEDISPRVSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR +TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM +KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>LFPAFLNI_01504 +MNTTAASAPSDAPLASTRIGEGPRRVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPDH +GASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLIV +EDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRRT +AGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVVDHPVLWLAGAESDYVQDEDVPRMK +ELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000874.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000874.fa new file mode 100644 index 0000000000000000000000000000000000000000..321d111d3628e6860e042989b29469f18e5c4069 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000874.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01348 +MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMAGAAANREL +PMIWRITKGSLRNKLLIILPALLLLDWLAPWVLPWLLLAGGTYLAYEGAHKVWGKLTGHS +PERDEPAVEKGPEAEDKVVRGAITTDFILSAEIMVISMNEVADVDFWLKAVILVVVAILI +TAVVYGAVALIVKMDDVGLHMTQNGRTAGGRRFGAGLVKAMPHVLTAITVIGTVAMLWVG +GHIVLVELAALGVPWPYDVQHGIVHAVEAAGGFVAWLVETLTSALWGLIWGSLALGVVLV +VNRLRGKKDTLAH +>MOLHKGIG_01576 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTETATSAVWGLLWGSVALGVV +LLVGRLRGNKAAPAH +>NAFOICDF_01241 +MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMEGAAAQREL +PMILRIVRGSLRNKLVFILPGLLLLDWLAPWALPWLLLAGGTYLSFEGAEKVWHKLTGHH +EPQEDTPAVEQGPEAEDKVVRGAITTDFILSLEIMVISMNEVSDQGFWMKAAILAIVAVV +ITVAVYGAVALIVKMDDVGLHMHENAHTSGARRFGLGLVKAMPVVMGVISVIGTVAMLWV +GGHIVLMELATLGLPWLYELQHTIVHAVEGAGSVIAWLVETLTSAIWGLVWGSLVVAVVG +LVRRLRT +>MHAAABBN_01286 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEETVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV +LLVGRLRGKKAAPAH +>LFPAFLNI_01503 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV +LLVGRLRGKKAAPAH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000875.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000875.fa new file mode 100644 index 0000000000000000000000000000000000000000..546d1903095c87300f907b08dbb9eb2294dfc619 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000875.fa @@ -0,0 +1,19 @@ +>ACLBLIBL_01349 +MTGVTAADGLDLSGMAAWLRHQADEEIVHANKFIDHVTDRGSDAAGDLSSRPLLNWFLEE +QIEGEATPPL +>MOLHKGIG_01575 +MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID +HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP +LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA +>NAFOICDF_01242 +MSIDKDLTRKFNEQITLEFEASMVYRQLAIAADMQDLSGMAAWLRHQADEEIVHANKFID +HVVDREASAVIGAIPAPDVPEHITPVQIFEAALAHERKVSEAIRELYRAAEAAGDLSSRP +LLNWFLEEQIEEEATVGEIVGQLKLVGEDGSGLLRIDSALGARPVETTENAG +>MHAAABBN_01285 +MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID +HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP +LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA +>LFPAFLNI_01502 +MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMASWLRHQADEEIVHANKFID +HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP +LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000877.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000877.fa new file mode 100644 index 0000000000000000000000000000000000000000..fecc58f93d8729caa958f9ed52253d6f40c3ce2b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000877.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_01351 +MRTPMTSNVTDTALLFEGGGMRASLTSAVVAELLRERIHVDFVAGISAGSSNSVNYLARD +PERARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFQANPARL +VLVGFDAVTGQTRWWDRSDMGTLADLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG +IPVTAAEEAGFEKLFVVMTRERSYVKRPERFPAFYQRTFRRYPAVAEALISRWRRYNETR +ERLFEMERQGRAYLFVPESMPVSNGERSVAKLAAAHELGLAQVRREMPAIREFLGL +>MOLHKGIG_01573 +MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD +PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL +VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG +IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR +ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR +>NAFOICDF_01244 +MAEQQDHTAEALTSNVTDTALLFEGGGMRASHTSAVVAELLRAGVHVDFVAGISAGSSNA +VNYLARDPLRARQAFVDFADDPRFGNWRTFLRGKGMFNAEYIYEHAGLPEADLPYDFAAY +RANPARLALAGFDAVTGETRWWGREDMTTLQDLMVRVRASSTMPILMPPVHLEDTVYVDG +ALGVDGGIPVTAAEEAGLAKLLVVMTRERSYVKRPERFPAFYQRAFRRYPAVAEALVTRW +QRYNATRERLFEMEREGTAYLFVPEVMPVSNGERSVAKLAAAHELGLAQARREMPAIKEF +LGL +>MHAAABBN_01283 +MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD +PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL +VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG +IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR +ERLFEMERQGRAYLFVPATMPISNGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR +>LFPAFLNI_01500 +MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD +PARARRSFVDFADDPRFGNWLSFLRGKGLFNAEYIYEHAGLPEADLPYDFAAFRANPARL +VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG +IPLTAAEDAGFKKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR +ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000878.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000878.fa new file mode 100644 index 0000000000000000000000000000000000000000..c221a630bb2c9d8913f504b5c0d57b959a26a628 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000878.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01352 +MATTHMKSTPVQTVGDLPEVGAPAPDFTLTGADLSPVTLQELRGRRVILNVFPSLDTGVC +AASVREFNSRATDLEDTTVLAVSADLPFAAARFCSAEGIENVRSGSVFRSSFGDDYGVTM +VDGPLEGLLARAVVVVDAEGVVRHAQLVPEITEEPDYEAALAAAQA +>MOLHKGIG_01572 +MATTHMKSTPVHTVGELPQVGSPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGGDYGVRM +TDGPLEGLLARAVVMVDADGVVRHAQLVPEISEEPDYEAALAAARG +>NAFOICDF_01245 +MATTHFKGTSVHTVGELPEVGSAAPEFTLTGSDLSSVTLADLKGRTVVLNIFPSLDTGVC +AASVRRFNQEAAGLEDTTVLAVSADLPFAAGRFCSAEGIENVVTGSVFRSDFGTAYGAEL +ADGPMRGLLARAVVVVDAEGTVAYTELVPEITTEPDYEAALAVVRG +>MHAAABBN_01282 +MATTHMKSTPVHTVGELPPVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLEDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM +TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG +>LFPAFLNI_01499 +MATTHMKSTPVHTVGGLPQVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM +TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000880.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000880.fa new file mode 100644 index 0000000000000000000000000000000000000000..0568ef0c646da7e2c0957c12d8dccb8fcd866b31 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000880.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01354 +MDPLWIALALTAFAGLATVLGGVLAVVGKEPSGRGLGAALGLAAGVMIAVSFLEMLPVAV +EGLAGAVGGAATALAVGALAVGTAGYVLLERAVPVPAAGVPDDVDGPDGLSRLRLMRLGM +VTALAIGLHNVPEGFVTFAGALQDPSVGVALAVAMAVHNVPEGIAVAVPVRRATGSRRKA +FAWTAFTGLAEPVGALVGWLLLAPFLTPALVAVVFAAVTGVMITVSLDALLPAARAAGGR +AATLAGVLLGVAAMAISLDLLG +>MOLHKGIG_01570 +MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPAAV +EGLGGAVGPAATAVAVAALILGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT +VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA +FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR +AAALGGVLLGVAAMALSLDLLS +>NAFOICDF_01247 +MEPFWTAVALTSLAGAATIVGGALGALGRPVSDRALAAALGLAAGVMLTVGAVEMGPAAA +RGLATAVGDGPGVLAAGAAVGGGALAYLLIDRLLPEAATPSGSSASAAREARVGRLGVAT +ALAIGAHNLPEGFVTFAGALEDSAVGLALAVAMAVHNVPEGIAVSVPVRRATGSARTGFL +WAATAGILEPAGALLGYWLLRPLLTDAVLGGVYGAVTGVMAALSLAALLPGAVRCGGVPT +ALAGAAAGAAAMLGSLSLLA +>MHAAABBN_01280 +MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLSAGVMLAVSFLEMLPAAV +EGLGGAVGPAATAVAVAALALGAGAYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT +VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRCKA +FAWAAFTGIAEPLGALIGWLLLAPFLTPALVAAVFAAVAGVMVTVSLDALLPAARAAGGR +GAALGGVLLGVAAMALSLDLLA +>LFPAFLNI_01497 +MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPASV +EGLGGAVGPAATAVAVAALTLGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT +VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA +FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR +AAALGGVLLGVAAMALSLDLLS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000882.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000882.fa new file mode 100644 index 0000000000000000000000000000000000000000..5c1a1ebd378fe8409305e08abfe50a77a29b4474 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000882.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01359 +MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ +PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSSAAASTLRLVVLATVLAIIIGIA +IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG +VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA +AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI +LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD +AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLSERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL +VTGTAAVLMNLVADVLYAVLDPRIRV +>MOLHKGIG_01567 +MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ +PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA +IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG +VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA +AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI +LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD +AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL +VTGTAAVLMNLVADVLYAVLDPRIRV +>NAFOICDF_01250 +MLKFILRRLGSSALVLFGASILLYVLTVNSGDPLKDLRESQASNREQLMQARIDYMGLDD +PWYERYWNWLTGVVKYLIGAGTLGTDRSGVQVESLLGNAAASTLRLVVLATVLAIVIGVA +IGIITAIRQYSGLDYAVTFLIFLFFSLPVFWAAVLLKEYLAIGFNNWIARPTMDWPLVIG +LAVVLGLALQAAMGGRLVRRLLTFAATVAVIVLGGYLLFALDMWRNPRMGPLVQLLIGLA +VAVGGTALVAGLKNRSVLKAALATVAVGVVAYYATYGVLMQSPSGWLIAGLGVIAVLVGV +LAGRLLGGFSKGSAVSVSVVTALVMGLSILAEHMMNYWPQLLKAKPRPIATIGAETPNLT +GHFWVLFLDKGTQLLLPTVLLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLGERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITESVFGWKGMGELFRTGLDQVDPAPVMAFFL +VTGTAAVLMNLVADILYAVLDPRIRV +>MHAAABBN_01277 +MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ +PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA +IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG +VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA +AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI +LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD +AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL +VTGTAAVLMNLVADVLYAVLDPRIRV +>LFPAFLNI_01494 +MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ +PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSNAAASTLRLVVLATVLAIIIGIA +IGIITAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG +VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA +AAVGATAVISGLRNRSVLKAALVTAAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI +LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD +AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL +VTGTAAVLMNLVADVLYAVLDPRIRV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000883.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000883.fa new file mode 100644 index 0000000000000000000000000000000000000000..a376e8a49d3e8e3465d910f670029c7054633f6b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000883.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01360 +MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRVKAGKSYSQGALVRKRFFRHKAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGANMGILPLALVLGLVTWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRVIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISLYQNS +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAAAGRKRGLFSRRAAKTDAGAT +TAGGLGTAPTARDGEADDLIADPDAPEHRRGGAGGPAGGVGQ +>MOLHKGIG_01566 +MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSLLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGGGAHRRLRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR +>NAFOICDF_01251 +MTMSHSAQQNPRSTSPAVVDLAEAEDLKLQQKTGKSYSQGALIRMRFFRHKAAMVSLVVL +AFIALMAFTSIGFAGIPGWWDESYSAASTVVDGGRPTLSVVPQFLGGEGLRWGAHPFGQT +STGTDFFALVMRGTQQSLIIAFIVGLISTAIGALVGAASAYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGKMAGGLQLGILPLAFVLGIVSWTSLARLVRGEILSLREKEFVAAAVAMGA +KPGRIIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSYLGFGVKSPDSSLGLLISDYQTA +FTTRPWLFWWPGMTILAIALSVNFLGDGLRDAFDPRQSGSGRRKRGLFSRRAAVTEATPT +TAGGLQASPASAPAGHADVVTDSRGLDAPAAWTVTDADGTSRPAGDDVDTTEGDAR +>MHAAABBN_01276 +MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEAAGGSARISDADEDGQR +>LFPAFLNI_01493 +MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHKAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000885.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000885.fa new file mode 100644 index 0000000000000000000000000000000000000000..1025962a1c6120b28585b6f146d0d719dc9755ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000885.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01362 +MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQGGAFAAHGEVAERVMDSGDLEREKGI +TILAKNTTVFYSGPSAPEGQTVTFNVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL +PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLADEVEDLDLDS +VLNLPVVFASGKAGRASLNQPEDGSLPDSEDLEPLFATMMEHIPAPAYTKGEVLQAHVTN +LDASPFLGRLALLRIFNGTLKKGQQVAWARQDGTLKTVKITELLGTKGLSREPIEEAGPG +EIVAVAGIEDIMIGETLTDVENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDAELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK +TVDGKVHEPMELMTIDTPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFSVPARGLIG +FRTQFLTDTRGAGIASSIANGYEPWAGTIEYRNNGSLVADRAGTATPFAMINLQERGSFF +IQPGSEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSDSFEGLTPPRQLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA +>MOLHKGIG_01564 +MTSTETRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI +TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL +PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS +VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN +LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG +EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR +TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG +FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF +VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA +>NAFOICDF_01253 +MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI +TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDASEGPL +PQTRFVLRKALAAKLPVVLVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPELDLDS +VLDVPVVYASGKAGRASREQPGDGALPDSEDLEPLFNVIMEHIPAPVYDESEVLQAHVTN +LDASPFLGRLALVRIVNGTLKKGQTVAWARQDGQLKSVKITELLATKGLERVPADEAGAG +EIVAVAGIEDIMIGETLTDLEDPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK +QIDGKLHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG +FRTRFLTDTRGAGIASSEAAGYEPWTGDIEYRTNGSLVADRAGTATPFAMINLQERGTFF +IQPGAEVYEGMIVGENARADDMDVNITKEKKLTNMRAASSESFEGLTPPRTLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA +>MHAAABBN_01274 +MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI +TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL +PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS +VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN +LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLGRVPAEEAGPG +EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR +TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG +FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF +VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA +>LFPAFLNI_01491 +MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI +TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL +PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS +VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN +LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG +EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR +TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG +FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGTATPFAMINLQERGTFF +VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000888.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000888.fa new file mode 100644 index 0000000000000000000000000000000000000000..ddf27785cbffe89901bf17f603fb857c28e8ed9f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000888.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01366 +MTQNESVRLTVGEQSLDLGVERATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDEGILRYRGYAIEDLAANSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYEIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRTIQSDGIKPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILSKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +PLRQYPQR +>MOLHKGIG_01560 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDQEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPAAKIGRPRQIYVGE +QLRQYPQR +>NAFOICDF_01257 +MSEIESARLTVGEKTLDLGVEKAAEGNDGIVVAPLLKETGKVTYDPGFMNTANAKSAITY +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKEALEAWETNILRHNMVHEDL +KMFFNGFPRDAHPMPVLSSSVSALSTFYADSLDPKDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNNLNYVENFLRLCFGVPAEEYEIDPDMVKALDLLLMLHADHEQNASTST +VRLVGSTDANLFASVSAGINALYGPLHGGANEAVLNMLRRIQAEGIKPEDFMEKVKHKED +GVRLMGFGHRVYKNYDPRAKIVKKTAEDILAKLGGNDELLEIAMRLEEKALADDYFVERR +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELTEDPATKIGRPRQIYVGE +QLRQYPQR +>MHAAABBN_01270 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTY +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +QLRQYPQR +>LFPAFLNI_01487 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +QLRQYPQR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000889.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000889.fa new file mode 100644 index 0000000000000000000000000000000000000000..1d7f64b06bbf8a894f5181ad36df311afbc27bcf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000889.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01367 +MTETAAQHPSARLVSGHGLATTAADGTVLDVWFPAPVAGPLADADATLAETLRSLAADDA +DRGTTQSVVELEADLDAAPATAEDAWLRLHALSHRLVRPNELNLDGVFGLLANVVWTNFG +PCAVEGFELTRARLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTV +MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLL +GANSGVGISIGDDCVVEAGLYVTAGALVTVVRPGEEPRTVKAVELSGVPNLLFRRNSATG +VVEVLPRAGRTVELNAALHAN +>MOLHKGIG_01558 +MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA +DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG +PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV +MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL +GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAAHTVKAVDLSGVPNLLFRRNSTTG +GVEALPRAGRTVELNAALHAN +>NAFOICDF_01258 +MTDTSQTSSARLVSGHGLATRAADGAVLDVWFPAPVTGPLASADASLAGTLEGLAAADAD +RGTTQDIVALEADLDVAPASAEDAWLRLHALSHRLVRPNELNLDGVFGLLTNVVWTNFGP +CAVEGFEATRAKLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTVM +HEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLLG +ANSGVGISIGDDSVVEAGLYVTAGTVVTVVEPGRKPRTVKAVELSGVTNLLFRRNSVTGG +VEVLPRDGRTVALNAELHAN +>MHAAABBN_01268 +MTQTAAQQPSPRLVSGHGLATTAADGAVLDVWFPTPVAGPLSAADASLRDTLRALAADDA +DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLARPNELNLDGVFGLLTNVVWTNHG +PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV +MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL +GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG +GVEALPRAGRTVELNAALHAN +>LFPAFLNI_01485 +MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA +DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG +PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV +MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL +GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG +GVEALPRAGRTVELNAALHAN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000890.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000890.fa new file mode 100644 index 0000000000000000000000000000000000000000..0c4382e16cb5f8c33121e2da144181ffdf9e59fb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000890.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01368 +MTETSAPALPDLADPGLDVAELTAVLLDVPSVSGDEGPLADAVETALRALGGLEVRRFGD +AVVARTDLGRDTRVILAGHLDTVPLPTVPGSRGTVPSAWEGDVLYGRGAVDMKSGVAVQL +ALAGRYGRADGPAPAHDVTWVFYDHEEVASDLSGLARVARQAPELLEGDFAVLLEPTDGV +VEGGCNGTCRYRVSFSGVAAHSGRAWRGENAIHKLGAVLTALAAHEPATVTVEGLDYREG +LNAIRVAGGVAGNVIPDAAHVDVNYRFAPDKTLEQAHARVREVLEGAGVDWDAQVRIDDA +SPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDEH +VHRAAVHACLDALDAWLAG +>MOLHKGIG_01557 +MSLTPNTLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFGDA +VVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +SREAVHACLAALTAWLAG +>NAFOICDF_01259 +MTDAVAPVLPDLAAADLDVAALTATLLDAPSVSDDEGPLADAVEAALARLPRLGVRRFGD +AIVARTELGLPGRVILAGHLDTVPLPTAPGARGTVPSAWEGDVLYGRGAVDMKSGVAVQL +ALAGLFGRADGPDPVHDVTWVFYDHEEVDSARSGLARIARQAPELLEGDFAVLLEPTDGV +VEGGCNGTCRYRVRFEGVAAHSGRAWRGDNAIHKLGALLSALAAYEPATVTVEGLDYREG +LNAIRVSGGVAGNVIPDAAATEVNYRFAPDKTLEQAHAHVREVFAAAGVDWDAQVEVTDA +SPAARPGLDRPAAAAFVAAVGGEPMPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDEH +VERAAVERCRDALEAWLRG +>MHAAABBN_01267 +MSLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEHALRALGGLEVRRFGDA +VVARTALGRPTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +SREAVHACLAALTAWLAG +>LFPAFLNI_01484 +MSLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFGDA +VVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRTVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +HREAVHACLAALAAWLAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000896.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000896.fa new file mode 100644 index 0000000000000000000000000000000000000000..a104efdd807049468e5693e038b639dd3c093f44 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000896.fa @@ -0,0 +1,18 @@ +>ACLBLIBL_01374 +MSTPLWIAVIAALVVVVAALAAAAAGRLTLRAGEPAGQAPVHPVALPERPRADDVAFVRL +AVAVPGYQRDQVDAVLLRLRDALADHEDEVAALRARLAELEADAARDAERTGPR +>MOLHKGIG_01551 +MRAPLGGEGRRVSGPQWIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQCEDEVTALRARVAELEAADPSRSD +PAGRA +>NAFOICDF_01265 +MTQPIWIAVLVVAVVAVAALAAAALGRALPRPADPAGQAPPHPVLLPEHPRAADVDRLRL +ATAVPGYQRDQVDEVLARLRAALAADEERIAALEARLGEGDGVGR +>MHAAABBN_01261 +MRAPLGGEGRRVSGPQGIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEVTALRARVAELEAADPSRSD +PAGRA +>LFPAFLNI_01478 +MRAPLGGEGRRVSGPQGIVLVAVLVVVLGALAASLAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEAAALRARLAELEAADPSRSD +PAARA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000898.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000898.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a3b2221e44570630df272700089b07b37ace354 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000898.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01377 +MGRGHTLRHLDAYLEDALPSASRRRIARHLDGCPDCRAAVRARARVLDAARTVHQRPAGV +VASPVLRSRGISGRVVVGLLAFVVLVGGLLAAVWMAGAPRAGVARLAPSPTDAVGLVSGG +SADGRAAVAQLRGHGWTVPSLLGAGLEPLTVDAAQTPRDVEVVVGWGLQEPTVTVRECRP +RIAGAAPEGCASAAPLPEDAQERTLTGGDVYRIQPAEADGAWTAELTTAQAAYRVEARLP +DERADAVLTHLLVSERSRVRELGGPDAVEERLERGIERIVESVPRVRD +>MOLHKGIG_01548 +MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA +VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAAVRTAPTPTDTVALPAAG +TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC +RPRIVGATPKGCASTAPLSTGVQERRLAGGGVYRIVPAGEQDGWTAELTTPQAAYRVEAS +LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG +>NAFOICDF_01268 +MGVLARGHCLPVLDSYLEGVLAPRASRRVEAHLSRCPDCRAVAGQRARVLDAARSVDARP +AAGAVMRPRGVSGRAVVCGLLVLVVLAGLVAAVWMLGGPASTAAPADVDPVRAVSAPVSA +SADEDDVATRVDELRGQGWALPSLSASGMRPLSVHADRVGEAAEVSVAWGRTSPVVTVRE +CRGADADERTRCARQGGVGVSGASEARLPVGMDYRIADHADGGWEAWLSTSDAVYRVDAS +VPRSQAEALLSQLVVVERSGLAPPRRDEDPRDRLERGLDRLLDGRVGGAAVRNPAAGAR +>MHAAABBN_01258 +MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA +VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAAVRTAPTPTDTVALPAAG +TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC +RPRIVGATPKGCASTAPLSTGVQERRLAGGGVYRIVPAGEQDGWTAELTTPQASYRVEAS +LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG +>LFPAFLNI_01475 +MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA +VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAALRTAPTPTDTVALPAAG +TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC +RPRIVGAAPEGCASTAPLSTGAQERRLAGGGVYRIVPAGEQDGWTAELTTPQAAYRVEAS +LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000900.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000900.fa new file mode 100644 index 0000000000000000000000000000000000000000..f09bf9c88983ebc5f5533fa412447e807c90eb17 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000900.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01379 +MSDLGLHVPEVRTDLERRVLDRLATVQDPEIRRPVTELGMVESVVETAPGTVEVTVLLTI +EACPMRGTIQGDVAAAVADVPGCDAVDVRTGVMSPERRLALQDALRAARPANPFGEGSLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTASPTKLDRM +ILPPVVRDVKVISIGMFLDEDRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQAVAGVIENMGPMTLPDGTVL +DVFGAGGGQEVAERLERVLGSAVPLLGSVPLDPALRRGGDAGDPVVLSAPDSPAGRALAG +VAERLAVRPRGLVGRRLPLSPR +>MOLHKGIG_01546 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ +IAQRVAVRPRGLAGRRLPVTPR +>NAFOICDF_01270 +MSAPALPRPEVRTPLEAAVLAALDGVVDPEIRRPITELGMVRSVAETGGGHVAVEVLLTI +AGCPLKGTIQADVAAAVADVPGCAGVDVRLGVMTPTERAALQEALRGARPANPFAEDSLT +RVLAVASGKGGVGKSTVTANLAVALAGRGLSVGLIDADVHGYSIPGLLGVQASPTRVGEL +ILPPVSRGVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELVVVTTPQHAAAQVAARAGQLAAQTGQRVAGVVENMGPMALPDGTVL +DVFGAGGGQEVADRLSGALGTSVPLLGTVPLDPALRRGGDAGEPVVVSAPESPAAAALQE +VAARLAVRPGSLRGRGLPVSPR +>MHAAABBN_01256 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ +IAQRVAVRPRGLAGRRLPVTPR +>LFPAFLNI_01473 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVADVPGCGSVDVRVGVMEPERRLALQDALRAARPTNPFGKDTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLGTQVPLLGTVPLDPALRAGGDAGDPVVVSAPESPAGRALAE +IAQRLAVRPRGLAGRPLPFTPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000901.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000901.fa new file mode 100644 index 0000000000000000000000000000000000000000..183ae3a633c40aa807c8f993d35622e674162f78 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000901.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01380 +MSQTSRDARPSRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF +CAAWLGWNTFGPEDLRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED +RDRAERNLADTEFLTREISGLRLAVQEVATRDFVRGELRGVQEDLRDELREALRAELREE +IRAELRAELAEGRRERTDPGAEPRPRKQKKHKGRDRGRDERRAGDDGVDPSTTTLAVIAA +REAAQAAQSAQAGQDAGPEAGRAVDGRDDADGAAR +>MOLHKGIG_01545 +MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF +CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED +RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE +IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG +SGPAAGPADGAGPVDGGGR +>NAFOICDF_01271 +MPQSPRDPRDTRATGLDTPMRARERVMPRLTPNPDAFGEWTEGIARFMGTPQFLLWMTLF +CLVWVGWNSYAPEPWRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED +RDRAERNLADTEFLTREISGLRIALQDMATRDYVRGELRAMNEDLVAALREVVREEVREE +LRAEEAGPAVAPKPKEKSKKKSSRREPGRPDGTEAHTTTLAIIAAQEAADQGGAAPDAAH +AADDAGQDAP +>MHAAABBN_01255 +MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF +CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED +RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE +IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG +SGPAAGPADGAGPVDGGGR +>LFPAFLNI_01472 +MTQTARYLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF +CAAWLGWNTFGPMAWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED +RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE +IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAQEARE +AGGSGPVTGPAGGAGPVDGGGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000902.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000902.fa new file mode 100644 index 0000000000000000000000000000000000000000..5172d32ac0b4062a7963cb7110df40afd9051933 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000902.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01381 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAVPPFATGLVIEVPGKKRVFVPM +TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAADLFDRRVRLTDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLDWDEARWTGQAEPQAATSFLAAHEDLKPA +DLADMLHEMPEKRRVEVARELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEEAEDVRRLLEYEEGTAGSVMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAVGNIMDKDLEPV +SDLAPIAHVTRELATYNLTSIPVVNEHHRVVGAVSVDDVLDHILPDDWRAMDHDDHDPRP +AA +>MOLHKGIG_01544 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP +AT +>NAFOICDF_01272 +MNSPRIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGRGARSAATGLVIEVPGKKRVFVPM +TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAGDLFDRRVHLTDGSGRAVVEDLGIEQQR +NGDWLVTDYYVRRDDGRTAFGRPRGEHLLVSWDEVAWGAAAEPQGASSFVAAHDDLKPAD +LADMLHEMTDKRRVEVANELQDERLADVLQELPDDDQVQILSHLDIERAADVLEEMDPDD +AADLLNELPDSQQELLLELMEPEDAEDVRRLLEYEEDTVGSIMTPVPVVLPPEATVAEAM +ATIRQQEISPALASLVIVARPPLETPTGRYLGVVHFQRLLRYPPPEAIGNIMDKDLEPVS +DMDSVAHVTRELATYNLTSIPVVNAQHRVVGAVSVDDVLDHILPEDWRAMDPEDHPETEG +QD +>MHAAABBN_01254 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP +AT +>LFPAFLNI_01471 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVARELQNERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEAV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP +AT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000903.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000903.fa new file mode 100644 index 0000000000000000000000000000000000000000..87f778c2a14109c1703d8712a567c3b6c6c2c2ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000903.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01382 +MSFMMSSPPPGADRGLPRGELLATYASYADAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLFLLTPEGGAGQILTSMLLGLAVWLIFGVIGF +GMRKGRHGFASSQAVVPTGYDLVVAFEHAARARTELGLGGAAATAAAAVSTSPATPAPAA +PQAGPNQNGAGQVDAPRPDAPQADAQHAPQAGAPSSGGSHAAPDADAQPAGAEAAPAAGA +VPTGLDRSYGVTLPPEEVAKLIQARGGQASRPQEDPRD +>MOLHKGIG_01543 +MSIMMPNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPPAASQPAPAPAAEA +EDGSVQATPAPAPSSGGSHAAPAPGGPEAPARPAPEADPAPTGLDRSYGVTLPPEEVAKL +IEARGGHPPRPQDEPRG +>NAFOICDF_01273 +MMMSGPAAGGLPQGELLATYSTYEQAREQVDRLAEADFPVTALSIVGKDLRVVERVRGRL +NYGRVALGAAVQGALFGAMIGAFLLLLDSSAGGMQIVTSALLGVAVWVIFGVVGFASRKG +RHGFASTQALVPGGYDLVVAFEHAGRARQELGLGARGAATPAPAPMPVQESAPAPAPAPA +PSGSAVSGPSGSHAAPASSAEPAPAHVDGPAQDPAAPAGLDRSYGVTLPPEEVARLIEAR +GGRPRQDPQAPQGQPHPWDRPQS +>MHAAABBN_01253 +MSFMMSNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPQPAPQPAPAPAAEE +AGGGSVQATPAAAPSSGGSHAAPAPGGPEASARPTPEADTAPTGLDRSYGVTLPPEEVAK +LIEARGGHPPRPQDEPRG +>LFPAFLNI_01470 +MSIMMPNPQPGAEQGLPRGELLATYATYAQARDQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPPAASQPAPAPAAEA +EDGSVQATPAPAPSSGGSHAAPAPGGPEAPARPAPEADPAPTGLDRSYGVTLPPEEVAKL +IEARGGHPPRPQDEPRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000904.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000904.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a627f5bae471274f3fe5f9472be567b2d8064ba --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000904.fa @@ -0,0 +1,59 @@ +>ACLBLIBL_01383 +MDIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQDALS +DVGLSSLGRMEAGVLGHVDAVLAAARALDGEDAPSPDDDALTPARGREILARDADRLLGP +ARPDRAARIMVTLPSEAAQDPDLVARMAEAGMDLARVNCAHDDEAAWAAMIEAVRACATP +ERPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARTPAGLVTEPSRVWLAAAGAADAPAGA +VVVPVTEAGAEVLAGLAAGDEVELTDARGSHHVLTVEQAGAAGALVRADKTVYWGTGLAV +DTPRGTLTVGELAPLEQSMRVRRRDQVVLTRSLDPVPAASAPPYRIGLTLAQAFEDVAVG +DRVSIDDGKIDAVVRAANADEITLEVTEAGPNGTKLKAEKGVNFPDTALSIPALTDEDLA +HIPFVARHADMVNLSFVRSAEDVAQLIDALAAEDATDVDITLKIETVGAFEQLPRMLLEA +MRWRDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAIWATQILESLAKTGLPSR +AEITDAAMAQRAEAAMLNKGPYIEEAITALGDILGRMGGHARKKRDMLRRLESWSL +>MOLHKGIG_01542 +MGIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQEALS +DAGLSSLGRMEAGVLGHVDAVLAAARALDGDLATAPEDDALTSAEGRAILARNAASLLGP +ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA +GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVAVAD +RPDGAVVVPLAAPDGKTLAGLQRGDEIELTDARGAHRRLEVERVSGEGVLVRADKTVYWA +TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA +DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT +DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR +MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT +GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS +L +>NAFOICDF_01274 +MSTLPENAPDSRPTAESPVVAPGAAVTELIEAIDALRARIVAAEQAHAERLDRVADRHRA +SARNLVHYVTLRGEDLRPLQDALSAVGLSSLGRMEAGVLGHLDAVRTALHPLGGRPAPDP +ADDDPLSPAEGRALLAANAESLLGPSRPGRETRIMVTMPSEAATNAALVQGMADAGMDLA +RVNAAHDGEAAWAAMVANIRGVARDGGRPAPRICMDLAGPKLRTGPLEPGPGVVKVKPRR +DVDGTVLERSRVWLGEADAPEAADAVVLPLDPAGSGHSPVLSALRPGDHAMLTDARDSDR +TLHVLAATEAGVLLACRKTVYWHTGLEVDTPRGTLVVGALPSVPQAMRVHAGDEIVLTRS +MDPRPAVSEGPFTIGCSLPQAFQDVRPGERVLIDDGKITGEVVSNDGEAITLTVTEAGPT +GAKLRAEKGVNFPDTDLRLPALTDEDRSHLPFAAAHADVVNMSFVRSPADVAALIDALDA +EDARGVGVSLKIETVGAFERLPAMLLEAMRWNDVGVMIARGDLAVEAGFERMAELQEEIL +WLCEAAHVPAVWATQILETLAKQGLPSRAEITDAAMAQRAEAAMLNKGPYIDEAIGALSD +ILTRMGGHADKKRDMLRRLRSWSL +>MHAAABBN_01252 +MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS +DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP +ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA +GLPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVATAD +RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA +TGTALTTPHGPLEVGPLPPLEQSMRVHEGEEIVLARSLEPVPAVDTPPYRIGLTLAQAFA +DAAVGDRVSLDDGRIGARITAVSADEITLEVTQAGPRGAKLKAEKGVNFPDTHLAIPALT +DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR +MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT +GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS +L +>LFPAFLNI_01469 +MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS +DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP +ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA +GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPTRDPSGTVTEPSRVWLAAGPHDAVAAAD +RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA +TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA +DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT +DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR +MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT +GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS +L diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000905.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000905.fa new file mode 100644 index 0000000000000000000000000000000000000000..bddc22cba00f4cd0d68a4146fdd6998c8f77370c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000905.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01384 +MTDAAQHPAQHADQDRPQDPAATPEAGVDAEGAVSPQPLAQRVENRSQRPSSDAFRAFMG +ADWAPSSDELPAQDASAPHAARRRAAVSARYPGERIVVPAGRLKVRSNDTDYRFRAHSAF +AHLTGLGVDHEPDAVLVLEPTDPGAGDGGSDHAATLYFRPLAGRDTEQFYADARAGEFWI +GPRPTLAGLAARTGLRTAGLEELESAVTKNVCADGTAVRLLREADQDMDALLAGVRAEAG +MDAEAAASADAQVAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE +RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGTVREGDLLLLDAGVEDDSLY +TADITRTLPVSGSFTDVQRRIYQAVLDSADAAYAIVRPGIRFREIHAEAMRVLVERLADW +GLLPVSAEVALSEDGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP +GLYFKEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA +>MOLHKGIG_01541 +MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA +PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT +GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP +TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA +AAAEADAQTAEFLSELRLVKDAWEVDRMRASVAATIAGFEDVVRALPRAVGHDRGERVVE +GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI +TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP +VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF +KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA +>NAFOICDF_01275 +MTDASAQQNDDLAPEAAADSGAALSPQPLAERVENRSQKPTSDAFRAFMASQWAPASREL +PGPDASAPFAARRRAAVSAMFPGERIVVPAGRPKVRSNDTDYRFRAHSAFAHLTGLGVDH +EPDAVLVLEPTDAGAGDAGTDHAATLYFRPLAGRDTEQFYSDPRAGEFWIGPRPTLAELA +ARTGLRTAGLEELENAVTKDVAATAVRLLREADQDMDAVVAAARADAGVDAQAAGAADAA +LAEALSELRLVKDEWEVERMRASVASTIAGFEDVVRALPRAVGHARGERVVEGAFFARAR +EEGNDLGYDTIAASGNNATVLHWIRNTGRVREGELILVDAGVEDDSLYTADITRTLPVSG +TYSDVQRRVYQAVLDAADAAFALVKPGIRFREIHAEAMRVLAGRLHGWGLLPVSPEEALS +EAGQHHRRWMPHGTSHHLGLDVHDCAQARRELYLDAVLEPGMVFTIEPGLYFKAEDLAIP +EEYRGIGVRIEDDILVTEDGAENLSAALPRTPEDVEAWMARLQG +>MHAAABBN_01251 +MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA +PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT +GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP +TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA +AAAEADAQTAEFLSELRLVKDAWEIERMRASVAATIAGFEDVVRALPRAVGHDRGERVVE +GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI +TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP +VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF +KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAVLPRTPDEIEAWMARLQA +>LFPAFLNI_01468 +MMGGMTDAAQHPAQTAPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMA +SDWAPSSDALPDADASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAF +AHLTGLGVDHEPDAVLVLEPADPGTGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWI +GPRPTLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAG +VDLTAAAEADAQTAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE +RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLY +TADITRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGW +GLLPVSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP +GLYFKEEDLAVPEEYRGIGVRIEDDILVNEDGAENLSAALPRTPDEIEAWMARLQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000907.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000907.fa new file mode 100644 index 0000000000000000000000000000000000000000..08001515b463e63809b5453eb7f212847037f666 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000907.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01387 +MPHRAVALRGRPDPALIERLAALRTELELPAGFPPEVLEEADAAARDVLAALASDPAYAD +RTDVPFVTVDPAGSTDLDQALYLEAADGDAITVRYAIADVPAFVAPGGAVDVEARRRGQT +VYLPDGRVPLHPEALSEDAASLLPDRERPAFVWTFVLDAAGAVVDTSLERARIRSRAQLT +YAQVQAFLDALPDAKAPAAPRPGLDEADHAAHRGWDAPLRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVHVAEDGRHCLVQRAPLPAEDHNAQLSLMTGMAAARLMLEAGVGILRTM +PAPDAEAVAAFRSRTRALGAPWEEGQDYGAYLRTLDPADPGHLAVLHEATSLFRGAGYTA +FDAHAEDPELRTPPSEPEQAALAAPYAHATAPLRRLVDRFVLALCHAHATGAPAPEWARA +ALPEVPALMTESSRRTSAADRAATDLVEAAALQDHVCAELEGIAVRRVKGGAEVWLLDPA +VTLRVPGEAEPGTRVRVRIEGVDRASGEVTASGVDWPHSSR +>MOLHKGIG_01538 +MTPHALGLRGPADPTLLERLAALRTELELPPAFPAPVLAEAEAAAREVHAGLTGSPDHAD +RTALPFVTVDPAGSTDLDQALLLTPADDDGILVRYAIADVPAFVTPGGAVDGEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDREHPAFVWTFLLDAAGAVVETGLERARIRSRAQLT +YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS +ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR +>NAFOICDF_01278 +MPHHALEVRGGPDAALAARLRALRAELDVPGEFPADVLTEAERAAAEVPGRVAADPDRAD +LTAVPFVTVDPAGSTDLDQALHLQAGPGRDELTVRYAIADVPGFVAPEGAVDAEARRRGQ +TVYLPDGRVPLHPEVLSEDAASLLPEVERPTFVWTFVLDAEGAVASTDLVRARIRSRAQL +AYPQVQALLDDDAAPEAADWPAEVRASLALLPEVGARRTAQEAARGGASLSMPDQEISVV +DGAYTLVQRVPLAAEDHNAQLSLMTGMAAARIMLEAGVGILRTMPAPDPDAVDAFRARTR +ALGLPWGEELDYGAYLRTVDPTDPRGLAVMHAATTLFRGAGYTAFDRGSVDPALRALPED +PEQAALAAPYAHTTAPLRRLVDRFVLVLCHAHVAGEPVPDWVRRALPDLPALMAESGRRA +SAADRAATDLVEAALLAARVGSVLEGTAVRTSEKGTDVQLTDPAVSLRVPGRAEPGTVVR +VRVDAVDVAAGKVTASGVDWPHSAR +>MHAAABBN_01248 +MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD +RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARVRSRAQLT +YGQVQAFLDARPGAQAPATPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVLVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDADAVAAFRERTRALGVPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPAEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHASGAPAPAWVRS +ALPELPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWSHSSR +>LFPAFLNI_01465 +MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD +RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARIRSRAQLT +YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS +ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000910.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000910.fa new file mode 100644 index 0000000000000000000000000000000000000000..b6c8979dad6113189c146afb1981b4153ac09b75 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000910.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01390 +MADVVTVFSLVASHQHLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD +ESGVEAAREGLVAAVAAHSSLPDEAVRSAFRVLDSEATARHLFEVGAGLDSAVVGEREIA +GQVRRALSMARESGTASGSLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLTEELRG +LADDDAKAAFWADASVLLIGTGAYAGTTLAQLAERGATAVAVHSASGRAEQFVEDRGGWA +LALGGGAVAGAVAEADVIIGSSGGERQISPERLQELREDVDRPLTVVDLALSRDFDPAVG +DLPDVDLITLESVRLAAPEQARAAVAEARVLVDGAVAEYRAAQRGRSADASIKALRRHTL +AALDREMERVRARHGCTAAAEEVEFALRRMVNQLLHEPIVRAKRLAAEGRLDRYEDGLEA +VFGIEPPGSTSSPAERPDAGCPAHEDEAGTARIA +>MOLHKGIG_01535 +MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV +EAARAGLLSAVAASTSLPDEDVHAAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR +RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA +AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG +GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD +VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD +RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI +EAPGRPAPAVGTVEAVCPAHEDEGGAARIA +>NAFOICDF_01281 +MDVAVTVFSLVASHKDLSLDTVARLSAGSAGVGSALASSTDDGAVVLATCNRVEVYADAR +DADAARERIVAAIAEQSGLPEDAVRSAFRVLDDDASARHLFEVGAGLDSAVVGEREIAGQ +VRRALVDARDAGTATGSLTRLFESATRTAKDVGSHTALGATGRSVVSVALDLAEELRGLT +DAMARRTFWQEANVLLIGTGAYAGTTLAQLADRGAQAVGVHSASGRAAQFVADRGGWALA +LGGADVAGAVAEADVIIGSSGGDRQISPERMAGLRRGAERPVTVVDLALSRDFDPAVGEL +EGVDLITLESVRLAAPEQAQAAVAEARGLVETALEEYTSARRGRTADAAIKALRGHTMAA +LDREMERVRARHGCTAAADEVQFALRRMVNQLLHTPSVRARELAAQGRLDEFEHALEVLF +DIPVPGTRPADAPGDACPATEADDARRTA +>MHAAABBN_01245 +MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV +EAARAGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR +RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA +AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG +GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD +VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD +RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI +EAPGRPAPAVGTVEAACPAHEDDGGAARIA +>LFPAFLNI_01462 +MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAIVLATCNRVEIYAEADGAGV +EAARTGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR +RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA +AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG +GEAVAGAVAEADVIIGSSGGERQISPERLQELREGGRRPLTVVDLALSRDFDPAVADLPD +VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD +RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI +EAPGRPAPAVGTVEAACPAHEDDGGAARIA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000912.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000912.fa new file mode 100644 index 0000000000000000000000000000000000000000..a92d7948bfb6646f2f4a55d21d2754a7557eddb5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000912.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01392 +MTGTALVVGGGIAGLVAAHRLCAAGWEVTLAEATSVLGGAVSARFLDVPSHGETGAPESQ +TLELDAGAESFAVRGTAVRALLEELGLGGKVVAPEPLGSWLHGPAGPVPAPRLGLVSIPG +DLEAEDLAAALSGPGLARAREDAVAPMDRWADALAAGEPVTVAAIVADRLGEEVLKRLVA +PVVAGVHSADPAVVELERVAPGLLASAVEHGGLAAGVAALRGSSTPGSLVAGVDGGMSRV +TGRLVDALREAGATVLRGVRVAALSRVPAMGGWWAQISDRDDEVVRGLDVDRVVLAVDGA +TAWDLLAPLSGGDLDPDAGPALGDGVALTTLVVEAPGLDAAPRGTGMLVGAGTDVAAKAL +THATAKWAWLREVVARPDHDGVARHPHRHVVRLSYGRSGAEPGGLGHRSTDEELLARAVV +DAAALTGVPLSEQDVVARAVVRWRPSIPPQAGPDREAADALIAWSRGQAGLDLVGSWVHG +TGLAAVVASVDRAFDAPPPAG +>MOLHKGIG_01533 +MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ +TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG +DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA +PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL +TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV +TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL +THVTAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV +DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG +TGLAAVVAGVDRTLGADAPPAG +>NAFOICDF_01283 +MSGSALVVGGGIAGLLAARRLNQQGWEVTLAEATSVLGGTLSARFLDVPSVSDSGAVERQ +TLELDGGAESFAVRGAAVRALVDELGLGDDVVSPEPLGSWLHGPAGAVPAPRVGLVGIPG +DLDAPDVAAALSPAGLERARRDLTEPMDRWAAARAAGEPVTVAALVADRLGDDVLERLVV +PVVGGVHSADPAVVDVERVAPGLLAAAVEQGSLARGVAALRGGQTPGAAVAGVDGGMAKV +TGRLVQTLREDGVTVLRGVRVAALSRLGADGRWWAQISDRDEEVVRGLEADRVVLAVDGV +AAWELLAPVSGDAVDPDAGPALGEGVALATLVVEAPGMDAAPRGTGLLVAPGTDVRAKAL +THSTAKWAWLRSVVDRPDESGAPRHPHRHVLRLSYGRHGGAAGDLGFRSADEDLLAAAVA +DAEALTGVELSADDVLASTVTRWRRPIPPQHGPDREAMDRLIAWAQDVPGLDLVGSWVHG +TGLAAVVAGVERTVAPAAA +>MHAAABBN_01243 +MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ +TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG +DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA +PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL +TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV +TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL +THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV +DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG +TGLAAVVAGVDRTLGADAPPAG +>LFPAFLNI_01460 +MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ +TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG +DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA +PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL +TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV +TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL +THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV +DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG +TGLAAVVAGVDRTLGADAPPAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000913.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000913.fa new file mode 100644 index 0000000000000000000000000000000000000000..53d975a89f8968b3db1dcd322e04b4ffc3e8aef0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000913.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01393 +MTKDTATTPAEAGKDWFTTYTVFARPQGQPGWLGLEGRDAKKAVQEFDALVADLAKAGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRRLRRTRLLERTTMVLSAMGADRLAEFN +KDHIPAFAMGRKALPWLCFYPFVRSYDWYLMEPKERARMLREHGQLGQEFPQVWANTTSA +FGLNDWEWLLGLEAPELKDLVDMMRHLRNNETRLYVRAEVPFYTGRRVETADLLEVLA +>MOLHKGIG_01532 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA +>NAFOICDF_01284 +MSNTAAQPGQDWFTTYTVFARPQGEPGWLGLDGREAKKAVKEFDGVVKSLATRGVTVRGV +YDVSGMRAEGDVMVWMYAHAPEDLQAAIRDLRRTRLLDGTNMVLSAMGADRMAEFNKDHI +PAFAMGRKPLDWLCFYPFVRSYDWYTLDPKERARMLREHGKLGQDFPQVWANTTSAFALN +DWEWLLGLEAPKLNDLVDMMRHLRDNETRHYVREEVPFYTGRRLETSELPEVLA +>MHAAABBN_01242 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA +>LFPAFLNI_01459 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000915.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000915.fa new file mode 100644 index 0000000000000000000000000000000000000000..bf462f50aaa74a4e64cc2b823a8d134f5053cdca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000915.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01395 +MSTLRIGTRGSALATTQTTHVAQALAERAGLEHELVVIRTEGDVTTGSLASLGGTGVFAS +ALRAAILDGAVDLAVHSLKDLPAAQPDTLEIAAVPERADLRDALCARDGLTLATLPEGAR +VGTGSPRRVAQLKALRPDLVLVDIRGNVQTRLARVPGLEQHDDGAPAAAGSPRGDLDAVI +LACAGLDRLGLDHVITERIDPDVMVPAPGQGALAVEVRAEDESFLGAALLEPDAPVGRLR +AGLELVDDRATHVAVTAERALLRRLEAGCAAPIGAVARVVDGEAGAPRIEMTAMVAAVDG +SRVLRRTSSVQLDPVPEDLAADPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT +VRGVDRGDGAPQPDDPA +>MOLHKGIG_01530 +MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS +ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR +VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI +LACAGLNRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH +AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG +SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT +VRGVDRGDGAPRPDDPA +>NAFOICDF_01286 +MSGPGAPAGDGLRVGTRGSALATTQTTHVAEALTDRSGMPHELVVIRTEGDVTTGSLASL +GGTGVFASALRSAVLDGRVDLAVHSLKDLPAAQPAGLEIAAVPPRADLRDALCARDGLTL +ATLPEGARVGTGSPRRVAQLRALRPDLELVDIRGNVQTRLARVAGHEVHDDDAPAAAGAP +RGDLDAVVLACAGLDRLGLQHVITERIDPEVMLPAPGQGALAVEIREEDGPLLGPSAVDP +DSHAGRLRAALELVDDRDTHVAVTAERALLLRLEAGCAAPIGAVARVEEGTAVDGSPAPR +IVMSAMVAAVDGSQVLRRTSSVQLDAVPEDVAGDPAEADEWIEDTLFMAAGALGVHLAEL +FVAEGADLLPGTVRGVAKPDPEA +>MHAAABBN_01240 +MTPLRIGTRGSALATTQTTHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS +ALRAAVLDGVVDAAVHSLKDLPAVQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR +VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI +LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH +AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG +SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT +VRGVDRGDGAPRPDDPA +>LFPAFLNI_01457 +MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS +ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR +VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI +LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRMH +AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVSDGEAGAPRIEMTAMVAALDG +SRVLRRTSSVQLDPVPADVAGDPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT +VRGVDRGDGAPRPDDPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000917.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000917.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b2ebf3fa6ee07330e08715a645fa9becd5dc85f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000917.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01397 +MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASQLLSNTGFNNVAVAILREPRVDL +MASATGVPQDEKHDAGPAPTEDDATDPDGDRPD +>MOLHKGIG_01528 +MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI +MAAATGVPQDERHDAGPAPTEDDAPDPDGGRPD +>NAFOICDF_01288 +MPDSVRMANTLEFLRGVDRLHAFYTENVRMLAHAYDLSDEEASRLLAHTGFANVSVAILR +EPRVDLLAGLGASVEDEVHTHPVVDDASAPAEEPPASGGADDPEEPPAGSAPADPDDGAR +>MHAAABBN_01238 +MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI +MAAATGVPQDERHDAGPAPTEDDAPDPDGGRPD +>LFPAFLNI_01455 +MGNTLGFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI +MAAATGVPQDERHDAGPAPSEDDAPDPDGDRPD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000919.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000919.fa new file mode 100644 index 0000000000000000000000000000000000000000..4863af749c62e81a8be190e87c1b12e6888cc973 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000919.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01399 +MPPHLRPGQTLLLASLVFGLFFGAGNLIFPASLGRDAGAAVTPATLGFLVTAVGLPVLGI +VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGS +LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVTPMSTGALPSP +APAYADGALVRGLLDGYTTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA +AMAVVYASLAYIGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG +LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMLLYPIAVVVILL +GLAWAWVRDRPAVARWVVACTGLAAVFDLLGALPEALGTTALVTALTGLAGRVLPGYAVG +FGWVVPALVGLVVGAVAAASRPRPRRGEREATPIAAGHGRTAAD +>MOLHKGIG_01526 +MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI +VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG +LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALMAAAVVAPMSTGALPSP +TPAYADGALVRGLLDGYNTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA +AMAVVYASLAYVGATSHGAFAQAANGGDVLARSASHFFGAAGVYLIAAIVVVACLKTCIG +LIVACTEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL +GLAWAWVRDHPAVARWVVACTGLAAFFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG +FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD +>NAFOICDF_00047 +MSARLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGSAVVPATLGFLLTAVGLPVLGI +IASALTRSRSVREMTAPISPWFATAFTCLLYLAIGPLFAIPRTATVSYEIGVAPLAGDGP +WLPVFTLVFFGVAAVAAFRPGRLLDWVGRFLTPVFLLLLGALAVAAVVAPMSSGDLPAPA +GPYADGALTAGILDGYNTMDALASLAFAVLIVEAAGRLGVDSPRRLAVELGKAGIVGGLG +MAVVYGALAYIGATSHGALPGAASGGAVLAGTASHYFGPAGTWLIAAIVLAACLKTSIGL +IVACGEMFAEMFPGSYRVWASVFLLVSLVIANLGLEAIIAWSIPVLMFLYPLAIVIIALG +LGWGWVRHHLTVARAVVAFTAVAAVFDLLAALPETLAATGPVTALTDLAGRILPWYENGF +GWVVPALVGLVVGLVLEAARGRGRSAAVADA +>MHAAABBN_01235 +MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI +VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG +LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP +TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA +AMTVVYASLAYVGATSHGAFAQATNGGDVLARSASHFFGTAGAYLIAAIVFVACLKTCIG +LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL +GLAWAWVRDRPAVARWVVACTGLAAFFDLLGALPEALVTTPPVTALTGLAGRVLPGYAVG +FGWVVPALVGLVVGTLAAASRPRSRRGEREAIPVTAGHGRTAAD +>LFPAFLNI_01453 +MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI +VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG +LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP +TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA +AMAVVYASLAYVGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG +LIVACAEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL +GLAWAWVRGRPAVARWVVACTGLAASFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG +FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000920.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000920.fa new file mode 100644 index 0000000000000000000000000000000000000000..c663c6b806a46dd3dfc2b80cb1de666e62f3cf13 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000920.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01400 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAPEPIAIASMPGVVQHTSDT +LKAAAAEAAELGLGGIMLFGVPETRDAVGSISLDPEGVLNQAIRDVKSEVGDALVVMSDL +CLDEFTDHGHCGVLTEDGAVDNDATLEIYAQMGVAQAEAGADVLGPSGMMDGQVRVIREA +LDAAGHVDTGILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRTEALHEVALDLE +EGADMVMVKPAMSYLDIVRDVAELADVPVSAYQISGEYAMIEAAAANGWIDRKASIVESV +LSIRRAGADTVLTYWATELGRWMKEGSL +>MOLHKGIG_01525 +MSFPLHRPRRLRRSAAMRRLAAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGAVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>NAFOICDF_01299 +MSFPLNRPRRLRQSAAMRRLVAETRLHPNELILPAFIKEGAAEPVPIASMPGVVQHTTDT +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALREVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>MHAAABBN_01234 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>LFPAFLNI_01452 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRGVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000923.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000923.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b7fff7fc1f4549760a37f08c3967832e7ecc3f9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000923.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01403 +MTTPPADPRPVPDGPLTLGEGLEAVARLVPAGRAVSYGDLAGLLGVGGPRQAGRAMAKSA +PGTPWWRVVSADGSLPGELARRAAVEHAREGTPVRPGGRVDLPRARWEPDEAALGAVAAI +AARIVSGPGARMQA +>MOLHKGIG_01522 +MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE +SSPGTPWWRVVRADGSLPPELAARAAVEHEREAMPRTPAGRVDLPRARWEPDDGAARAIR +AIADRIVSGPGARMRP +>NAFOICDF_01302 +MSPVPSTPPDPDPHLPTDGPVTLGEALAAAARLIPSGRAASYGALAGLLGRGGPRQAGRA +MAESEPGTPWWRVVRADGSLPEPLRRQARERWAAEGTPVRGSGTVRDQRVDLAQAGWEPD +AAARAALADLAARVG +>MHAAABBN_01231 +MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGHAVSYGGLAGLLGVGGPRQAGRAMAE +SSPGTPWWRVVRADGSLPPELAARAAVEHEREATPRTPAGRVDLPRARWEPDDGAARAIR +AIADRIVSGPGARMRP +>LFPAFLNI_01449 +MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE +SSPGTPWWRVVRADGSLPPELAARAAVEHEREGTPRTPAGRVDLRRARWEPDDGAARAIR +AIADRIVSGPGARMGP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000927.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000927.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b44c69cb3fd2074a4d6abed4dad51fba0aac8ca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000927.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01407 +MPVPDPAAPAPEPRHDPAPAPAPAAPLALPLAREEVDRGAVARLDPGHLAAAWEREGTEV +LWLQGGRAPVADGRLRFTTPSGPVPPQAAYLGRGTAADLGPGGRERAVVAVALEPPAVLP +PDAAAALGDAAWVGLRDAAAALSDADAGLFVAAVANANWHAAHRFCSFCGGATAVEAAGW +VRRCEACGREHFPRTDPAVIVAVTDPDGRILLGRNAAWPAGRYSCLAGFVEPGESLEHAV +VREVAEESGVTVADPRYRGSQPWPFPRSLMLGFTAQAPAGAEPVADGTEILSVRWFEREE +LAALAREGEITLPGAVSIARALIEDWYGGTLPDAQTLIT +>MOLHKGIG_01518 +MASCPPSSSDPTVAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV +ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA +VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE +QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV +TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV +TLPGAVSIARALIEDWYGGTLPDAQTLIT +>NAFOICDF_01306 +MPVPSAPDAVPAALPHLTLAREALDRSGAEREDPGLLGRLAADPATGVLHLVGGRAPVRD +GALVLVPPAGPFPPEAVFLGRRLTDAAAPSAAGRPLVLVARESAPGSSGDGGPTRPAEPT +DAPTRDPLAGAAWLGLRDVAAGLSDADTGLFVEAVAIANWHAGHGFCSRCGGRTDTESAG +WVRRCRDCSARHFPRTDPAVIMAVMDDQDRILLGSNAAWPAGRHSCLAGFVEPGESLEHA +VAREVLEEAGIVVVDAAYRGSQPWPFPRSLMVGYRAHALPGQEPVADGHEIRSVRWFTRD +ELAAEVRAGAVTLPGAVSIARALIEDWYGGTLPDPTTLIS +>MHAAABBN_01227 +MASCPPSSSDPTAAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV +ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA +VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE +QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV +TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV +TLPGAVSIARALIEDWYGGTLPDAQTLIT +>LFPAFLNI_01445 +MASCPPSSSDLTAAPPLALPLAREELDRGAVARLDPGHLAAVWAREGTEVLWLQGGRAPV +ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA +VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE +QFPRTDPAVIVAVTDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGI +TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELAHLAREGDV +TLPGAVSIARALIEDWYGGTLPDAQTLIT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000930.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000930.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ed7e269cba328d837f510b8cfedaee1b12629a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000930.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_01410 +MADNGRMPPADAAVPVPAEHERGEPVPAAAAVSALARRPVRRGAVRQSTDLDWEGTPVRL +VRSTARTRTVSAAWREGRLQVNVPARLTPAHEREWIARMVEQVARRAGAGASPGRPGAGS +QPGSGPGAGSGGDEALMAWAQRLSAAHLGGRARPASVAWSARQRRRWGSCTPSRGTIRLS +DRLRGMPDWVVAAVLVHELAHLLESGHGPAFRRLVAAYPRYAEAMAFLDGVAFAESRGRT +AQDTWVDDEDAMDADAPDDGPTEDERA +>MOLHKGIG_01515 +MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD +GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR +GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR +WAEDEDAG +>NAFOICDF_01309 +MSPSRTVTDLDWHGTPVRLVRSARRTRTVAAVWREGRLQVSVPARLSRAEERRWIERMVD +RAGPAPAAHPAPSASAPSTGLGSAPDPRGDADLLARADALASAHLDGAAPGGRAPRPASV +TWSSRQRQRWGSCTPARGTIRLSAQLRGMPDWVVDAVLVHELAHLSERGHGPRFQALVGR +LPRYTEAMAFLAGVTYATSRGLPGAYPADADVADHARGWPGGDDDVVEG +>MHAAABBN_01224 +MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD +GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR +GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR +WAEDEDAG +>LFPAFLNI_01442 +MPDNGRMRPVPPAPGRPPRAVPAAHRGPARESTDLDWEGTPVRLVRSTARTRTVSAAWRD +GRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPDGRPADARSDDALLAWAGRL +SAAHLGGRARPVSVTWSARQRRRWGSCTPGRGTIRLSTQLRGMPDWVVAAVLVHELAHLL +ESGHGPAFRRLVDRYPRYAEAMAFLDGVTFAEGRGRTAPDRWAEDEDAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000931.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000931.fa new file mode 100644 index 0000000000000000000000000000000000000000..21830b41d8990e7f6350d77cf01959fee79fe388 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000931.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01412 +MRAVPPRTTRAYRLPASGWLALGSAGLALLLPTPYILESPGPAVDLLGERDGAEVLRVEG +GTPDEGEGTLDMTTVMVGGPPISTTSVIDLARSLVDPAVDVVPRELMYPTGMSSEEVGAA +NTAAMSDSQDTAAAAALHALGRPVPSTLVVHELVPGGPSEGVLRPGDEVIAAAGEPAEDL +EDLRAAVGAAGPDPVTLTVRRDGAVTELRVPVAAAPEGAPQPWQMGALIETVVDVPLDVE +LTVPDIGGPSAGLMFALTVLERLTPGAMTGGAPIAGTGTITPDGVVGPIGGIPQKVRGAA +QAGATTFLAPTANCGELDGRVPEGLQVYAVDTLAQAREIVEAVGRGEPPESARTCG +>MOLHKGIG_01513 +MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG +GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA +NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL +EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE +LTVPDIGGPSAGLMFALTVIERLTPGAMTGGASIAGTGTITGDGVVGPIGGIPQKVRGAA +EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG +>NAFOICDF_01311 +MPYILEGPGPAIDVLGEQDGTPVLTVEGGTADPGEGRLDMTTVLVSGPPGGTTGLGDLVT +ALADGTVDAQPRELVHPSGVSADTVAQSNAAAMTDSQDVATAAALRALGRDVPAHLAVHA +TVPGAPAEGILREGDVILAAAGRSVTDMAGIRAAVDAAGPGDLALTLRRDGTERQVSVPV +TAADPATGRSWQLGVLLEQRFDLPVQVEFALEDIGGPSAGMMFALAVIERLTPGDMTGGA +RIAGTGTITADGVVGPIGGIPQKMQGAARDGADVFLAPRENCADLAGRVPAGMTVYAVDT +LATARAVVEAVGRGERPDDVPTCS +>MHAAABBN_01222 +MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG +GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA +NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL +EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE +LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTITGDGVVGPIGGIPQKVRGAA +EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGETPAAARTCG +>LFPAFLNI_01440 +MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG +GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA +NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL +EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIESAYDVPVDVE +LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTISGDGVVGPIGGIPQKVRGAA +EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000932.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000932.fa new file mode 100644 index 0000000000000000000000000000000000000000..a7e94ba3466c76b0204bd88422718ad6ab965f8b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000932.fa @@ -0,0 +1,94 @@ +>ACLBLIBL_01413 +MSFGQGGGGPFGGPPRDGGGSAGGSSGPFGAFGPFGGAPQGPGGDGRDGGQGGGPFGPFG +GGAGGSSAADRPRSGRPGRPSALVLTVIAVAILVGLFVLFTNVYTEVLWFSQLGFTEVFW +TEVLAKAALFLLGALGMALAVWLAIRTAWRHRPSDASAAGRDSLSQAQRQLEPIRRLVFL +GVPVVLGLFAGSAAMNGWDTVLLFLNQVPYGQADPEFGLDMMFFMATLPFLSLVAGYLTS +VVLVAGIAGVLVHYLYGSVRVEEGGGIRVAPAARVHVGVVLALFLLLQAVNFWLNRYRTA +QSQSGSWAGALYTDVNAVIPTSAILAVTAVIVAGLFVWTVFSGKWRLSLIGTAVLVITAL +VVGTAYPFVVQEYQVKPSERTLEAEYISRNIELTREAYGLDAVEVTNYEGVTETEAGALA +GEEANTANVRLMDPNLISQTFGQLQQFRPYYAFPDTLHVDRYEVDGQTRDTILAARDVNV +DDTQSWVNRHTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDEDYEPRIYFGQ +NSPSYSVVGAPEGAPAVERDRPQTADSQDDTAYTFSGDGGPSVGGLFNRLAYAVKFGSPE +LVLSSDVNEASQILYDRDPADRVSKVAPYLTVDTSPYPAIVDGRVQWIVDAYTTSDQFPY +STAQQLGEVTVDSLSQGPNAALQGRVNYIRNSVKATVDAYDGSVTLYAWDDQDPLLQAWQ +KVYPSSLRPYSEMSAALMDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPT +RDGDVKQPPYYMTLQMPGQEEPAFSLTSNYIPQITQGSQQRNVLYGFLSAAGDAGTGEDG +VKAEDYGTLRLLELPRSTTVPGPGQAQANFDSNATVSRELNLLRQGASEVLNGNMITLPV +AGGVLYVQPVYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEG +QAGDPPQGEDGAAPAPGSVQEELSSALAEAQDALTRGQERLAEGDWAGYGEQQDRLNEAL +RRATAADDALDGDAPADGEAPAEGQPPAEGSEAPSPAPEG +>MOLHKGIG_01512 +MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS +AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVLAKAAL +FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF +AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLMVGYLISVVLVSGITG +LLVHYLYGAVRVEEGGSVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG +ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI +VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDPEAGALAGEEANTANV +RLMDPNLISQTFGQLQQFRPYYSFPTTLHVDRYEVDGQTRDTILAARDVNVDDMQSWVNR +HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGLNSPSYSVVG +APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE +ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV +TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP +YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP +YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL +RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP +VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEAPAPGE +EPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG +GDAPAQEQAPAEASPAPSSSPSPTPSG +>NAFOICDF_01312 +MSFGQEGAGPFGGPPHHDGDGGAHAARRVRAGGGRPSALLLTVIAVAALVALYMLFTQVY +TEVLWFDQLGFSEVFWTEVLTKAALFVVAGAVMALAVWLSLRTAWRHRPGTAGADGRDSL +SRARRQLEPMRRLVWAALPAVLGLFAGSAAMNGWKTVQLFLHQVPYGKADPEFGLDLMFY +LATLPFLTMAVGYLISVVLVAGLAGLAVHYLYGALGVGDDGRVHVSVPARVHLGVLAGLF +LLLQAATFWLNRYRTLQSQAGNWAGAMYTDVNAAIPTSAILAVTAALVAALFVWAAFTGR +FRLPLVGAAVLVITALVVGTAYPYVVQQYQVKPSERTLESPYIARNIEMTREAYGLDQVQ +VANYEGTTDAQAGDLKGEEANTANVRLMDPNLISQTFGQLQQFRPYYAFPGTLHVDRYEV +DGQTRDTILAARDVNVDPEQSWVNRHTIYTHGYGVVAADASAVGAGGRPQWMLSEIPSRG +VLGDDSTYEPRIYFGLNSPAYSVVGAPEGAPAVERDRPQTADSTDDTAYTFQGDGGPSVG +GLFNRLAYAVKFGSPELVLSSDVNEASQILYDRDPVDRVAKVAPYLTVDTAPYPAIVGGR +VKWIVDAYTTSDQFPYSTAQQLGEATQDSLSEGQAAALQGRVNYIRNSVKATVDAYDGSV +ELYAWDAEDPLLKSWQGVYPASLKPYSEMSAALLDHVRYPEDMFKVQRELLGRYHVTNPG +DFYENNDAWSVPSDPTTDKDVKQPPYYMSLRLPGQEETAFSLTSTYIPQITDNGQQRNVL +YGFLSADGDAGTGRDGERAPGYGTLRLLELPRSTTVPGPGQAQANFDSNAQVSQELNLLR +QGASEVLNGNMITLPVAGGILYVQPVYVRSSGGTTYPTLRKVLVSFGDKVGFADTLDEAL +NQVFGGDSGATTPDAGEPAQEPRGTAEEELSSALAEAQDALAEGQERLAQGDWAGYGEQQ +TRLNEALKRATAADDAAKGAQESADPAPEG +>MHAAABBN_01221 +MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS +AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVVAKAAL +FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF +AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLVVGYLISVVLVSGITG +LLVHYLYGAVRVEEGGGVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG +ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI +VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDTEAGALAGEEANTANV +RLMDPNLISQTFGQLQQFRPYYAFPTTLHVDRYEVDGQTRDTILAARDVNVDDSQSWVNR +HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGLNSPSYSVVG +APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE +ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV +TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP +YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP +YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL +RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP +VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEAPAPGE +EPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG +GDAPAQEQAPAEASPAPSSSPSPTPSG +>LFPAFLNI_01439 +MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS +AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVVAKAAL +FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF +AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLVVGYLISVVLVSGITG +LLVHYLYGAVRVEEGGGVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG +ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI +VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDTEAGALAGEEANTANV +RLMDPNLISQTFGQLQQFRPYYAFPTTLHVDRYEVDGQTRDTILAARDVNVDDSQSWVNR +HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGHNSPSYSVVG +APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE +ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV +TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP +YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP +YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL +RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP +VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEVPAPGE +KPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG +GDAPAQDQAPAEASPAPSSSPSPTPSG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000933.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000933.fa new file mode 100644 index 0000000000000000000000000000000000000000..88b5b15366b252744b71caaf236d0562c147f002 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000933.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_01415 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVIKPLQTLMIPASVIAGILGLVLGPNVLGWL +PFSTQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGSFASYGVLIYASQVAIGALVALL +VLQPLFSTPDSFAALLFAGWAGGFGSAAAVGQAYAANGDMTVTSLAYTSATVGMIVGVVG +GIIQAKIGARRGHAKEFAGLTSIPDELRTGVLDQVQERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVTWITAVWPNIVGEDGPKLIIPAFAVAFILGLIGRVVFQATKTAKFLDP +GSLNSVSGTATDILIVCGIASIAPTVVVDYWQPLLVLFVIGLALALFLGLVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +IAGLSWAVVGIWGAIAIAAILAAIWLRRTDPGVRSPAQQAVRAASR +>MOLHKGIG_01487 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLVLGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYASQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITSVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR +>NAFOICDF_01314 +MTWFQGVWPSIVGPEGPKLMIPAFAVAFVLGIIGRLLLQVTKTATFLDSASLNSVSGTAT +DILIVCGIASIAPKVVLDYWQPLLILFVVGLALAVLLGLVVAPHVMTESWFEKQLFTWGW +ATGAVATGVAMLRIVDPKLKSGTMEQFGVAYITVVPVEIAAVSFVPLLIIAGLSWAVVGI +WDAIAEAAIIAAVFLVRSDPARKSAVPA +>MHAAABBN_01219 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR +>LFPAFLNI_01437 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +IAGLSWAVVGIWGAIAIIAIIAAVWLRRTDPGRRTPAQQAVRASSR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000934.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000934.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7c93959d0048619e5322962d198901c9773ded2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000934.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01416 +MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI +EDDYREDQDAARSWGQKALAASQKADDFRTKGDAASAEKFDNLAKVAIERQMDSERQAKS +AEPTITSQREIVERLKTGLDQMKVKRQQLVSKRDELTARAKSAHAQSAVADAVKSIDLLD +PTSEVSRFEEKVRREEARVRGQQELAASSLDAQFESLEDLGEKTEVEARLAALKSGGAGQ +SALTAGGSEGSDLALDYGAETTAEQGAEQTRVERG +>MOLHKGIG_01486 +MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI +EDDYREDQDASRSWGQKALAASQKADDFRAKGDTASADKFDNLAKVAIERQMDFERQAKS +AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD +PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ +AALTSGDVDADETLTLDYAAEGTAEETGTARG +>NAFOICDF_01316 +MVKQSILGRITTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMM +EDDYREDQEAARSWGQKALAASQKADEFRTKGEAANADKFDNLAKVAIERQMDAERQAKT +AEPTITSQREIVDRLKTGLDQMKVKRQQLVSKRDELTARSRTAEAQTKVNEAVKSIDIMD +PTSEISRYEEKVRREEARVRGQQELAASSLDAQFESLEDLGEQTEVEARLAALKSGSAPS +ALTAGSEELTLDYSGAETGTQTGTAERA +>MHAAABBN_01218 +MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI +EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS +AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD +PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ +AALTSGDVDADETLTLDYAAEGTAEETGTARG +>LFPAFLNI_01436 +MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI +EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS +AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD +PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ +AALTSGDVDADETLTLDYAAEGTAEETGTARG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000937.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000937.fa new file mode 100644 index 0000000000000000000000000000000000000000..1778e3d9f3ef8cde31d43e595996549e1afc2ee1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000937.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_01419 +MTTPITPAALAAEHGWRTVLAVGAHPDDLDFGAAATLAGLSAAGLRVELCVVTDGDAGGF +DSEGPEAMTARRHAEQRAAAAVVGAHEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVV +LSTHPERDWELMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRHLLLYS +APAARRNTVVDVTGLEDVKLRALDAHISQHPDVAAMRRHVLAQMTEHHRRAAGPAAAPGL +AEAFHLVTVNGPGTISGF +>MOLHKGIG_01483 +MAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGGFDSEGAEAMTARRHAEQRAA +AAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVVLSTHPERDWERMQAAHPDH +LACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRNLLLYAAPAARRNTVVDVTGLAEQK +LRALDAHLSQHPDVDAMRRHVLAQMAEHHRHAAGPAAGPGHAEAFHLVTVNGPGTIAGF +>NAFOICDF_01319 +MSAVPESLPTPADLAVRHGWRTVLAFGAHPDDLDFDASATLAGLAAAGVRVELCVVTDGD +AGGFDSDGPEAMTARRHAEQRAAAAVIGAADVHFLGERDGHLEPTHEVRRRIVELMRRVR +PDVVLCPHPERDWESMQASHPDHLACGEAVVRAAYPAVENPYAYPELADAGLDAFRIRHL +MLYTAPAARRNLTVDVTGLEDVKLRALDAHVSQHPDAPAMREAVRAKLTRRHREAAGPDA +PAGSGEAYHLVTVNGDGVIAGF +>MHAAABBN_01215 +MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGG +FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV +VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKVRNLLLY +AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG +HAEAFHLVTVNGPGTIAGF +>LFPAFLNI_01433 +MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFRAAGLHIELCIVTDGDAGG +FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV +VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAAENPYAYPELAAEGLEAFKVRNLLLY +AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG +HAEAFHLVTVNGPSTIAGF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000939.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000939.fa new file mode 100644 index 0000000000000000000000000000000000000000..acb8f80581300ef58dd52e7f79586a4a1e6aa9b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000939.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_01421 +MEPLGFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGRVRHDRVDY +RPGDVLLFGRESTGLPEEVVADPRVAETVALPMQPSRRSLNLANAVSIAVYEAWRQHGFA +GAASETDSLD +>MOLHKGIG_01481 +MPDSPTPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL +GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD +VLLFGRESTGLPEEVLTDPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAA +RPDSLD +>NAFOICDF_01321 +MPQTPPDPSPAAPPPAARNPHLDAERAPAPGTPGFRILFHTPEIPGNTGNAIRLAAITGA +ELHLVEPLGFDFSDAHLRRAGLDYHDLAVMTVHPDLDTALAALAPARVFAFSARGRVRHD +RVAYEAGDVLLFGRESTGLPEDVLSDPRVTDTVSLPMQPSRRSLNLANAASIAVYEAWRQ +HGFAGAGSPAADSLH +>MHAAABBN_01213 +MPDSPAPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL +GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD +VLLFGRESTGLPEEVLADPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAV +RPDSLD +>LFPAFLNI_01431 +MPDSPTPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL +GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD +VLLFGRESTGLPEEVLTDPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAA +RPDSLD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000940.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000940.fa new file mode 100644 index 0000000000000000000000000000000000000000..f8a48f0bdc5a546a3cf5b61f2b03abfed7ece670 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000940.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01422 +MSAADEHCTAYEVLGVDRDADDAAVRRAYRAAARRTHPDAGGDPAEFRAVSRAWQVLGDA +DARRRYDLSLPAPGAGRAPASGGAARPGRAAASRPARGAAGRPARTVRYEPPPGEGESDA +AVLDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLAGR +WGRPLDVDHAVLCGHRLALVGSVMVPEGAYTWDGSDLRSRGRPVAPPLLGPAMMAWQQVL +PQVTVGGFVHVMTDRDALHGPVVRHARGADDPGARADLLTVPPAPGREFVRDLLLFLGTG +EDPDLVDRRVLGTLVERLH +>MOLHKGIG_01480 +MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA +EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV +LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG +RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ +VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD +PDLVDRRALGALVGRLH +>NAFOICDF_01322 +MSGTGDRRTAYEVLGVPRDADAERIRRAWRAAARRTHPDAGGDARDFRAVTRAWEQLGDP +EARRRYDLSLPPEPAGTTGRTASAGRSAAQAWPPAGVRERDRPAPGSVVYDPPPGQGEHD +SSVLDLVRSSQRLHGAPRPRGILPDEHRVVRQARTLDLLARTLPPVLPAVRILTGLHLGG +RFGRGLDVDHAVLCGRRLALVGSVQVPDGTYTWDGADLRAGARGRPVAPPLLGPAMQAWQ +HALPQVTVGGFVLVMTDRDAVHSPVIRQARGADRPEAQADLLTAAPAAGRDLLRELQLFL +GSGPDPDVVDRRALAVLVRHLH +>MHAAABBN_01212 +MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA +EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV +LDLPRSSQRVHGAPRPRGILPDERRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG +RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ +VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD +PDLVDRRALGALVDRLH +>LFPAFLNI_01430 +MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA +EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV +LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG +RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRSRPVAPPLLGPAMMAWQQALPQ +VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD +PDLVDRRALGALVDRLH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000942.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000942.fa new file mode 100644 index 0000000000000000000000000000000000000000..e80ae4545725fb9cdcb7982a58edbc03d86ddbb1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000942.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01424 +MRQNVAMALTELALRHPVRRFARREVDFRRRILTMAVVNRTPDSFYDDGAAFALEAAVDQ +ARAAAEAGAEWVDVGGVPFAPGPALDPGEEARRVVPLIAALRGEAAEHSEAVAGLILSAD +TFEPAVAEAAIAAGADVVNDTSGLVHADLGRVVAASQAHLVLTHSLAHVHGPRAVVPRPR +YGDVVAEVREHLLRTVERAVALGVPEERIIVDPGHDLNKNTLHTLEITRRLDEIAGLGLP +VLAAVSNKDFIGESLDQHRHERLAGSLAAAVACVHGGARILRMHDAAASVSAARLLECVF +GWREPARLVHNMGEANPAPDRTSLAEHRAGRVRAGGTR +>MOLHKGIG_01478 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA +>NAFOICDF_01324 +MPTPSVPLAHPVHRFAHHEIDFRRRIVTMAVVNRTPDSFFDDGAGFAFDAALAQVHTAAD +AGAEWVDVGGVPFAPGRELDPAEEAARVAPFVAAVRAGRGEGASEAARRLILSADTFQPA +VAEAAIDAGADVVNDTTGLYYPDLGRVVAASNAHLVVTHSLAHVSGPRTVVPRPRYDDVV +AEVREHLLRTVDRAVALGVPEERIIVDPGHDLNKTTVHTLEVTRRLDEIADLGFPVLAAV +SNKDFIGESLDRHRHDRLAGTLASAAFCALAGARILRMHDADASVSTAHMLECILGWREP +LLAVHNTGDVNPAADRTTPADRVPADRPPAAVPAPTHDPEEARP +>MHAAABBN_01210 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA +>LFPAFLNI_01428 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000943.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000943.fa new file mode 100644 index 0000000000000000000000000000000000000000..83b6b7a5f1cfe7ceb4732c0b49610250fb7584b3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000943.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_01425 +MPSAATPRPLGERVHLDHAATTAVRPSALAALAEAAALPGNPASLHASGRRAKLALEQAR +EAVAAALGAHPSEVVLTSGGTEADNLAVQGLFRARRAADPQRLRIVLTGAEHHAVLDAVD +WLAAHEGAEPVIVPVDADGVVDLAAWEAALAAAPERTALAALMWANNEIGTVQPVAEAAR +IAAAHGVPLHTDAVQAVGAVPVDFAASGAATLAVSGHKAGAPVGVGALLVRRDVALTPVV +HGGGQERRLRSGTVSVALAAALAAALTEAVAEQPAEAVRLGVLRDRVIEAVEALETVVLT +GPRDADPATGEPLPPGTRRLPGNVHVTVPGRTADALLFTFDTAGLDTSSGSACTAGVAEP +SHVVAALPGRTEADARATQRFTLGRTSTSADVDALIAALRALAPAPRRGAPTPKGAPTTK +EESR +>MOLHKGIG_01475 +MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLRLEEARERIAAAL +GAHPTEVILTSGGTEADNLAIQGLYRARRAAAPERTRIVLTGIEHHAVLDVVDWLAAHEG +AEPVLVPVDDDGRVDLAAWGAALATAPERTALATLMWANNEIGTVQPVAEAARLAADHGV +PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER +RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP +ATGQALSPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL +PGRTEADARATQRFTLGRTTTPAEAAALIDALRTLLGPGV +>NAFOICDF_01327 +MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL +GAHPTEVILTSGGTEADNLAVQGLYRARRAAAPERTRIVLTGIEHHAVLDVVGWLAAHEG +AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGV +PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER +RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP +ATGEPLPPGTRRLPGNVHITVPGRTADALLFFFDMAGLDTSSGSACTAGVAEPSHVVAAL +PGRTEADARATQRFTLGRTTTPAEAAALIDGLRTLLGPASRLDRPSVVERGVRP +>MHAAABBN_01207 +MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL +GAHPPEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG +AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI +PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER +RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP +ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL +PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV +>LFPAFLNI_01425 +MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL +GAHPSEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG +AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI +PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER +RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP +ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL +PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000946.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000946.fa new file mode 100644 index 0000000000000000000000000000000000000000..1321bc1b4335a52b27e6ed9f94cfeda18c627859 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000946.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01428 +MPEAHDDGARPVALGGSPWAGTDAAEAQRVTLGELGAEHWPVLPELPSRGPGADATGRSA +ALLSELAVDLQPHGWRVSPPGAAGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLAVR +VRGPLSLLGGLWLPGGERVLADHGARRDVAASYLEGLLEAVPRLRAATGAAGLGLLVDEP +WAAAVLAGALPTASGYRTVRSLPRDEARGLWRELLAGLTALPGVASVWLAPGRRTASAAD +VPATAELAALAGECLPAAGGEDDDAGAPVRLVVPVGDLDDGPDGTAGTRAAWESAAGWAD +AGRGLTLSPAAHLRPADVVTTWERLGADPAHLRGTGLTAPGRHDATVLRRLRTDAAELAA +RLDDALG +>MOLHKGIG_01472 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR +SAALLQQLAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA +VRVRGPLSLLACLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD +EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP +GAELPGPAALSTLTGESLPRPDAAADAPAPAPVSLVVGVGALDDGADGTPGTREAWEAAA +GWADIGRGLTLAPEPGVRPVEVVRTWERLGVDPGRVGDVGLTAAGLHDPVVLHTLRRDAE +ELTARLAELRG +>NAFOICDF_01330 +MPEASDDVGAVRVAALGGAPWRGTDAAEAQLATLGELGAEHWPVLPELPDRGPGADATGR +SAALLHELAVDLQPHGWRVSPPGVVGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLG +VRLRGPLSLLGSLWLPGGERVLVDHGARRDVAASYVEGLRDAVPRLAAATGARTLGVVLD +EPWAAAVLAGALPTASGYRTVRSVPRDEVRALWRDALAALADLPGVGRVWLAPGRRSAGV +DVPLPDVSALAALAGESLPAAAPSADDDAPAPTRVDLVVPVGALDPGPDGTGGTRAGWET +AAGWTDAGRGLTLSTATGVRPADVARTWERLGADPGHLAGVGLTVPGPHDAAVLGRLRAD +AEELAARVGELLG +>MHAAABBN_01204 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR +SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWHEDAHRWADTAGAEGAVVERLA +VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD +EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP +GAELPGPAALATLTGESLPRPDAAADAPVPAPVSLVVGVGALDDGADGTPGTREAWEAAA +GWADIGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGSHDPAVLRTLRRDAE +ELTARLAELRG +>LFPAFLNI_01422 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPERGPGADATGR +SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA +VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAARLGVVVD +EPWAGAVLAGTLPTASGYRTVRSLPREEARGLWRAALARLTALPDVARVWLAPGRRAASP +GAELPGPAALATLTGESLPRPDAAADAPARAPVSLVVGVGPLDDGADGSPGTREAWEAAA +GWADVGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGPHDPAVLRTLRRDAE +ELAARLAELRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000947.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000947.fa new file mode 100644 index 0000000000000000000000000000000000000000..551887e16f21bbc12dd66e2fa6c3533a76c4e752 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000947.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01429 +MSRAKILVVDDDEALAEMIGIVLRNDGFEAAFAADGTAALPAFHRERPDLVLLDLMLPGM +DGIEVCKLLRSESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEAKPAEVLQIGDLEIDVAGHQVTRDGAAISLTPLEFDLLVALARRPRQVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG +>MOLHKGIG_01471 +MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI +DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG +>NAFOICDF_01331 +MSKARILVVDDDEALAEMIGIVLRNDDFEPSFAVDGTSALPAFRSARPDLVLLDLMLPGI +DGIEVCKQIRAESDVPIIMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEQRPAEALAIGDVRIDVAGHQVSRGGAPISLTPLEFDLLVALARKPRQVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRAKVEPDPENPTVVLTVRGVGYKAGQV +>MHAAABBN_01203 +MGKAKILVVDDDEALAEMIGIVLRNDGFEPTFAADGTSALPAFHRERPDLVLLDLMLPGI +DGIEVCKLIRAESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEAKPAEVLHIGDLEIDVAGHQVTRAGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG +>LFPAFLNI_01421 +MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI +DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000948.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000948.fa new file mode 100644 index 0000000000000000000000000000000000000000..369e77178094f0c3283bee61bed638e31fd38b71 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000948.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01431 +MSPTRPTGPRRARRLAGVGLAAALALALGGCTQIPQSSDVRSAEPLDGATAAPEAPQFRP +PGPSADDTAEDVIRGFLLAGTSPQDDYAVAREFLDGPAAARWAPGQRTLVYSAQPRITRG +EGTGNYQVQVEVDSEIDEFGLRTIAPEGTTRAWQVSVQERPEGMRITATENGTLLSQSQF +GQLFAPHELAFYDTAQRYAVPDVRWFVNRGTTVTAVTRALLRGPAPYLTGAVETAFPLRT +GADLAGPTVPVDEDGVAHVDLTEAAAEGADADRRHRMREQLEITLLGLQSVSDVRVTVDG +AELSASGENPPPPVQDEPTTGSVQVGIDSATGDLAYFQGMSVGPVGGAPDVSALDPVDPT +MSRDRSRFAFVTRDRTAVHVAGTDGSLREAMRGTGLTSPSIDGLGWVWAADGAETSRVRA +VPAEPGQEARIVTATWLRPAERIVDLRVSRSGARAALLVDDGDRRTVRVAGIVRGSDGVP +SALTEPILLPSTGRAASVEWAGDTNLLVSPRAATPDERVVPRIVSIDGTVRELNPLGGLT +GVSAGDGGALYAETDELVFLLVGSSWRAQELERGVRDLSFPG +>MOLHKGIG_01469 +MTTVDPQPPRPPRVAVVAVIVALVLALSGCTQIPQSSEVRSADPVDGASAAADAPQFHPP +GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD +GDGDYQIQVEVDSEIDEYGLRTVAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG +QLFAPHELAFYDTAKRYIVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVETAFPLRTG +TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA +QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM +SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV +SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN +ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG +ISAGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD +>NAFOICDF_01333 +MRPSGPARPRRRLCAAALAGALALAGCAQIPQSSPVRSGAPLDVGSRAADAPQFRPPGPA +EDATAEQLVRGFAQAGIAPEDGYAIARQYLSAEASDGWEPDRGVVVYSGEPTVTRGLGEG +TYEVQLEVESEVDEFGQRTMAPPNTTQAREVTVEEVDGVLRITGVQDGVLLSRSQFAQLY +APHPLYFFDQSQAFAVPDVRWFVNRGTAVTALTRALLRGPAPYLTGAVATAFPLRTGADL +TGPSVPVAEDGTAAVDLTGATVDGADPARLSRMREQLERTLTGVSGVERVEVTVEGRSLT +SSAPSGSVPSARIGEDPGTVQVGVSDAGELVFFQGLDAVPVGGLPSVADLGPEDPAMDRE +RRRFVFLDRTRTVLHGVGTDGGEHRLLDGGRLTAPSLDSSGWAWTVDRARSSRISVVRAD +GSEPARVVTTPWLAEGESIVALHIGPAGARAALIVDDGQQRTLRVAGVVRGGDGVPTALT +PPVYIPTLDPPDDVEWMGDGSLVSTPLAPDAETRVRPEVVSLDGTSRQLNPLAGLTGISA +REEGTLYAETAEDVFLLVGSSWRAQDVATPVHDLAFPD +>MHAAABBN_01201 +MTTVDPQSPRPPRLAVVGVIVALMLALSGCTQIPQSSEVRSADPVDGATADADAPQFHPP +GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD +GAGDYQIQVEVDSEIDEYGLRTIAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG +QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG +TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA +QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM +SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV +SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN +ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAAKPDERVVPRIVSVDGTVRELNPLGGLRG +ISAGDDGAYYAETEEFVFLLVGSSWRAQELDRGVRDLSFPD +>LFPAFLNI_01419 +MTTVDPQPPRPLRVAVFAVIVALVLALSGCTQIPQSSEVRSADPVDGATAAADAPQFHPP +GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD +GAGDYQIQVEVDSEIDEYGLRTVAPPGTTQAWAVTVQERPQGMRITSTENGTLLSQAQFG +QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG +TDLAAPTVPVDDDGVAHVDLTQAAAEGADADRRHRMREQLELTLTGLQSVKEVEVTVAGA +QLSTSGDDGPAPVQTDPAVGSVQVGIDTATGGLVYVQGTSVTPVGGAPDVTALDPVRPTM +SGDRSRFVFVTRDRTAVHVAGTDGTLREVLRGTGLTVPSLDLLGWVWAADRETTSRIRAV +PAQPGGQERIVTATWLRPGERIVDLRLSRSGAQAAMLVDDGQRTTLRVSGVVRGSDGVPN +ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG +ISVGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000949.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000949.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e690bbc97096285e57efe0b641117439963dd60 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000949.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01432 +MPHAPAPEPLLESDSGLPAARRAIAALAALGEAFVDLVLPAECAVCAAPGHRLCAPCRLE +LNAALARPFRAEHGAAALPLGPGGVPLPVVAAGRYADALAAAVLAFKDHHGLHLRAVLGE +ALCRSAAVARLAPDVPEAAHALLVPVPGGAAGFRRRGYDPLAELVRALPAPWVVSDAVRA +PRGPGRARRAGPSHAGAGSAQRRRRARRWRPVPGRLPAGAPVLLVDDVLTTGATLGALAE +AVRRAGGRPVGAVVLAAVAPPADDPGPVTGAGVG +>MOLHKGIG_01468 +MRSPPSSPSPPSVFGTLGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQ +DAPALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEP +DLPGARHALLVPVPGGAVGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGG +PSHAGAGAGQRRRRARDWRVAAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVG +AVVLAAVAPPRDPAEPGPRPGPRVG +>NAFOICDF_01334 +MHPLLESVVDLVLPADCAVCGAPGHRLCPDCRCLLGRELSAPHRAEEPALALPLGPDGAP +LPVWAAGDYRDGLAAALLAFKDHHGFGLRPILGDALARTVAAARLDPGLQEAAHALLVPV +PGSASGFRRRGYDPLAELVRSLPAPWVRDDVVRAAPAWSAWPPGGGPSHGGAGSRERRSR +RRGWRVREGALRPGTPVLLVDDVLTTGATLAALHRAVRRAGGRPVGGVVVAAVAPPTGDG +GAGVGGAGSTLAGAEPGE +>MHAAABBN_01200 +MRSPPSSPSPAFGALGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQDA +PALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEPDL +PGARHALLVPVPGGAVGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGGPS +HAGAGAGQRRRRARDWRVAAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVGAV +VLAAVAPPRDPAEPGPRPGPRVG +>LFPAFLNI_01418 +MRSPPSSPSPPSVFGTLGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQ +DAPALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEP +DLPGAPHALLVPVPGGAAGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGG +PSHAGAGAGQRRRRARDWRVVAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVG +AVVLAAVAPPRDPAEPGPRPRPRVG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000951.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000951.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f920c86fc9cb7bf7d2e1f3b93827aab14dd3a8b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000951.fa @@ -0,0 +1,85 @@ +>ACLBLIBL_01434 +MPSIIDRVLKISDNRVLRRMQGTVDAVNLLEEDFRALSDAELRAETDTLKARHADGESLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL +TGRGVHVITVNDFLASYQAELMGRVFRFLGMETGVVVAGQLPAVRREQYAADITYGTNNE +FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEEGSDYEVDHKKRTVGVLGPGIEKVEDHLGIANLYETQNTTLIQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYDKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV +VEDIAERHERRQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPQVLAEAEAAVED +ANREVLEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA +QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYADR +RSILEGEDLKDRVRRFVEDAVGNIVDATTEEGHAADWDLDQLWRDLSELYPVGITQEDVL +EEVGGRGRLKAEDLRRELVSDALLAYEDREAQVGSEALREAERRVVLSAIGRRWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAGIREDSVSTLFKAQITAAPAPTSLP +GIKDARGLTMTPQISVEGVEAPQRPSQLRFTGPSEDGQGAVTRAGTETGATVEAGTNRRS +RREAERRERRS +>MOLHKGIG_01466 +MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL +SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE +FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV +VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAQAEAAVED +AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA +QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYTDR +RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL +DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPASTSLP +GVQDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS +RRQAERRGRRG +>NAFOICDF_01337 +MPSIIDRVLKISDNRVLKRMRGTVDAVNLLEDDFRALSDAELRAETDSFKKRLADGETLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGLALHQGNIAEMKTGEGKTLVATAPAYLNAL +TGKGVHVVTVNDFLASYQADLMGRVYRFLGMETGVIVSGQDPATRRAQYAADITYGTNNE +FGFDFLRDNMAWSKEELVQRGHHFAIVDEVDSILIDEARTPLIISGPAQGDISRWYGEFA +RLVRSLERGTDYEVDEKKRTVGVLEPGIEKVEDHLGIANLYESQNTTLVQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLAGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYEKLSGMTGTAETEAAEFTSTYGLGVVVIPPNREKQRVDRNDLVYKNEKVKFDAV +VKDIAERHATGQPVLVGTTSVEKSEYLSTLLTKAGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLEQAEAAVQD +AREKVREAGGLYVLGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDDLMRNFNPGAA +QRIMNSASIPDDMALEFKMVSSAIQNAQSQVEGRNAEQRKNVLKYDDVMNRQREAIYADR +RAILEGDSLGERVRGFVEDAVGAVVDAATEEGAPVDWDLEKLWETLREVYPVGISPEDVL +EQVGGRGRLKAADLKRELVSDALLAYDDREAQVGSEALREAERRVVLAMIGRHWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGFTMFQAMLAAIKEDSARTLFHAQIAAAPAPTQLP +GVKDARAMTMVPQISVEGVETPRQPARLHLSGPSEDGEGVEEKDLAADGAQTPAGANRAS +RRAEARRRRRGED +>MHAAABBN_01198 +MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL +SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE +FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEANTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNREPQRVDRNDVVYKNEKVKFDAV +VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED +AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA +QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVLNRQREAIYTDR +RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGQATDWDLDQLWRDLAEIYPVGVSQEDVL +DEVGGRGRLTAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRHWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP +GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS +RRQAERRGRRG +>LFPAFLNI_01416 +MPSIIDRVLKISDHRVLKRMQATVDAVNLLEDDFRALSDAELRAETDALRARHADGESLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL +SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE +FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV +VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED +AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA +QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLQYDDVMNRQREAIYTDR +RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL +DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP +GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS +RRQAERRGRRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000952.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000952.fa new file mode 100644 index 0000000000000000000000000000000000000000..657c586c9af44e7d55fac0f34fb6d7be055806da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000952.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01435 +MIAVACVEVETGRRALRDLSAWLSPEVLDKMTRRMDLLGLAEQDRPRARSAAAGVSRAPA +AAPRPVGARVCEVAPGRVEASATVLCDGRARAFALRLERRISRWKVTSVEIG +>MOLHKGIG_01465 +MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI +AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPKSA +PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG +>NAFOICDF_01338 +MTHSVRADRTMIRTSADRPAHRPAQEDPMTTLAPALAHGPTRPRPVSRTAPSRRDTESAL +LRGPARRMSAVPTGEDLVRRAEQEDDREELRRLRSLAAVVAVACVETEAGRRPVRDLAGW +LAPETYEKMCRRVDLLERTGTRPPSGSAPRPVGARVCAVRPGAVEASATVLVAGRARAVA +LRIERRLSRWKVTHLEIG +>MHAAABBN_01197 +MTALATRPRTASARRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI +AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA +PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG +>LFPAFLNI_01415 +MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI +AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA +PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000954.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000954.fa new file mode 100644 index 0000000000000000000000000000000000000000..27ba347bb07ddfa7b33e83093ef0cd09be6ca69e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000954.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01437 +MRWDGLFDDLEARWADLGWRQSEAEAAELTRAEWMALTLADRLRGERGRPVRLHLAWGEA +LDGVLHAVGEDWAGLHLSGGRSAVVPLPGVAAVEAGLHRAVPAPTGPATGLGAVLRGIAR +ERVPVVVTGTRGVTLVEGTVDRVGRDHLDVSRHPRDEARRAAAVRGRLVVPFTALGVVRT +ASRLA +>MOLHKGIG_01463 +MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV +VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAVAAPELAAAGWGTVLRGIAR +TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT +ALRPA +>NAFOICDF_01340 +MRWDGLFEDLEARWSALEWDATRAEAAELTRGEWAALTLEERLRGARGETVRLHLVWGEH +RDVRLGTVGDGWVSVNAAAADSLLVPLTSVVAWEGPLGAASTAPEGVRSRPGLPAALRQL +ARARAAVRVVAGNGVELGEGTIDRVGRDHVDLARHPRDEARRAGQVRGRLVVPLAALGLV +ATPGPLG +>MHAAABBN_01195 +MRWNGLFDDLEAHWVDLGWQETVAEAAELTRAEWMALSLVDRLRGARGRQVRLHLAWGEV +VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR +TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPLDEARRAAAVRGRLVIPFGALGTVRT +ALRPA +>LFPAFLNI_01413 +MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV +VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR +TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT +ALRPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000955.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000955.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c0c2943a613b8f758e29f630f1dd9e13881b35c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000955.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01438 +MQRFLTLTDVAETLNISGQAARALIRSGELQAIQVGGRGQWRIEESWLQEYVDRQREATR +ARVQEWAEADAKSR +>MOLHKGIG_01462 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTEADAKAR +>NAFOICDF_01341 +MPQFLTLTDVAEVLNVSVGQARTLVRTGQLQAIQVGGRGQWRIEAGWLDEYVERQRELTR +SRVAERTREDAGHGA +>MHAAABBN_01194 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTETDAQAR +>LFPAFLNI_01412 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTETDAKAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000956.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000956.fa new file mode 100644 index 0000000000000000000000000000000000000000..48eb42ff50c83c51c0f6662e4175d732bd5f635e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000956.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01439 +MSTSTSASAEGGRLRRPRWRDPRLLVGLVLVLASVAGVVALVASSQRTSAYWAAAVDLPP +GTPLEAGQLRAVEVNLADAEGKYVAAAPDSAPSGRMVASTVRAGELLPAAALVDADPEGR +RPVGVRLREPLAGGVGVGDRVDVWVAMPAEGGRGHADPERLAEALEIAEVATEQGSIGGS +GETRVQLLAPEATLPRVVDAQVKDARITLVPAHGVR +>MOLHKGIG_01461 +MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQQTAAYWTAAEDLPPGTPI +ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV +ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVAAEQNGFGGSGTTRV +QLLAPEETLPRIVDAKVKDARVTLVPAHGVR +>NAFOICDF_01342 +MTTDPTAPAEGARLRRPRWRDPRLLVGLVLVLASLAGVTAIVAGAQRTQTYWAAARDLAP +GAPVPADAFVPVDANLADAAGHYLRADAPAPAGKVVGAVVRAGELVPADALADVDPQRRR +PVGVQLAEPLPAGTSAGDRVDVWVAARQDDGRDYEAPRRIAEGLEISELTEAEGGFGTGA +TTRLQLMAGEDVLAQLLDAKVSEARITVVPALGEG +>MHAAABBN_01193 +MSASAEGGRLRRPRWRDPRLLVGLMLVLASIAGVVALVASSQRTAAYWTAAEDLPPGTPI +AAGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV +ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQSGFGGSGTTRV +QLLAPEETLPRIVDAKVKDARVTLVPAHGVR +>LFPAFLNI_01411 +MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQRTAAYWTAAEDLPPGTPI +ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV +ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQNGFGGSGTTRV +QLLAPEETLPRIVDAKVKDARVTLVPAHGVR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000957.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000957.fa new file mode 100644 index 0000000000000000000000000000000000000000..7fc056379d634e7fc6016d81468188342c96746f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000957.fa @@ -0,0 +1,51 @@ +>ACLBLIBL_01440 +MTVRIALATTVLPGLDHIGPLERHQTRITVVRRAEDLAELLAIARSGLVDAVLVAGATEA +VTGAFLEELARLPRPVGAAAISEVRAERRRLRALGVPCVRADAGPEPLAAAVVEAALAAA +DGRRARADAVAEDEGGEDPVDGLDGIELTYGVLDDDPRLGPPLLGGDPERSAVSAARPEA +GAGDEAVDDGRRGGRAGDDLVPADAAQGGVTRDGVAQDRAQDGFARDDAQDFAAWDADAA +GRSVPDVDRPDPRDPDGDAAEHAEDRPDVEASGTPGDARVIVVWGPTGAPGRTTVAVNLA +AEHAVAGRSTLLVDLDTYGPSVGAHLGLTEESAGVARAVRRADHGPLGPADLEAAGVRVR +VAGAELTVLTGLTRVDRWPELRPSALTSLLAAARGRWERVVVDVGFGLEQDEELSFDVPA +PQRNGATLAALAAADEVLAVGGPDAVSLPRLVRGTEELVEAAPEARLRVVVNRLRPAAAG +VSPRSQVEAVWSRYASAGIPLAAFLPWDPAAADRALLGGQVLAEAAPNSALRRALAELAD +VDPRGARRTGRRRRPTGQGPAGAARRHPQDEGAARPSRRRTLMPWSARSRRTP +>MOLHKGIG_01460 +MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDLAELLAIARSGLVDAVLVAGDTESLT +AAFLEETARLPRPVGVAALSEVRTERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG +RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRGADEPDDAGPGAAPAA +ATPDGGPATADEGADPAPSPEEGEPAGPARESLVTVVWGPTGAPGRTTVAVNLAAEHAVA +GRNTLLIDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL +TVLTGLTRVDRWPELRPAAVSALIAAARERWDRVVVDVGFGLEQDEELSFDVPAPQRNGA +TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEVAPAARLRVVVNRLRPAAAGVAPRGQ +VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA +RRGRHRARPSQTIAAVSSDAARDATDTGRPARRRTLIPWSVRSRRTP +>NAFOICDF_01343 +MRVALATTLMPGRDHVGPLEQAQAEVTVVRRAEDLAELLAAARSGLVDAVLVAGDLSALA +RGFVDEVREAPRPVAVVAMGEVRAERERVRTLGVPCLSADADPLALAAAVQSAVRARLTG +ARPELGSETPPADPPAPAPGTPDGGDPEAVRVAAVRDREGTPRLPEPNPVRVDALAASEV +DALFTEETSPVAAADEAGPASPDAAGPDAVTASPADTAPEDGPEGGPERGRTGRTVAVWG +PTGAPGRTTVAVNLAAESAVAGLRTLLVDLDTYGPSVGVHLGLTEETAGLARAVHRAERG +SVTREDLVDAAVRVRVAGGDLDVLTGLTRPDRWPEVRPGALREVLQAARDGWDRVVLDLG +FCVEEDEELSFDVPAPQRNGATLAGLAAADRVLVVGGADAVAMPRLLRAVEALPAGVEQD +RVRVVVNRVRPQASGVAPQAQVAGVWERYGPPIPLVAQLPWDPGAADRALLGGQVLAEAA +PGSALRAAVLELARLDPAVAARTQSAGRGRRPAVRGLRRRLAPWSAPSPRTP +>MHAAABBN_01192 +MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT +AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG +RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA +ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA +GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL +TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA +TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ +VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA +RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP +>LFPAFLNI_01410 +MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT +AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG +RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA +ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA +GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL +TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA +TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ +VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA +RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000958.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000958.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c6fce9562784eb1462f2445cbfa00fdc39fce06 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000958.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01441 +MVSSLAQDPLTSHPDLADEDRSWLQLLVGDWQLVADLALADLVLWCPAPRPDPAEGFVAV +AQVRPFTAPTLFHRDIVGSRARADLRAVVASTWSGGERPEGAGPVETPDGTLQVRLWPVV +RRGRVVAVLSAHGDPNGRPSRSVIEENYIRTADSLLDMMQHGRWPAPEESAGLWAGGTPR +VGDGLVVLGPDSVARFTSPNAVSALRRLGIGATLEGHRLTDVLAGTDAARQPSEEGTWAV +LTGLRAGRREVQSRGASLTVRSVPLLGPDGWHGALLLLRDVTELRRQEQRLVSKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEADRALRQAMRRVDTIALVHQTLSEEIDGQVPVD +DLLKRQFRLAVEVSGDGRPLEAAASGEFGELPSHVTTPLALVLNELAANAVEHGTAPAGG +RVELHAERELTPAGSVLVVSVTDGGSGVQDGWSPGEFQPAADGAGLGLRIVQTMVEGDLR +GTLRWERLPDGGTRVVLRIPTA +>MOLHKGIG_01459 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT +>NAFOICDF_01344 +MVSTIASDPLNTHPDLGAEDRAWLQQLVGDWQLIADLALADLVLWCPLPVEVDGTGHLAM +AQVRPFTAPTLFHRDIVGSRARADLRALVDRVWAAGAPADGTGPLVEPGATLKVRLWPVV +RAGRVVGVVSAHEDPRTRPARSAVEDNYRTSADTLLDMVQHGRWPNPEDPPAYWIGGTPR +VGDGLVVLGDDSRATFTSPNAVSALRRLGLPTTLAGHSLTELLGGTEAARRPVEEGSWAM +LNGQRAGRTEVQANGATLTVRSVPLRNRDGWCGALIMLRDVTELRRQEQRLISKDATIRE +IHHRVKNNLQTVGSLLRMQARRSDSPETGRALRQAMQRVDTIALVHQTLSEQIDAQLSVD +ALMARQFRLAVEVAGDGRPLGTRVEGTFGELASHVVTSVALVLNELATNAVEHGTGEEGG +VVSLQAHREDTPAGDVLVFSVTDGASVEDGPGEGFVPQPAPNGLGLRIVHSLVEGDLRGS +IQWRRMPDGGTRVTVRLPVE +>MHAAABBN_01191 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT +>LFPAFLNI_01409 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000959.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000959.fa new file mode 100644 index 0000000000000000000000000000000000000000..517238e395d7bb5f65b75bc0def559ba57cc1f71 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000959.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01442 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS +>MOLHKGIG_01458 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS +>NAFOICDF_01345 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRTCEVIDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS +>MHAAABBN_01190 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS +>LFPAFLNI_01408 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000960.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000960.fa new file mode 100644 index 0000000000000000000000000000000000000000..df91c8953a42f7ca399b2173f10f4b768c55df80 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000960.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01443 +MAQSRRPDPVDPREAPAAPAPEGPRTGGRAPVAALVVAAALALQAAALLWLAGDAIAHLG +DGVLPAGARVMLIVIYVLLGLWILVTSVALLRGRAWSRGAATAVQLFGVLLSSRLLSVGE +PVVGGVLLAVSGIALVTLFSRPVTAHLSQAAREPSAE +>MOLHKGIG_01457 +MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA +ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAAVAIQLFGVLLSSWLFSVD +AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA +>NAFOICDF_01346 +MSSSIPASPSGRRRMPAQAVVVAGVLGLEALTLVWLAVDGVAHLGAGALPTAAGVFLVVV +YVLLAAWVGAVCGGMVRGRRFSRGAAVAIQLFAVILSTWLMSIGAPIAGGLLLVGSGAAL +LCLFSGAVQAHLAGPDAGRPDAGRPDVG +>MHAAABBN_01189 +MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA +ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD +AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA +>LFPAFLNI_01407 +MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA +ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD +AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000961.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000961.fa new file mode 100644 index 0000000000000000000000000000000000000000..236f639da04106498ff79641f1ecb5ab552cc157 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000961.fa @@ -0,0 +1,19 @@ +>ACLBLIBL_01444 +MTDERQAHDANDQDSPAEVRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELVDL +DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG +PVN +>MOLHKGIG_01456 +MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP +DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK +GPGEKFTGPVN +>NAFOICDF_01347 +MTDQNQHQHAAGEDVPTEVREIHEVPAVEVITTTAVHLMTAAAVKVGLADSPDAREMTDL +DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG +PVN +>MHAAABBN_01188 +MDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELIDLDEARKLITALAG +LVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTGPVN +>LFPAFLNI_01406 +MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP +DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK +GPGEKFTGPVN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000962.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000962.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b6c5a0316b5366877c82889a14facef1170590c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000962.fa @@ -0,0 +1,39 @@ +>ACLBLIBL_01445 +MNPSSQHRSSTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAEADLDLVEVAP +TAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGHAKKFL +SQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVIGPLRT +KADARADQRKNSEDSHRERQGGGSRRDQAAREAKARAAEKAAANAAPVKNSVGDAFPEQL +KAMAARTQESAPAAPAASAEPKQAPKAPAKPAAQAAPKQAPKAPAKPAAAAKPAAKPAAA +PKPAAASKPASSGKPAAPASAPKPAAKPMPAPPKPAAPRGGAAKPGPRA +>MOLHKGIG_01455 +MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA +GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL +RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID +KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR +QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS +APVRNSVGDAFPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSA +TPASAPKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAP +KPGPRA +>NAFOICDF_01348 +MESSSHPRQQDVRHGRAELPGHRVSAAVAPGSDDPWRPGGTAKGPIRGRFEASRLHPQGR +PSAWRAPGVRSHQRPANRSGTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAE +ADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKKQVNTVLKEVRFRLKIDQHDYE +TKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIRLLQKFAEDVAELGTVESQPRQDGRN +MVMVIGPLKAKAEAREEQRKSTEGTQRERKGGGSRRDQAAREAKAAAAEKAAANSAPVRN +SIGDAFPEQLRSFAAQQTEAPAEQAPVPAPKAAPAKATPAKAPAPKPAATPAPKPPASAP +KPPAAPKPAAAPKPAAKPMPAPPKPAAPKGAPKPGPRG +>MHAAABBN_01187 +MEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGH +AKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVV +GPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDSAPVRNSVGDA +FPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSATPASAPKPAA +TPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKSGPRA +>LFPAFLNI_01405 +MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA +GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL +RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID +KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR +QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS +APVRNSVGDAFPEQLKAMAARTQENASAAPAETKQAPKTPAPAAPRPATKPASSATPASS +PKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKPGPR +A diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000963.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000963.fa new file mode 100644 index 0000000000000000000000000000000000000000..0a028fd7cda83b63dc6269619a0f02f10bd2a83b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000963.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01446 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDKLVSKGSLKQIKR +MLGI +>MOLHKGIG_01454 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR +MLGI +>NAFOICDF_01349 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLAGDKVVSKGSIKQIKR +MLGI +>MHAAABBN_01186 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR +MLGI +>LFPAFLNI_01404 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR +MLGI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000964.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000964.fa new file mode 100644 index 0000000000000000000000000000000000000000..b946682a0d76b8b2fb62fbbae214cffd572130ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000964.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_01447 +MARVKRAVNAHKKRRTMLELASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL +WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD +VNAPRRLPLVGPGTPGSPPRVRRGHRRRRGGPSDEEARPVGVCAPAPRRTRPGEPMTPPA +EPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAVRQWPAGH +VLTQVYVSAGLAERDPDLAALVERVADGGPGGERVLVREASDEVLTAMADAVTGQGIVAV +ARIPDQPPLADAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVDPFNPKV +VRSTAGSLFHLPVLTGAEAAAVADASRGAGLQVWAADGYGDDRLDALAPETTAAPTAWLF +GNEAQGLDEAELALADRRVAVPLYGAAESLNVGTAATVCLYASAMAAAVRRDG +>MOLHKGIG_01452 +MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPTAAAGQ +WRAGRVLTQVYVSGGLVDRDPALAELVARVRDRPTPGGERVLVREASDEVLTAMADAVTG +QDIVAVARMPEPQAVEAVLEEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD +PFNPKVVRSTAGSLFHLPVATAVPAEAAAAAARAAGLQVWAADGYASDRLDALAPGVVAA +PTAWLFGNEAQGLDDGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG +>NAFOICDF_01351 +MSRAPQPDDELMQNPRAERVRAVAALAGRAARRRSGTFVVEGPQSCREALRAHLGEGPER +TRAQWRPGAVLTQLFVAPDLFARDPGLGDLVARLHDLTGPDRVLVREATDEVLTAMSDAV +TAQGIVAVARIPQPLTAEDAWSDARLAAVLCRVQDPGNAGTIVRAADAAGADLVAFTAGS +VDPFGPKAVRSTAGSLFHVPLVVGTEADAAADAARAAGMQVWAADGYGADRLDALEQDVL +GAPTAWLLGNEAQGLSAAELELADRRVAVPLYGAAESLNVATAATVCLYASAMAAPHA +>MHAAABBN_01184 +MTPPAEPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAARQ +WPAGRVLTQVYVSAGLADRDSELAALVERVAADGPDGGERVFVREASDEVLTAMADAVTG +QGVVAVARVPDQPALEDAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVD +PFNPKVVRSTAGSLFHLPVLAGVQAEDVAVTARAAGLQVWAADGHGSDRLDALSPASLGA +RTAWLFGNEAQGLDEAELALAERRVAVPLYGAAESLNVGTAATVCLYASAMASPTTRD +>LFPAFLNI_01402 +MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPAAAAGQ +WRAGRVLTQVYMSVGLVDRDPALAELVARVRDRPTPGGECVLVRQASDEVLTAMADAVTG +QDIVAVARMPEPQAVEAVLGEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD +PFNPKVVRSTAGSLFHLPVVTAVPAEAAAAAAWAAGLQVWAADGYGSDRLDALAPGVVAA +PTAWLFGNEAQGLDGGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000967.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000967.fa new file mode 100644 index 0000000000000000000000000000000000000000..1ff61718601f1c77493d899fa857aae4478f3bdf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000967.fa @@ -0,0 +1,37 @@ +>ACLBLIBL_01451 +MRWEAQTLRSESGAQRAAAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNAV +PAASAMPFRWTVNPYRGCTHACRYCYARSTHAFLDLDAGEDFDRQIVVKVNVAQVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYSLMPGIIEALADSGTPFSVLTKGTLLARDVPLLQ +AASRSVPVQVSLSLAMLDPAVAAAVEPGTPSPAARLRLIERLAAAGADVTVMAMPLLPWL +TDGDRDLDALMRALAAAGAARVMPGALHLRPGAKEWYLRWIRQEHPDLLAGYEQMYARSA +YAPESYRRTLARAAGEAAARHGLTRGGAHGIRREDGPVARPVPRSTPVAVPAPAAPAQPA +LF +>MOLHKGIG_01448 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF +>NAFOICDF_01355 +MRWEAQTLRTGGGAQRPGAGTPAGSPATLPLPGLQRIVSPPEFAGVTFHEVLARSALNKV +PASSAMPFRWTVNPYRGCTHACVYCYARGTHRYLDLGPGEDFDRQIVVKTNAPEVLRAEL +SRPGWTREPVALGTNTDPYQRAEGRYRLMPGIITALADTGTPFSILTKGTLLGRDAPALQ +AAAAQTSVQVGLSLALLDPSLAAAVEPGTPSPAARLRLISRLAEAGVEVSVMAMPLLPWL +TDSDRQLDRLMAALADAGAHSVLAGTLHLRPGAREWFLGWIDREHPHLAADYRRMYARSA +YAPQAYRRVVSQAAREAAARHGLRHGGAHTITREDGPGPRGGASAPLSAPAGTTGAEQAD +TAADAVRPVIAQPTLF +>MHAAABBN_01180 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF +>LFPAFLNI_01398 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000968.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000968.fa new file mode 100644 index 0000000000000000000000000000000000000000..b23eae719f98a2a49f0ec60fb74e6b7f181c2e91 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000968.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_01452 +MTTPASASAVRVLLTGFEPFGGDGHNPSIVAARDAVALLAERGVAAEAVELPCAFAAAGP +ALAAALERTRPEAAVAVGLAGGTAAVRVERIAMNLQDARIPDNAGDQPVDRPVRAEGPAA +HFATLPVKRAVEAVRAAGVPAEPSLSAGAFVCNHVLYALLDAPGTARAAGFVHVPWDLAH +RPRPDAPALPAEDLARAVAEVALVALEGGADLDVPGGTLH +>MOLHKGIG_01447 +MFESTRKRVRVRAWRGRRDAPTVVAMTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDA +VGILADRGVTAEAVELPCAFGAAGPALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNL +QDARIPDNAGEQPVDRPVRADGPAALFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHV +MYSLLDGPGTARAAGFIHVPWDTEHRPTPDTPALPAADLARAVAEAALTALAGGPDLDVP +GGTLH +>NAFOICDF_01356 +MTDPVRVLLTGFEPFGGDDHNPSIEAARAAAAALTADGTPAVAVELPCVFAAAGPALAAA +LEAHRPEIAVAVGLAGGTAAVRVERVAVNLQDARIPDNAGDRPADRPVRSGGPAAHFATL +PVKRAVAAVREAGVPAEPSLSAGSFVCNHVMYSLLDAPAPARAAGFVHVPWSREHAPTPQ +TPALPAADLARAVAAVARAALVEGPDLDVPGGALH +>MHAAABBN_01179 +MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGS +ALTAALDRVRPEVAIAVGLAGGTAAVRVERVAVNLQDARIPDNAGDQPVDRPVRADGPAA +LFATLPAKRAVAAIRAAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFLHVPWDAEH +RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTMH +>LFPAFLNI_01397 +MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGP +ALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNLQDARIPDNAGEQPVDRPVRADGPAA +LFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFIHVPWDTEH +RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTLH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000970.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000970.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f9d7514aad687e5133cb070d03244d891854949 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000970.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01454 +MTPSPETGAEPTAPAAEISPVDAAAVDAAVQAALAAFDAATDLDELKAARLAHTGDRAPL +TLANKGIGALPKERKAEAGKLMGDARGRLNKALAARTEVLEAEQAERILREETVDVTAAV +RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF +FVEPSEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV +DRGLTMAHLRGTLEYFARQMFGEEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG +GCGMVHPNVLRAAGLDPEEFSGFAFGMGVERTLMFRNEVPDMRDMIEGDVRFSQHFGMEV +>MOLHKGIG_01444 +MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL +TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV +RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF +FVDPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV +DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG +GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV +>NAFOICDF_01362 +MTSSPETGASEDAPQLSPVDGPAVDAAVAEALAAFEAAADLEELKAARLAHQGDRAPLTL +ANKAIGTLPKEQKAEAGKTMGAARSRIGKALAARTEVLEAEHAARMLAEETVDVTAAAAR +RLPGARHPLSLLQERVSDIFVGMGWEIAEGPELEHDWFNFNALNFPPDHPAREMQDTFFV +EPLESNLLLRTHTSPVQVRSMLERGAPVYVLCPGRTFRTDELDATHTPVFHQFEGLAVDR +GLTMADLRGTLEYFARQMFGPEAEIRLRPNFFPFTEPSAEMDIWHPQAKGGPRWIEWGGC +GMVHPNVLRSAGIDPEEFSGFAFGMGIERTLMFRNEVPDMRDMIEGDVRFSQHFGMEL +>MHAAABBN_01176 +MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL +TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV +RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF +FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV +DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG +GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV +>LFPAFLNI_01394 +MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL +TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAERAARILREETVDVTTAV +RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF +FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV +DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG +GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000971.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000971.fa new file mode 100644 index 0000000000000000000000000000000000000000..243bf1045eae069de54ef24a2bc839f8b4ccfcd7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000971.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_01455 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPSDELRGPIVVGQVLSKEPEP +QKNGKTINWCTVRVVPEGAEQTLTGEGIDPSGVQGVVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASVRELGIGDDHDGILVLSTLGLDPEPGTDALEVLDLQGEAA +EINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAALTPPAADDAGHPVRIADDAPIYGAP +GATRFVARTVSGVDASRPTPPWMAARLRLAGIRSISLPVDISNYVMWELGQPLHFYDAQK +LAGEIVVRRARAGETLRTLDDKERTLDPEDLLITDDSGPIGLAGVMGGLATEVTDATTTI +VIESANFDPISIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEPG +VTDVGTRPELAVVEMAADFPTALVGVEYTADEVAETLRALGAQVEAAEAADGAAPRLRVT +APSWRTDLRIPEDLVEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGHT +EVLAYPFVSAEQNRRFGVDSEEQGEALEMVALANPISSQYRYMRLSLLPGLVEIARRNLG +RGFRDLALYEAGLVFLPGTQLGSASIPPRAAHPAPEVLADLEAGIPAQPWRVAGLYAGHD +SAPGPDHAPRPVDWQDAVSGALAVADVLGVELAVRQGRHHAFHPGRVAELVVLGERGDQV +VGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPPAVVAVPLSTYPMSTQDVALVVEE +AVVAGDVRASLAEGAGELLESVELFDVYRGPGVPEGSKSLAFSLRFRAPDRTLTAEEASE +ARAAATALAAQRHGAVQR +>MOLHKGIG_01443 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVALPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS +EARAAATALAAQRHGAVQR +>NAFOICDF_01363 +MRIPLDWLREFAQVPADATAEDVLADLVTVGLEEEDVHRPSDELTGPLVVGQVLTREPEP +QKNGKTINWCSVRVVPEGAEQTLTGEGIDPSGVQGIVCGAHNFEVGDKVVVCLPGAVLPG +DFRISPRSTYGHVSAGMMASARELGLGDDHDGIIVLGDMGLDPEVGTDVVDLFHLREEAA +EVNVTPDRSYAFSIRGIAREYAHATGTAFTDPAAAVTAPEANDAGPAVTLADGAGIYGVP +GCDRFVARVVEGIDPAAATPPWMAARLRLAGIRPHSLAVDVSNYVMWELGQPLHFYDADR +LTGGITVRRAAAGETLRTLDDKERTLDPEDLVIADESGAIGLAGVMGGAATEVSEGTTRV +LIESAHFDAVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTPAQG +VTDVGTRPEPVVVELDPEYPARRIGVDYPRERVVELLTGLGASVEDAGDLLQVTAPTWRH +DLRIPEDLVEEVARLDGYANIPSTLPVAPPGRGLTRAQVHRRRVADTLAAAGLTEVLDYP +FVSEGQNRLFGSATPEEGAAQRMVRLANPISSEFGWMRTTLLPNLLETVRRNVSRGFKDV +ALFEVGAVFLPGDGALGSPSNEPIGVKPSAETLAELDAGIPAQPRHVAGAFAGHEAAPGA +GFAPRAFDWQDPIAAALAVGRAVGVELTVVQGTHQAFHPGRTATLSLPDGTAVGVAGELL +PAWLEDADMPARTGAFELDLDAVLAAAADRVVARPLSTYPASQQDVALVVADDVVAGDVR +ATLAEGAGELLEEVALFDVYAGKGVPEGHKSLAFSLRFRAPDRTLTADEASEAREAATAL +AAERHGAVQR +>MHAAABBN_01175 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGVGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS +EARAAATALAAQRHGAVQR +>LFPAFLNI_01393 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEVADEAAERAVQMLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVTEAADGAAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQVPAMVALANPIASQYRHLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSPEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHAPRPVDWQDAVAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARMSVWELDLDALCAAAPETVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEAS +EARAAATALAAQRHGAVQR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000972.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000972.fa new file mode 100644 index 0000000000000000000000000000000000000000..f11fdeb18831bf7672963f39675b360ffe9ace94 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000972.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_01456 +MPGGDGDGAEDAAGPDDGPAAAPGLGLDVERVDAPAFADRDALGEVGFSTAERAWVAALP +RSERPAARARLWTRKEALVKAAGTGFTGDPADVAALHPPPGVVLLDVAAGLPDGIVGSVA +LRRA +>MOLHKGIG_01442 +MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH +GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA +DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV +PADVVLVDLTDRLPGGLLGALALRGR +>NAFOICDF_01364 +MTTAPTSPTRGIEVGAVGVSRTEGTAQVLAALGTRLGLGPRALALAHSCPGCGATDHGAP +ALRRAGDGTTPGGAPGDDGGPVLPAVSLTHVDGPRPVTVLAWCTPSVAGTAWGIGVDAED +PTAPQTLRAFAAGADGAAEIDAVAFAAEERAALAGLSPEGALAERVRLWTVKEALVKARG +TGLDRDPAEVRPQLGEAVVPLADPRLPPGVVGTVAWRPAS +>MHAAABBN_01174 +MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH +GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA +DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV +PADVVLVDLTDRLPGGLLGALALRGR +>LFPAFLNI_01392 +MSAATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACAGCGSAAH +GVPALTGLPPGRVALVSFTHVRMPGAEDRARIGAWWAPARPADGLGLGVDVERADAAAFA +DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV +PADVVLVDLTDRLPGGLLGALALRGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000973.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000973.fa new file mode 100644 index 0000000000000000000000000000000000000000..4283db0be2e9a7a2dbc6c713562669d42ebec5d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000973.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01457 +MSTDPYVPGVGTDAAVIEHVVLDLDVRLAANRVSGTAVLSVRLTRQSRRIELDLHRLRVS +KVGAAVDGRALPASFSQPRRWPSRLVVDLGESRPEGTLVELTVAYAGTPTPRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPVSRSTADITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLTQPVPAYLLTVQIGRYRLVDAAAPADGLPPLRLVASTRTEQRARAALATQPAM +MAAFIAAYGPYPFEEYTAVVADDVLEIPLEAAGMSLFGTNHLDGSWESERLIAHEMAHQW +FGNAVTLGRWADLWLHEGFACWSEWLWAEASGRSSIASMARRAWQRLAEDPVEHVLTEPG +AAEMFEDWVYKRGALTVEALRVLLGREVFGSMLRAWVDEHRFGTVDTAGLRAHVHAWAPR +AQVTPEQVDELFEAWTRRPELPPFPG +>MOLHKGIG_01441 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLHQRVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM +MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW +FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG +PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH +AGVSRAQVDELFDAWTLRPELPPFPG +>NAFOICDF_01365 +MSTDPYIPGVGSDTATIEHLRVELDVRLASNRVAGVAELHVRLCRQSDTVELDLHRLAVD +GAAGTHDGRPLKVRATTPRNRPHRVVVHLGASLPEGSLVVLRLSYSGHPRPRRSPWGTIG +WEELTDGVLVAGQPHGASTWVPCIDSPAVRQTADITVTCDAGYLPVANGRGTRLRSRGSR +ETWRWVMDRPVPAYLLTLQIGRYRQVTAPGSGTPESAAAGGVPPLRLVVSPRLQARAEAA +MAGQGRMMEAFTAAYGPYPFDDYAAVVADDVLEIPLEAAGLSLFGVNHLDGSWESERLIA +HEMAHQWFGNAVTLGRWSDLWLHEGFACYSEWLWAEASGRAALRHEAKQAWHGLKRQGED +LVLAAPGAADMFDDRVYKRGALTVLAVRTLLGDAVFGEMLRDWVARHRFATVDTPGFRAH +VLAWAPRADVAPEDVDALFDAWTLRPELPAFPG +>MHAAABBN_01173 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM +MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW +FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG +PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH +AGVSRAQVDELFDAWTLRPELPPFPG +>LFPAFLNI_01391 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM +MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW +FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG +PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH +AGVSRAQVDELFDAWTLRPELPPFPG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000974.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000974.fa new file mode 100644 index 0000000000000000000000000000000000000000..46e49d2a068a953abc958da60459b9e1e3fb2c51 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000974.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01459 +MPHASSPAVPRTHHAVVVAETGGPEVLRWTQADVPAPGPGRVLVRTAAVGLNYIETYQRA +GVYPMDLPFVPGTEASGTVVGLGEGVDPTLLGARVATATAQGAYAEHFTAPADRLLTVPE +GVDLADAAALPLQGMTAHYLCRSTFPVEEGQTVVVTAGAGGVGLLLTQLAAARGARVITT +ASTEAKRELSRAAGAAAAVDYPELAATVDRLTDGHGAHAVFDGVGKDTFETSLRVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGGLYVTRPSLVHYTRTEEETRGRSDELFAAWAAGELD +VRIGERIPLAEAAAAHAALESRATTGKVLLTLG +>MOLHKGIG_01439 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS +>NAFOICDF_01367 +MSTHAEIPARHHAIIAEEVGGPEVLRWTETAVPTPGAGEVLVRTAAAGLNFIETYQRSGV +YAVPHPFTPGSEGSGVVVALGPGVDEALRGARVATAAGRGTYAEHFTAPADQLLHVPAGV +DLADAAALPLQGMTAHYLCRSTFPVEPGHVVALTAGAGGVGLLLTQLAAARGATVITAAS +TEDKRALSAAAGASAAVPYAELRQTVLDATGGEGAHAVFDGVGADTFEDSLASLRVRGTL +VLFGGASGQVPPFDLQRLNSGGGLYVTRPSLAHYTRTAEETAWRGRELFDAWSAGALDVR +IGARVPLAEAGRAHTLLASRATTGKVLLPLS +>MHAAABBN_01171 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GTYAMDLPFTPGTEGSGEVVALGEGVDAALLGARVATATATGAYAEHFTAPADRLLAVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS +>LFPAFLNI_01389 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHAVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000975.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000975.fa new file mode 100644 index 0000000000000000000000000000000000000000..c9e69508cf8f67ca294e28756cb50eee6d9a2fe7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000975.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01460 +MTHTVAVSGASGYAGGEALRLLAGHPDVAVGAITAHSNAGERLGALQPHLHSLADRVLEE +TTADVLAGHDVVILALPHGASGALAAQIAERSPETLVIDAGADHRLESAADWEAFYGSEH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLSQAAGERVQISFTPTLAPMAR +GILATATARLRPGADPAAVRGAWERAYADERFVHLLPEGLWPATKSVLGSNHVQMQLAVD +ERAGRVIVTAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>MOLHKGIG_01438 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMPR +GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAVLDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>NAFOICDF_01368 +MTFTVAVSGASGYAGGEVLRLLAGHPEVQIGAISAHSNAGERLGSLQPHLHALADRVLDD +TTADVLAGHDVVVLALPHGASAAVAAELAERSPRTLVIDAGADHRLESAADWERFYGTDH +AGTWPYGLPELPGQRERLAGATRIAVPGCYPTTSILALAPGFAAGLLETRDVVIVAASGT +SGAGRAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVQISFTPTLAPMPR +GILATATARLKEGVTADRVRAAWEDAYGPERFVHLLPEGQWPTTKAVVGSNHVVMQLAVD +PHAGRVIVTAALDNLTKGTAGGALQSMNIALGLPEQLGLEIQGVAP +>MHAAABBN_01170 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTADVLAGHDVVILALPHEASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR +GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>LFPAFLNI_01388 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR +GILATATARLRPGVAAADVRDAWAEAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000976.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000976.fa new file mode 100644 index 0000000000000000000000000000000000000000..1dc1e8b34d65c31698708bab5e1c9fa79673c191 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000976.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01461 +MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNDGPRRAAAAVFTANRVAAAPVLWSRQAVS +DGRADAVVLNSGGANAATGAPGFQDAHATAEHAAEALGVSSGDVLVCSTGLIGERLDRER +LFAGVAAAAGALSADGGEDAAVAIKTTDTVAKTAQARGEGFIVGGMAKGAGMLAPGMATM +LCVITTDADVPAAVLDAALKDAVRTTFNRVDSDGCMSTNDTVILLASGAAGVAPDPEAFA +ATLHEVCADLSRQLVADAEGAAHDVAVRVHGAQTEDAAEAVARAVTRSNLFKAAIFGQDP +NWGRVIAAVGTVPEEVAAFDPYALDVSFNGVQVCRGSGVGEDRALVDLSAREVLVEVDLH +AGDAEATVWTNDLTHDYVHENSAYST +>MOLHKGIG_01437 +MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNQGPRDAAAAVLTENRVAAAPVVWTRRAVR +DGRATAVVLNSGGANAATGAEGLEDARRTAEHAAAALGTAADDVLVCSTGLIGERLPMDT +LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM +LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPAAFA +AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP +NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH +AGDAEATVWTNDLTHDYVHENSAYST +>NAFOICDF_01369 +MSVTAAQGFRAAGVTAGLKPSGKPDVAVVVNDGPSHTAAGVFTTNRVAAAPVRWSRQVLT +DGRADAVVLNSGGANAATGHAGFQDAHRTAEHAAEALGVSAGDVVVCSTGLIGERLPLDT +LLAGVDAAAAGLAEDGGADAALAIMTTDTVPKEAQASGEGWTVGGMAKGAGMLAPGMATM +LCVVTTDADLPAAALRAALEEAVRTTFNRVDSDGCMSTNDTVVLLASGASGVAPEPTQFG +AALHAVCADLARQLVGDAEGAGHDVLIRVVNASDEDAGEAVARAVSRSNLLKTAIFGQDP +NWGRVISAVGTVPEEVAPFDADALDVSFNGVQVCRAAGVGDSRAGVDLSGREVVIEIDLH +AGDAVVELWTNDLTHDYVHENSAYST +>MHAAABBN_01169 +MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRDAAAAVLTENRVAAAPVVWTRRAVR +DGRATAVVLNSGGANAATGAEGLEDARRPAEHAAAALGTSADDVLVCSTGLIGERLPMDT +LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM +LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA +AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP +NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLSAREVLVEVDLH +AGDAEATVWTNDLTHDYVHENSAYST +>LFPAFLNI_01387 +MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRRAAAAVLTENRVAAAPVVWTRRAVR +DGRATAVVLNSGGANAATGAEGLADARRTAEHAAAALATAADDVLVCSTGLIGERLPMDT +LTAGVSEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM +LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA +AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP +NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH +AGDAEATVWTNDLTHDYVHENSAYST diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000978.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000978.fa new file mode 100644 index 0000000000000000000000000000000000000000..63e521a89229198022ca67721aba8ad96e9bb692 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000978.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01463 +MSTTQDALLARYADSLTGVFGRPARVLVRGEGVHVWDADGRRYTDLLAGIAVNSLGHAHP +AVVRAVREQIAGLGHVSNLFTSEPQIRLAEELLAVADAPAGSTVFFANSGTEANEAAFKL +ARRHGGQDPSGSRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDVDA +LRAALAPGASGATVAAVVLEPVQGEAGVHGWPVGYLAQVRALTREAGALMILDEVQSGMG +RTGTWFGFQNPSVTGSDDPVLPDAFTLAKGLGGGVPIGALVCVGPEVSGLLSAGQHGTTF +GGNPLATAAGLAVLETIRSEGLLEHVRAAGERAAKLLADLPEVAAVRAHGLWIGVDLAAP +RGPVPDGGLAPAVVAAGLEAGWILNATGPDTLRLAPPLVIAAEDLERFVELLPALVAAAT +TEGDPS +>MOLHKGIG_01435 +MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP +ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL +ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVKHVPGGDAAA +LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG +RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF +GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP +AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL +TPAEGDRP +>NAFOICDF_01371 +MSTAPGTDPAAPQEELLARYAHALTGVFGAPARALVRGSGTSVWDADGREYTDLVAGIAV +NSLGHAHPAVVEAVSRQVATLGHVSNLFTSEPQVRLAEALLDRAGLPEGSSVFFCNSGTE +ANEAALKLARRHGTQDPTGRRTRVLALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEF +IAGGDAGALAAALAPDAEGRTVAAVVLEPVQGEAGVHGWPAAYLARVRDLTREAGALMIL +DEVQSGVGRTGTWFAFQNPQVTGSGAPVVPDAFTLAKGLGGGVPIGALVSVGPQVSRLLA +PGQHGTTFGGNPLATAAGLAVVETLEAEGLLDHVRTVGARVSERLETLAEVTAVRAYGLW +IGVDLADDAAASPTGGLAPAVVRAGLDAGWILNATGPRTLRLAPPLNVEAADLDRFADAL +PALVRAARAAAPTPHAPKEETA +>MHAAABBN_01167 +MSTDQSALLKRYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP +ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL +ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA +LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG +RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF +GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP +AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL +TPAEGDRP +>LFPAFLNI_01385 +MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP +ALVRAVSEQIATLGHVSNLFTSEPQIRLAERLLELAGVPAGSTVFFANSGTEANEAAFKL +ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA +LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG +RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSRLLTAGQHGTTF +GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP +AGPVPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL +TPAEGDRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000979.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000979.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ffa006d492726b3a39e1368674c42b20f9c6661 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000979.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01464 +MTPAPTPAPAAVRHFLVDTDLTPGEQAEVLDLAAQMKTDRFAHRPLAGPRTGVVFFDKTS +TRTRVSFAAGIAELGGSPLIVNPGESQLGHKESVADTARVLERMVGIIVWRTFAQSGLEE +MAAHSRVPVVNALSDDYHPCQILADLLTVREHLGGTQGRVLAYLGDAANNMAHSYLLGCA +TAGMHVRIAGPAGHLPAEHVVAAARERAAETGGSVLVTTDAAEALDGADVVVTDTWVSMG +QEDEKEARLALFRDYQVDAAAMARAGSDAIFLHCLPAYRGYEVSAEVIDGPQSVVFDEAE +NRLHAQKALMAWLLYRSGLAEDPR +>MOLHKGIG_01434 +MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV +SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS +SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRTLTYLGDAANNMAHSYLLGCATAGMH +VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAAEALAGADVVVTDTWVSMGQEEEK +EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA +QKALIAWLLYRSGLAEEPR +>NAFOICDF_01372 +MTAAPGTDVPVRHFLVDTDLSPAEQAEVLDLALEMKADRFRHRPLAGPQTGIVFFDKTST +RTRVSFAAGIADLGGTPLIVNPGESQLGHKESIADTARVLERMVGVIVWRTYAQSGLEEM +AAHSRVPVVNALSDDYHPCQLLADLLTVREHKGRTRGLTMAYLGDAANNMANSYLLGGVT +AGMHVRVAGPEGFLPDPAVVRAAEERAGETGGSVLVTTDAAAALDGADVVVTDTWVSMGQ +EDEKEERLRLFADYRVDAAAMARAASDAVFLHCLPAYRGYEVTEDVIDGPQSVVFDEAEN +RLHAQKALMAWLLYRSGLAQDPR +>MHAAABBN_01166 +MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV +SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS +SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH +VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK +EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA +QKALIAWLLYRSGLAEEPR +>LFPAFLNI_01384 +MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV +SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS +SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH +VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK +EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA +QKALIAWLLYRSGLAEEPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000980.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000980.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bd84a6075f8ff219ec17710e3b292487cff8f3c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000980.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01465 +MAVPTTKTARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +GGMVYALPAEGDDGALPGRGSDAQLSRLSSMARELLISAEPTENLVVLHTPPGAAQFLAS +VIDQARVENVMGTIAGDDTILLITTGVSAAPVVAAHLLGLAG +>MOLHKGIG_01433 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG +>NAFOICDF_01373 +MATPATKTARQAAIRDVLQTRAIRSQAELSDALAERGLSVTQGTLSRDLVDLGAVRLRGA +EGMVYAVPADGEEAVAGRSAESQTGRLASMARELLLSAEPTENLVVLRTPPGAAQFLASV +VDQARVEGIVGTIAGDDTVLLITAGTREAPAVAARLLGMAG +>MHAAABBN_01165 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG +>LFPAFLNI_01383 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000981.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000981.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5463cd97f96508c27efc169af4cae18b5182dc8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000981.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_01467 +MDTMTLFTSTRTRRTTASVAAGMTLMGAAAVGFSAPAQAATEETWDAIAFCESTNRWDIN +TGNGFYGGLQFTLSSWQGVGGQGYPHQASKAEQIKRAEMLQDLQGWGAWPKCAAGLTQAD +ADATDAAPVAVERTSSVQRQAAAEQAAAEEAAAEQAAAEEAAAEQAAAEQWAAEQAAAEQ +AAAERAEAKRAAAAEKAAAKKAAAAERAAAHQAAAEQAVVAEAETIVVKAGDSLWKLAAE +HEVEGGWTALYEANKDTVSDAAMIYVGQELVLPQA +>MOLHKGIG_01432 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESSGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVDAAPVAVERTATVQRQSAADETAADQAAAEQAAADQAAAEQAAADQAAAE +RWAAKQAAADQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAEKAAAQKAA +AAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKG +AVSDAAVIYVGQELVLPQA +>NAFOICDF_01374 +MTFFTTSSRRATATALTGMTLVGAAAAFAAPAQAASVETWDKIAACESNGNWAINTGNGY +YGGLQFSLTSWRGVGGTGYPHEASKAEQIKRAEILQDMQGWRAWPVCSVKAGLSGADTAP +DAYSTTPVQRQSTQASASAAQDWAAEQSAAEQRAAEKAAAQRAAAAAHTPKSVLKAAEKA +NTENATELAAAEDTVFVKPGDSLWKIAKTHKVAGGWKALHEANKDIIEDASVIYVGQELV +LPTA +>MHAAABBN_01164 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESNGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA +AADQAAAERWAAEQAAAEQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE +KPAAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT +ALYEANKGAVSDAAVIYVGQELVLPQA +>LFPAFLNI_01382 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSALAQAATVDTWDRLAECESNGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA +AADQAAAERWAAEQAAADQAAAERWAAEQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE +KAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKGAVS +DAAVIYVGQELVLPQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000983.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000983.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae3a4ae0c58628d2196927c297137a3599011b46 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000983.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01469 +MTENPEARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHAA +GLLGAEDLEGMIAALDRLETDVRSGAYAPADSDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGLVATVDALLSQVQAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARTAVSPYGSGALAGSSLGLDPEAVAAELGFDSAVWNSID +GTASRDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVKLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLAGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFETERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +EEYAAISPALTPQVREVLSTEGSLNSRDAQGGTAPAAVAAQVEALERTLEPLRRWAQTPG +SVVDAR +>MOLHKGIG_01430 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPHAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALEPLRRWADTPG +SVVDAR +>NAFOICDF_01376 +MSENSTPRHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLTADELAGMIDALDRLEADVRSGAYAPAESDEDVHGSLERGLIERAGAELGGKLRAGR +SRNDQVATLGRMFLRDHARVVARGVLATVDALVEQAEAHPFAPMPGRTHLQHAQPVLLSH +HLLAHAWAFTRDLQRLVDWDARAAVSPYGSGALAGSTLGLDPNAVAAELGFDSAVWNSID +GTAARDVYAEFAWVAGMIGVDLSRISEEVIFWATKEAGFVRLHDSYSTGSSIMPQKKNPD +VAELARGKAGRLIGDLAGLMATLKGLPLAYNRDLQEDKEPVFDAVDTLELLLPAVSGMIA +TLSFNTERMAALAPQGFALATDIAEWLVRQGVPFRVAHELSGEAVQVAESRGVELWDLTD +EEYAGISAHLTPAVREVLSTEGSLNARRGQGGTAPEAVAEQLAALKAALEPLRAFAASAG +SVVDAR +>MHAAABBN_01162 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVAAELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVRLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVMAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG +SVVDAR +>LFPAFLNI_01380 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG +SVVDAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000984.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000984.fa new file mode 100644 index 0000000000000000000000000000000000000000..07b57d31551633959e90be3e27c644c447e093dd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000984.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_01470 +MTDAVSVRQSELELERARVAERYARLDALREEKERQLAAVRRTGLEGSLQNHSERDAFAS +LYEDRLAQLLAVDDRLVFGRLDLDPERAGDPDEERYIGRIGLTTEEHERLLVDWRAAEAG +AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDVLDPDLLGQEGVRADAQGALLAAVTARR +TGRMGDIVATIQAEQDEVIRAPLAGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPERDLDAAAVKGRLEMAQV +IAHAVAQRQRLLAQPRRLMIEGTAVKLKPAAVRRARDRARATGKPHNEARVTFVKILVRE +LAEKLSKKLEKSSGAPVQRDLLLEDVRTSRDVRVALNLCWMPLTPQKLVGDLLTREHLLR +AAAPWLSDGEVGALLRPADAPWTEADVPLLDEAAELLGRLEAPAKGGESAAQHERNLENA +RASLENMHQTLADMGVDGVVDAEQLAAANEARAVRRTTAETAAHDRTWTYGHVVVDEAQE +LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLEPEFGDRWRLEELTVNYRSP +ARVMRWASQVAQAAGLEVSRPRAVREGEHAPRLTVRPGADLVALTLDAVAGERDRVPEGL +VAVITAAAHAPELLAALRERWGRARVDTAPLPGVEIVVATPWETKGLEFDAVVLAAPERL +VDDARGVVGDLYVAMTRATQSLSVVSTAAVAALPAGLADPPA +>MOLHKGIG_01429 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS +LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG +AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR +TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA +VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE +LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR +AAAPWLSDAEVGALLRPADAPWTEADVPLLDEAAELLGRLDTPGRGGESAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE +LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP +ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEAERDRVPEAL +TAVIAPAERTGELLTALRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVLPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE +>NAFOICDF_01377 +MTDTVSSRQAELELERERVAVRYARLDALRAEKEEQLARVRRSGLQGSVQNHSERDAFAS +LYEDRLAQLYAVDERLVFGRLDLDADDAGDVEQRYIGRIGLTDEGQERLLVDWRAQEAGA +FYQATAARRLGVGRRRHLLLRGREVRDFEDDVLDPSLIAEGAAGAQSQGALLAAVTARRT +GRMGDIVATIQAEQDEVIRADTSGALVVQGGPGTGKTAVALHRAAYLLYTHRDRLAKSGV +LVVGPSNAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPDRSARAAELKGRLEMADVV +AAAVAQRQRLIPETRRLEIEGTVVKLKPAMVRRARDRARATGKPHNEARTTFVKILVREL +AEKLRKKLEKSSGVPVQRDLLLEDVRTARDVRVALNLCWMPLTPQKLVGDLLTKEHLLRA +AAPGLSDGDVAALLRTDPDAWVESDVPLLDEAAELLGELEEPHRPGESEAQHRRNVENAQ +ASLENMHQTLAELGVDGVVDAEQLAAANEVRAVRRTTAEQAAHDRTWTFGHVVVDEAQEL +SPMQWRLLARRCPLKSFTVVGDIAQASRRGGARSWKDVLGPEFGDRMRLEELTVNYRSPA +RITRWAAQVAQAAGLEISSPEAVREGEHEPLLTVEPGADPTRLAQRVVEAERGRVGDGLV +AVIVPADDAAEHLTHLQDRWGSLVDRAPAPGVEVVVVTARETKGLEFDAVVLVSPERIVA +DADGVVGDLYVAMTRCTQSISVVSGAAEEELPAGLMPVPA +>MHAAABBN_01161 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS +LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG +AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR +TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA +VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE +LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR +AAAPWLSDVEVGALLRPADAPWTEADVPLLDEAAELLGRLETPGRGGESAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANETRGVRRTTAETAAHDRTWTYGHVVVDEAQE +LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP +ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALEAVEVERDRVPEAL +TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE +>LFPAFLNI_01379 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS +LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG +AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR +TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA +VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE +LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR +AAAPWLSDAEVGTLLRPADAPWTEADVPLLDEAAELLGRLETPGRGGEFAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE +LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP +ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEVERDRVPEAL +TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000985.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000985.fa new file mode 100644 index 0000000000000000000000000000000000000000..ef9e817beaa961bd602435f77d6ebce0f0b65a8b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000985.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01471 +MAPDNEERAARLRAQANDPSFENVWQELLWRGLVHVSTDEAALEEALAGEPISYYCGFDP +TAASLHLGHLVQLLTLRRLQLAGHRPMALVGGATGLIGDPRQTSERVLNSQETVAGWVES +LREQIQPYLSFEGENAATMVNNLDWTAGMSALDFLREVGKNFRVGTMMKKEIVAKRLNSE +EGISYTEFSYQVLQGNDFLELYRRHGVSLQTGGSDQWGNLTAGTELIRKVEGVPAHALGT +PLITNADGTKFGKSEGNAIWLDAAMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQKRLAWEVTSLAHGEEATTKVIEASQAVFGGGDLGEVDAETLGAIL +SELPQADRTQWEGEPGTVTAVELLVSTGLVGSKSEARRTVKEGGASVNNERVSDADRVYT +REDALAGRHLLVRRGKKNMAGADFGSQDADRG +>MOLHKGIG_01428 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDALAGRHLLVRRGKKNMAGADLGEA +>NAFOICDF_01378 +MAETTVTRAERLRQQANDPSFENVWQELTWRGLVHVSTDEAALEEALAGEPISYYCGFDP +TAPSLHLGHLVQLLLMRRLQLAGHRPVALVGGATGLIGDPRQTSERVLNTREVVQEWVES +LRAQIEPYLAFEGDNGARMVNNLDWTASMSALDFLREVGKNFRVGTMVKKEIVAKRLHSE +EGISYTEFSYQVLQGNDFLELYRQHGVTLQSGGSDQWGNLTSGTELIRKVEGAHVHALGT +PLITNSDGTKFGKSEGNAIWLDADMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAAKVDAEPFRREAQKRLAWEVTALAHGEEAARTVIDASAAVFGGGDLSEVDVDVLSAVL +AELPQADAAQWGAAGKPTAVELLVSTGLVSSNSEARRTIKEGGASVNNVKVADAEQVFGA +DEALAGRYLLVRRGKKNMAAADLRSGE +>MHAAABBN_01159 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAKMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQKRLAWEVTALAHGEETTTKVIEASHAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDALAGRHLLVRRGKKSMAGADLGEG +>LFPAFLNI_01378 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDAFAGRHLLVRRGKKNMAGADLGEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000986.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000986.fa new file mode 100644 index 0000000000000000000000000000000000000000..25069b9d7277f3fc08cf0ead29b3f57851a45fed --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000986.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_01475 +MAEDTPRGRRDDRRSPGDGAGRSRGGSGDARRFGGPRDGRRSGGSGEGRSGQDRRDRSSE +GFRGGRSGDGPRRERSSDGPRRERSSDGFRRDRSSDGPRGERSGDGPRGPRAGGDRRQSG +AGSARGGFEGRRGGERREGAGGERRDRRSASSSPRWEGRGQDRTERTERRERPAHNPRDL +RAANRVDQERSPDIDADVTGQELDRGTLKEVNGLDERPASWVAKHLVMAGRYIDVDPALA +FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHVAAQVDSERA +LGRPAKALQLAAEIDTARLDRAARVELAMVVSGIREDAGDLQGAHDALQIPELDRRRGYP +FSPRLFQRQADVLLLLGRADEARLWARAVRVAEKALGIGGFAEPEIVDVDTEPVDDRRER +GPSPRERRYAENAAPAAEEVPDTPEADDEVAADADTEAPASTESELDAPPAAVAQADEVD +PNQMSLFDELDGGEGEGR +>MOLHKGIG_01424 +MTGKELDRGTLKEINGLDERAASWVAKHLVMAGRYLDVDPTLAFQHALAASRKGGRLSRV +REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS +RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG +RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRNRRPSPRERRHERYAAEAG +AEPTADGSPAEEPEAAAEPTLVPRQEAVAQPPAAVDTPDEVDPNQLSLFDALEAPEADER +>NAFOICDF_01383 +MAERSAREPRDDRRGDGHDGTRSGTPRGRRDGDGGRRQGEGRPFRPHRDGEGVGRSRNVG +GRDGAAPRPGRPERAQRERPAHSPSDLRAANRVDQQRSPDIDGDVTGKELDRGTLKEIGG +LDERPATWVAKHLVMAGRYIDEDPELAFQHALAASRKGGRLARVREAVALTAYAAGEYHE +ALREFRTYRRMTGDDTHIAAQVDSERALGRHEKALQLAGEVDTSRLDRAARVELAMVVSG +VREDLGDLEGALAALKIPELDRRRGYPFSPRLFQRQADVLTALGRTQEAAVWQRSVHVAE +RALGIGGFAEPEIVDVEVEPAEDDRPVRGHRERHTGPRVSDASQSSAESAPVGEGSAEEH +GQAAPAERES +>MHAAABBN_01155 +MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV +REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS +RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG +RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG +AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER +>LFPAFLNI_01374 +MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV +REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS +RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG +RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG +AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000987.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000987.fa new file mode 100644 index 0000000000000000000000000000000000000000..72060d6ad193c0ea6b4687fa3f04e75cdd4b102b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000987.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01476 +MSPTLPRGHDGLLCDLDGVVYAGGGAVPGAVETLTALAERGVPVGFVTNNASRAPESVAE +HLRSLGVPARPEQVFGSAPAGVDLLEETLGARTGRVLVVGSDYLRQVVRDRGFEVVAASQ +DRPDAVIQGFDPGVGWAELAQAAYAVNAGAAWVATNLDASIPRAEGIAPGNGALVGAVGQ +ATGTAPAAAGKPEPLLFRTAARALGLTRPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ENAGSAPEADRPTWIVEDLPALLSEPDGQAGTADGRRG +>MOLHKGIG_01423 +MSTTFFDGHDGLLCDLDGVVYAGDGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAEAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QCPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAADALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEASADPRRG +>NAFOICDF_01384 +MTDPAASTFFGGHDGLLCDLDGVVYAGGEAIPGAVETVSALAERGVPVGFVTNNASRPPE +AVAEQLRRFGLEVSPSHVFGSAPVGVDLLEERLTAAGHEGPARVLVVGSVHLADLVAARG +HHVVETAAERPDAVLQGFDPRVDWSRLAEAAYAVNAGAAWVATNLDLSIPRAEGVAPGNG +ALALAVTQATGVIPVAAGKPEPRLFHTAAAALGLQAPLMVGDRLDTDIRGGNAAGMETVL +VLTGVGSRHAAGEAPEEDRPTWIVDDMTALLGEPAEAARG +>MHAAABBN_01154 +MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG +>LFPAFLNI_01373 +MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000988.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000988.fa new file mode 100644 index 0000000000000000000000000000000000000000..257faa84fb080d4df508926e3d5e3e79000febcc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000988.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01477 +MAEAVRADVALAARGLARSRTEASALIRAGQVLVDGRPVRRASERVAPTASLTLADDGPR +WVSRAAHKLVSALEAFPDVAVRGRRALDAGASTGGFTQVLLEGGAARVAAVDVGHGQLVD +LVRTDPRVLVREGLNVRDLTVQDVEGEVDLVVSDLSFISLRLVMDALAGVCRPGADLLLM +VKPQFEVGRAALPRTGVVTDPAARRDVVAAVAAAALDSGLELRGLARSGLPGQDGNVEFF +LRLRRPAADAAGAPGTGLDDDAPAAEAVAAAWTAAAEVDWA +>MOLHKGIG_01422 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPADRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVGVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHNQLAP +PVRADPRVLVREGLNIRDLTAEDIDGPVDLVVSDLSFISLRLVLAPLASVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRHAVVGVTAAALGAGLAPRGLARSGLAGQDGNAEFF +LRLRRPDATAADNPAGGTSPAPPAGERAAGWVRGAHIDWS +>NAFOICDF_01385 +MGEARRADVALAADGLARSRTEAAALVKEGVVLVDGTPVRRPSQPVASGAVLSLLDQGPR +WVSRAAHKLVSALEAFPVPVAGRRALDAGASTGGFTQVLLERGAARVAAVDVGHGQLVQE +LRADPRVLVREGLNVRDLTATDVEGSVDLVVSDLSFISLRLVLDALAGVCRPDADLLLMV +KPQFEVGRAALPRTGVVTDPRARRSAVEGVVAAALGTGLAARGVARSGLPGQDGNVEFFL +HLRAPAAPRDGGAVAGDADEDERRRRAAALVAAADVDWS +>MHAAABBN_01153 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVAVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP +PVQADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSGLAGQDGNAEFF +LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS +>LFPAFLNI_01372 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVAVAGRQALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP +PVRADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSDLAGQDGNAEFF +LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000989.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000989.fa new file mode 100644 index 0000000000000000000000000000000000000000..bab6871da348e3b5998c5cf2d34ed086335813fb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000989.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01478 +MPHNPGRRVLVLAHTGREDAISAALQATRILEEEGLVSVMLEQDVAAIRENADAPAGFAP +QTLGVDCGLEDIVLGLVLGGDGSVLRAADFVRGYDVPLLAVNLGHVGFLAESERTDLQRT +VQAIASEAYVVIERMALDVVVRVEDREVARTWALNEASVEKSNRERMLEVVISVDNAPIS +SFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVTAQEREAVLREVETVEPRHAGPRPDVVEPATMPLSVLSAADIQRYRDRGARYPGE +DA +>MOLHKGIG_01421 +MPYTPGRRILVLTHTGREDAISAALQATRMFAEEGLVTVMLEQDVAAIRAAAGDPPEFAP +ETLGVDCELEDITLGLVLGGDGSVLRAADFVRGYNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVHVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +SFGCDGVVLATPTGSTAYAFSAGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARVEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVTAQERAGVLHEVETVEPRHAGPRPDVVEPATMPLSVPSPADIQRHRDRGARHPGE +DA +>NAFOICDF_01386 +MSETPSRRVLVLAHTGRADAIAAALQATAMLAEEGLDTVMLAEDVAAILESGTDAVGFRP +LTLGRDCTLDDVQLGLVLGGDGSVLRAADFVRGHGIPLVAVNLGHVGFLAESERTDLHRT +VKAIADGAYVVIERMALDVTVRVEGREVARTWALNEASVEKSNRERMLEVVVSVDDSPLT +SFGCDGVVLASPTGSTAYAFSAGGPVVWPGVEALLCVPISAHALFSRPLVVGPHSTVAVD +VLTRTRETGVLWCDGRRTVELPPRARIEVTRSAEPVRLARLRPTPFAERLVRKFRLPTEG +WRGPVTEADRRTGPLAEVETVEPRHAAPRPDVVPPPSEPLTVLSPEALARYRGRDGREGD +RTS +>MHAAABBN_01152 +MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP +EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE +DA +>LFPAFLNI_01371 +MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP +EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE +DA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000990.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000990.fa new file mode 100644 index 0000000000000000000000000000000000000000..05fc6b2b19859731b2e7ef41f64ccc556b0d526b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000990.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01479 +MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAA +RAVVDAGVRLPEAHAALALAEDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRT +VPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGGAELAASLRAYRADHAAVSAA +RRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE +AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAAD +LARYTADLDTDAASDLDAAQSRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGR +LEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQELHALFMPDASFHVDLAPVGG +DGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV +TLSAEERVEELARMLAGHGDSAAAREHARELLEASARERG +>MOLHKGIG_01420 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS +RAVVDAGVRVTADHAALRLAQEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRS +VPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA +RREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGD +LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR +LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG +DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV +TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG +>NAFOICDF_01387 +MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSR +RAAVDAGVRLPADHPALSLAVEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRA +VPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGGPQLVAAAAAYRADHTAYVAA +RRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG +GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAAD +LARFSADLDGDAVSDLDAAQTRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGR +IDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAELHALFMPDASFHVSLVPLDD +GDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV +DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVV +TLGQQERVDELARMLAGHGDSAAARAHARELLEASAAERA +>MHAAABBN_01151 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS +RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT +VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA +RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGD +LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR +LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG +DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV +TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG +>LFPAFLNI_01370 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS +RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT +VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA +RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGD +LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR +LEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEELHALFMPDASFHVGLTPVAG +DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV +TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000991.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000991.fa new file mode 100644 index 0000000000000000000000000000000000000000..d28b7f5cd4c29f04adb7a8b1dc8e58ff01c0ad51 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000991.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01480 +MPEISACAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRMDPEHKGQDPLTRELMVH +PGAVAVLAVRTQLSTVGPREQVALVRQYRHPVGMELWEVPAGLRDVDGEDLHQVAVRELA +EEADLRAREWHTLVDYYTSPGGSTEAIRVFLARQVEVIPEAERHARTDEEAAMPLAWVGL +DEVTDAVLDGRVHNPSTVVAILALCAHRAQGWRRLRPVDAPFVPDRHGPGADWPA +>MOLHKGIG_01419 +MPEISASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSREPLTRELMVH +PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA +EEADLRAREWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGL +DEVTDAVLDGRVHNPSTVVAVLALGAHRAQGWRRLRPVDAPFVPDRQAPGADWPA +>NAFOICDF_01388 +MAEVPASAGRSPLRDLSLPRRVKKSKTVFEGRVWDIARESFRMDPDDKGQEPLTRELMVH +PGAVAVLALRTHLTTAGPVEQVALVRQYRHPVGMELWEVPAGLRDVAGEPLVETARRELR +EEADLEAAEWHTLADFFTTPGGSTEAIRVFLARQVSAVPEGARHEREGEEASMPLAWVNT +DEVLDAVLDGRIHNPSTVVAVLALHAHRAQAWRRLRPPDAPFVPDRRGPGADRPA +>MHAAABBN_01150 +MPEIPASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSQDPLTRELMVH +PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA +EEADLRALEWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGV +DEVTDAVLDGRVHNPSTVVAILALCAHRAQGWRRLRPVDAPFVPDRHGPGADWPA +>LFPAFLNI_01369 +MPEIPASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSREPLTRELMVH +PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA +EEADLRAREWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGV +DEVTDAVLDGRVHNPSTVVAVLALGAHRAQGWRRLRPVDAPFVPDRQAPGADWSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000992.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000992.fa new file mode 100644 index 0000000000000000000000000000000000000000..b3a20370187c55f96f30655c623fcc18d3b7d77f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000992.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01481 +MSTDPAARGSGEAEARGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY +RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPFAVRSAARVLAAVRGLHRFWALEG +LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS +EVVGLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMT +GAARSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADV +RVVQELLGHASVTTTQVYTLVTVDSLREVYAAAHPRAR +>MOLHKGIG_01418 +MSADPAPRGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRWLEAQG +VRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPAL +DVHPPKPGARLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVD +DVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMAGAARSTPA +LFVNACGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLG +HASVTTTQVYTLVTVDSLREVYSAAHPRAR +>NAFOICDF_01389 +MSASPELHRALDRHLDHLAVERGLASATLAAYRRDLGRYLAWLEASRVDRPADVDPGHVA +GFLSALGTGDDGGRPLGARSAARVLSAVRGMHRFWALEGLTPTDPAADVAPPRPPERLPK +ALPVETVTRILEAVPTAEPADLRDRALLEFLYGTGARVSEAVGLDVDDVVGVAGDRGAGR +GDDDRLPVVRLFGKGSKERLVPVGSHAADALAAWLVRGRPALAAAATRPVPALFLNLRGG +RLSRQSAWSILKAAAERAGVAQDVSPHTLRHSFATHLMQGGADVRVVQELLGHASVTTTQ +VYTRVTAEALREVYASAHPRARWTT +>MHAAABBN_01149 +MSTDPAARGSGEAEARGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRW +LEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTP +ADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVV +GLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVT +RSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVV +QELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR +>LFPAFLNI_01368 +MSPHAPQTSALAAPFRRHLDHLAVERGLAENTLAAYRCDLARYRRWLEAAGVRAPGDVDP +GHVAGFLQALATGDDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPARDVHPPKPGD +RLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVDDVVGLAQTG +DDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVTRSTPALFVNARGGR +LSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLGHASVTTTQV +YTLVTVDSLREVYSAAHPRAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000994.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000994.fa new file mode 100644 index 0000000000000000000000000000000000000000..5ebd5cb21f2018d43c298ebf11d49691e50ae49a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000994.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01484 +MLYSTKTAEQKRVDLRAALAEGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVALRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ +FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI +YPVTLLRSAMGAAERVLDAIKDEGTQASQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIDENNANL +>MOLHKGIG_01415 +MLYSTKTAEQKRIDLRETLKQGGAQQFPGAFTPLSAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ +FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI +YPVTLLRSAMGAAERVLNAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIGANHADL +>NAFOICDF_01391 +MLYSKKTAAQKRIDLRETLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFEDAGLAGCHIEDQ +FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI +YPVTLLRSAMGAAERVLDAIREEGTQQSQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIDSNNANL +>MHAAABBN_01146 +MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ +FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI +YPVTLLRSAMGAAERVLHAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIGANHADL +>LFPAFLNI_01365 +MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ +FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI +YPVTLLRSAMGAAERVLDAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIGANHADL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000995.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000995.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3f34ae158295361e25d944c51f41262f3e49e00 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000995.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01485 +MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIVNRIIDNASVAVASLQR +GPIVAARAQALSHPVSTGGAGATVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH +PGDNIPPILAVAQHAGRSGKDLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG +IGTLLGLDTETVFQAVGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ +TSPVPIYEGEDGVIAWMLDGPDASYEVPLPEAGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLNKEHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV +ALQDGAWHHVDSYAPERAAREDTVALWHKVTTVEDPEWTRRYHSNDLTEKAFGGAVEITL +TDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVTQEEQDRFLDAVQRVSELGP +GELDQLNVTADPAFLSQADLDNAPKGLF +>MOLHKGIG_01414 +MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLRR +GPIVAARAQALSHPVSTGGEGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH +PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG +IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ +TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV +ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL +KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP +GELDQLNILADPAFLSEADLAAAPKGLF +>NAFOICDF_01392 +MKKHDVRVHPSADNLAREDQLAHKLAEVAVDPVEVLPEVEEMIINRIIDNASVAVASLKR +GPIVAARAQALSHPVSTGGAGATVFGVDQKVSPEWAAWANGVAVRELDYHDTFLAEEYSH +PGDNIPPILAVAQHAGRSGADLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG +IGTLLGLDAETVFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ +TSPVPIYEGEDGVIAWMLDGKDAHYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLHSEHPEAMDPENVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSVPYIFTV +ALQDGAWHHVDSYAPERAARPDTVALWHKVTTVEDPEWTRRYHSNDLSEKAFGGAVEITL +TDGTVITDQIAVADAHPLGARPFAREQYIQKFRTLAEGVVTPEEQDRFLDAVQRLSELQA +GELDQLNVLANPAFLSEADLAAAPKGLF +>MHAAABBN_01145 +MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR +GPIVAARAQALSHPVSTGGAGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH +PGDNIPPILAVAQHTGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG +IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ +TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV +ALQDGSWHHVDSYAPERAQREDTVALWHRVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL +KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP +GELDQLNILADPAFLSEADLAAAPKGLF +>LFPAFLNI_01364 +MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR +GPIVAARAQALSHPVSTGGEGASVFGVAQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH +PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG +IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ +TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV +ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL +KDGAVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP +GELDQLNILADPAFLSEADLAAAPKGLF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000996.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000996.fa new file mode 100644 index 0000000000000000000000000000000000000000..65cf512b9dcfe41204a90cb1e7db0d6e59c76357 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000996.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_01486 +MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPVREALSRLVADGLAEQAPG +RGTVVADLSLEQADQLFDLRIALESLLARRAAQRATPETAARFTALAARFQEAGEALRAG +TDPADYYAMTAELDASLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLATSAAEHAD +IADAVGSGAADLAEATTRVHLHHAFHHLTRRTRADETPTLLSPTEGDRP +>MOLHKGIG_01413 +MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG +RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG +TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD +IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP +>NAFOICDF_01393 +MPPFTPAGVSVYSGAMRVSDRAYAALRGEILDWTLPPGTVLGEVELADRLGISRTPVREA +LARLVADGLAAQAPGRGVVVADVSLEEAEQLFELRIALESLLARRAAERADADQAAAMGA +LADRFLAAVPRLEAGDEPAGYYTLTDELDAGLDAAAGNPYLVSTLRTLRLHLARLRRLAA +HDPARLASSAAEHADIAAAVAAGAADLAEATTRVHLHHAATHLTRRARAAESTTLLTPTP +FEGAHQ +>MHAAABBN_01144 +MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG +RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG +TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD +IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP +>LFPAFLNI_01363 +MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG +RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEVALRGG +TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD +IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000997.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000997.fa new file mode 100644 index 0000000000000000000000000000000000000000..eef1049072fcb38ceefa73a7caf01a57ca7c27a1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000997.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01487 +MMPPPNPAPPAPTPPPTPAPLHDPEGFWLEAAEAIDWTVPPTRALDDSAAPLYRWFPDGE +LNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRFTYAELTDAVARLAGALAARGVGKGD +RVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGIEPK +RRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADVDGRGGASWEDWGEAVAAAEPAE +CVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASDVGW +VVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIRRAD +PEGELLQDHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANPVGL +EQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQRYID +SYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECA +VIGVADPLKGQRPSGYVVLKSGVPVPEPGSEAEAALLDELRQAVRREVGPVADFRDVVVV +DALPKTRSGKILRKTMRQMADGEEYAVPSTIEDASVLDALAPVLRPGA +>MOLHKGIG_01412 +MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP +DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG +KGDRVLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI +EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD +VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR +RADPEGELLKAHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP +VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGSLPTLWRDDQR +YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALGSHPAVA +ECAVIGVADPLKGQRPSGYVVLKSGVETPEPGSEAEAALLDELRQAVRREVGPVADFRDV +VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR +>NAFOICDF_01394 +MATDTTAAPRSYADVHRRSLEDRESFWLAAAEAIDWTVPPTRALDDSAAPLYRWFPDGVL +NTAHNCLDRHVAAGRGEELALVHDSAMTGEVTRFTYAELTAEVARLAGALAERGVGKGDR +VLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRELAARIDDATPDVVLTCTGGIEPKR +RVEYLPAVAEALEIAEHPVRTVLVHHREGFATAREDVADRGGAEWEDWAEAVADAAPAGC +VDVAATDPLYILYTSGTTGRPKGVVRDHGGHAVALRWTMENIYDVGPGQVMCTASDVGWV +VGHSYIVYGPLLAGATTVLYEGKPVGTPDAGAFWRLIQDHGVRSFFTAPTALRAVRKADP +EAALLAEYDVSSLRHFFAAGERLDPETQKWIEGVLGMPVIDHWWQTETGWAIAANPVGLE +ELPVKTGSSSVPSPGFDVVVVDGLGTPVAPGEEGNIAIRLPLPPGTLPTLWKADQRYVDS +YLTAFPGHYATGDSGIVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECAV +IGVADTLKGQRPSGYVVLRAGVERPEPGGEAEEALLAELVQTVRREVGPVADFRDVAVVE +ALPKTRSGKILRKTMRQLADGEQVAVPSTIEDASVLEDLAAVLRPAG +>MHAAABBN_01143 +MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP +DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG +KGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI +EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD +VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR +RADPEGELLKDHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP +VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWGDDQR +YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVA +ECAVIGIADPLKGQRPSGYVVLKSGVETPEAGSEAEAALLDELRQAVRREVGPVADFRDV +VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR +>LFPAFLNI_01362 +MATHDAPTEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP +DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG +KGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI +EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD +VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR +RADPEGELLQAHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP +VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQR +YIDSYLSAFPGHYATGDSGLVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVA +ECAVIGVADQLKGQRPSGYVVLKSGVETPEAGSEAEAALMDELRQAVRREVGPVADFRDV +VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000999.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000999.fa new file mode 100644 index 0000000000000000000000000000000000000000..eafef1558094dd8d06c1198f9fea641a63901f7c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0000999.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01490 +MSAAAETAAAVPGALPAGIPQPVLVRGTGLLGASIGIGLSAAGADVLLHDLSPAALAVAA +DIGAGRPMRIDDDGADAGPAPALVVVAAPPDVTADVVVDSLRRWPEALVLDIASVKEAIA +AGVRAAVDDGRLGPSDPDRHLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTLPAAV +QAGRALALALRATPYRMDARAHDESVAMISHLPQIAASLVAARLQDTPDQALALAGNGLR +DTTRIAASDPQLWVQILSGNAERIVPALHGLRDDLDRLIRTLEAPGAPGSRLDMARLIAE +GNAGRARVPGKHGAPPQAFAVVTVIVDDTPGQIAAVLDEVGRTDVNVEDLRLEHASGHRA +GMVDISVLPGRRDELVAALSAAGWKVV +>MOLHKGIG_01406 +MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD +IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA +GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA +AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD +TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG +NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG +MVEISVLPGRRDELVAALTAAGWKVV +>NAFOICDF_01401 +MIPAEGGAGPAGLSGPVLVRGTGLLGASIGLGLRAAGADVLLDDPSPTALAVARDIGAGA +VVDLDDPALAPGLVVVGAPPDVTPAVVVDSLRRWPHAVVTDIASIKGAILAEVREAATRG +DIAPGDVARYLPGHPMAGSERSGPVAARGTLFTASPWVLCPAAETDPAALAAGEALARTL +QATVHRMSAADHDASVALISHLPQIAASLVASRLQDAPDPSLALAGNGLRDTTRIAASDP +HLWVQILAGNAPQIVPTLHGLREDLDRLIGTLEAPSAPGARLDVARLIAEGNAGRARIPG +KHGAPPQAFALVTVIVDDTPGQLAALFEEIGRAGVNVEDIRLDHASGYRVGMVDVSVLPG +RKDELVSALTDAGWKVV +>MHAAABBN_01136 +MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD +IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA +GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA +AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD +TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG +NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG +MVEISVPPGRRDELVAALTAAGWKVV +>LFPAFLNI_01356 +MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD +IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA +GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA +AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD +TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG +NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG +MVEISVLPGRRDELVAALTAAGWKVV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001000.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001000.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae404b4f5b658430a8aa2ba3b2845d8a28400a5c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001000.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01491 +MTEHTRDDVATTPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV +DLADADAVAAAAVAMELEQSTDPDVEAVRVGGTDVTEAIRGAEVTDTVSTVAVVIPVREE +LRRRQRETIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGEPGVD +AGTLHRQGGRAGRPRRHRVHVRPPRRGRGARGLHRARLRADRGGRPGRRRGPGRHPGREG +RPTMTDNPQHRSGDDEFVPAGEDQVAERLAAMTEEEAEARAASLRAGLADYELEDDDAAL +LDAWQLGPDEDLDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDA +EWNGREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSM +LRRKDRPVIVAANKVDDMVQEADAASLWSLGFGYPYPVSAVHGRGVADLLDAALEAMPEE +SAHGGLVPRGGPRRIALVGRPNVGKSSLLNRLAGSDRVVVDDLAGTTRDPVDELVELGGR +LWRFVDTAGIRRRQHMAHGADYYAALRTASALDRAEVAVVLLEAPSVISEQDVRILQMVL +DSGRALVIAFNKWDQVDEDRRHQLEKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDT +ALDSWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDP +GYRRFIVRRLRETFGFEGTPLEIGMRVREKRGLAPLSAAAADDDGVPRARRGSTDPAPAG +GRRRPTPSRGSSHGFLMFRA +>MOLHKGIG_01404 +MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLADYELEEDDAALLDA +WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN +GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR +KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH +GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR +FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG +RALVIAFNKWDQVGEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD +SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR +RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR +>NAFOICDF_01403 +MTENTPLTEGEEYQPAGEDHLAERLAAISDEEADARAASLRAGLGDYELEEDDAALLADW +DGDDEFDLDLPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYEAEWNG +RVFTVVDTGGWEHDAKGIHKRVADQAELAVDVADAVVFVVDATVGMTATDEAVVTMLRRK +DRPVIVAANKVDDMVQEADAASLWSLGFGYPWPVSAVHGRGVADLLDAALEELPEESAHG +GLVPRGGPRRIALVGRPNVGKSSLLNKLAGADRVVVDDYAGTTRDPVDELVELGGRLWRF +VDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPSVISEQDVRIVQMALESGR +ALVLAFNKWDQMDEDRRPQLEKEIERDLAHVAWAPRVNISALTGWHKDRLVPALDTALES +WDRRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQASTRPPTFVLFTTGFLDPGYRR +FIVRRLRETFGFEGTPIEIGMRIRERRGRKR +>MHAAABBN_01134 +MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA +WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN +GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR +KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH +GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR +FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG +RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD +SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR +RFIVRRLRETFGFEGTPLEIGMRVREKRGSRR +>LFPAFLNI_01354 +MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA +WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN +GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR +KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH +GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR +FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG +RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD +SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR +RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001002.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001002.fa new file mode 100644 index 0000000000000000000000000000000000000000..24b99154c4017dc26adac6a09947dbb5b32dedb3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001002.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01511 +MHTPQNPPTGHEPAVEPSARVAAPTAAAPDPAAAPDWHGRPFLGQPGPLANLFSVEMWER +FSFYGMQAMLVYYMSWTLAEGGLGIDVAVATGIVGAYGGMVYVFCILGGWIADRLLGSER +TMFYSAVTIMLGHIALALVPGIPGLALGLILVAVGSGGLKANAANLVGALYSQQDPKRDA +GFSIFYMGVNIGALFGPLLTGLARDSWGFHFGFGLAAVGMAIGLVQYALTRKNLPSDVHR +IPNPLPRSQYGRWVLIALAAVAVGVVLFLTGIVTVANLADAVVVLAAVAAIGIFAVLLTS +KKVTEEERSRVKAFIPLFIGTAVFFALFQQQFTVIALYSENRLDRNLFGWEMPMEWVNSI +NPIFIIAFAPVFAALWTKLGPRQPGTPVKFGIGIVLIGLAFLLFIPVADVLAVPLLWLAL +ILFVCTMGELLVSPVGLSLSTKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEENEV +GYFGVIGAVTVGVGLLMLAIAKPVRRGMRGVL +>MOLHKGIG_01381 +MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF +SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT +MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG +FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLTQYALTRKNLPTDVHRV +PDPLPRSQYGRWGLIGLGMVAVVVALFLTDVITLDNLSDAVVVLAAVAAIAIFAVLLTST +KVSEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSEHRLDRNLFGWLMPMEWVNSIN +PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVAAVPLLWLTLI +LFVCTMGELLVSPVGLSLATKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEQNEVG +YFGTIGAVTLGVGLIVLAIAKPVRRGMRGVL +>NAFOICDF_01406 +MTHSPDSGASVAPDADLGAAQAPAPDWHGRRFFGQPGPLANLFSVEMWERFSYYGMQAML +VYYMSWTAERGGLGIDEATATGIVGAYGGMVYVFCILGGWIADRLLGSERTMFFSAVGIM +LGHIALALVPGVPGLILGLVLVAVGSGGLKANAANLVGSLYAKGDQARDAGFSIFYMGVN +LGGLVGPLLTGWARQTWGFHVGFGLAAVGMAIGLTQYALTRKNLPSTVHGVPDPLPRSQY +GRWALIGLAGLAVVAVLLLTGVVNVGNLADAVVVLAALAAIAIFAVLLTSSKVSAEERSR +VKAFIPLFIGTAVFFALFQQQFTVVALYSENRLDRTLFGTEIPMEWVSSINPIFIIAFAP +VFAALWTRLGDRQPSTPVKFALGILLIGAAFLLFIPASGFLAVPLLWLTLILFVMTMGEL +MISPVGLSLSTKVAPAAFPVLMVALYNLSVALGTALAGSLAGSYTAENEAGYFGVIGGVT +IAVGVVMLLLAPAVRRGMRGVR +>MHAAABBN_01101 +MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF +SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT +MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG +FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLAQYALTRKNLPTDVHRV +PDPLPRSQYGRWGLIGLGMVAVVVALFLTGVVTLGNLSDAVVVLAAVAAIAIFAVLLTST +KVTEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSENRLDRNLFGWLMPMEWVNSIN +PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVVAVPLLWLTLI +LFVCTMGELLVSPVGLSLATKVAPRSYPVMMVSLYNLSVALGTALAGSLAGSYSEENEVG +YFGVIGAVTLGVGLLVLAIAKPVRRGMRGVL +>LFPAFLNI_01336 +MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF +SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT +MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG +FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLTQYALTRKNLPTDVHRV +PDPLPRSQYGRWGLIGLGMVAVVVALFLTDVITLDNLSDAVVVLAAVAAIAIFAVLLTST +KVSEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSEHRLDRNLFGWLMPMEWVNSIN +PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVAAVPLLWLTLI +LFVCTMGELLVSPVGLSLATKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEQNEVG +YFGTIGAVTLGVGLIVLAIAKPVRRGMRGVL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001004.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001004.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f3fb868876fd56773a3ffd0e905e101e6c05068 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001004.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01513 +MNQPGREPDLSTSSINLTELAPLVAADLSAEESDAIRALPAGSALLLADGGPEKAARFLL +DQDVVTVGRHPDADIFLDDVTVSRRHAEFRAEAGGHRLVDMNSLNGTFVNHDRVDDVLLR +SGTHVQIGKYRLTYFTSTQRG +>MOLHKGIG_01379 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DKDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAAPARG +>NAFOICDF_01408 +MTQQEPSLHTSSISLTDLAPVAETGLSPEETAAVRALPAGAALLVAHEGPDAGARFLLDT +PVVTVGRHPESDILLDDVTVSRRHAEFRAVDGGHELVDLSSLNGTYVNNDRVDQVRLRTG +MQLQIGRYRLSYHAAEPA +>MHAAABBN_01099 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAGPARG +>LFPAFLNI_01334 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAGPARG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001005.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001005.fa new file mode 100644 index 0000000000000000000000000000000000000000..04df89cf83bbef8b40f779a2f2ef4c22f5173df2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001005.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01514 +MTEPQHADAGPRTRPAGRLGIGEVVAALKSDFPGVSASKVRFLEDRGLVLPERTPAGYRR +YRPEDVDRLRFVLTVQRDHFLPLKVIAAQLAALDRGEVPADLPGGVVAPGASDASRLGRE +VAAGRRGWTRSELAEESGAGEELLAELDQYSLLPADEDGAYSSHAMEVARAAVVLAGHGL +EPRHLRPFRAAADRELGLVERAVAPLQARRDANMRPRVARSAQEIAQASLRLHSALVAEG +LEQWDDGAVG +>MOLHKGIG_01378 +MIDPRPLPDAVPTARPAGRLGIGEVVAALEAEFPGVTASKVRFLEDRGLVLPERTPAGYR +RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAVPASSDAARLGR +EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG +LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV +GLEQWDD +>NAFOICDF_01409 +MSAPHEPSAAPPPAGAALGIGDLVAALEPSFPGVSASKVRFLEDRGLVRPERTAAGYRRY +RPADVDRIRLVLTLQRDRFLPLKVIREHLDALDRGERPEDLGEAPAAAQEAVRLGHGIAD +PDRRWTRAELAREAEVPAPLVDELDQYALLPRAEDGLHPPAALGVVRAAGRLAAHGIEPR +HLRPFRAAADRELGLVQSAVAPLATRRDAGTRERAARTAEEIATACLALHAALVRAGLES +LDG +>MHAAABBN_01098 +MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEDRGLVLPERTSAGYR +RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAAPASSDAERLGR +EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG +LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV +GLEQWDD +>LFPAFLNI_01333 +MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEERGLVLPERTSAGYR +RFRPEDVDRLRFVLALQRDHFLPLKVIAEHLAALDRGERPTGLPGTAAAPASSDAERLGR +EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG +LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV +GLEQWDD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001006.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001006.fa new file mode 100644 index 0000000000000000000000000000000000000000..57403c1fb3a2d56f391e13ce788da947913e366e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001006.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01515 +MTEPRPEDAPEAGDVPMSVLGVRVELPEQHHVILLVDPPGRIMVPLWVGAPEAAAAALAL +EGVSAPRPLTHELLLSTVAALGAEVVRVRLTEVRNDVVHGELELSTGARVDARASDAVVL +ALRANAPVLASPAVLAEAGMSARSGEEDGQERTVEDFRDFLDSVRPEDFA +>MOLHKGIG_01377 +MTEPRPVPADDAGDVPLSVLGVRVELPEQHHVILLVDPPGRTMIPLWVGAPEAAAAALAL +EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV +ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA +>NAFOICDF_01410 +MAEPPEPAGDVPLTVLGVRVELPEQQHVILLLDPPGEIVLPLWVGSPEAAAAALALEGAP +SPRPGTHALLLAALAAAGSRLRGVRLTRIEDETVHAALLLDGGAEVDARASDAVVLAVRA +QVPVLCAAEVIAAAGMAARDAAAGDEDEVDDFRAFLDSVDPEDFA +>MHAAABBN_01097 +MTEPRPVPADDAGNVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL +EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRGEVVHAELVLSTGARVDARASDAVVV +ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA +>LFPAFLNI_01332 +MTEPRPVPADEVGDVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL +EGVRTPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV +ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001009.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001009.fa new file mode 100644 index 0000000000000000000000000000000000000000..49349c3ef136f8f6338b4886bb9d19846596889f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001009.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01518 +MATSTEHHDLLIIGSGSGNSLVTEHWEGRSVAIADSGVFGGTCLNVGCIPTKMYAYPAGL +AASAGAESERLGVGLEFTGADFPAIRDRIFQRIDAISEGGLRYRRDELEHTSVIQEEVRF +VGPRRVRTASGREVTADQVVIAAGSRPTLPRIPGVDLPSVHTSDTVMRLPRLPRRLLVIG +GGFIACEFASIFAALGSEVIHVNRGHRLLKAHDLSVSTAFTEIAARQWDVRTGWTPAGVE +PVADPDRAAQGWVRVRLDRAEGQEQTGTVEEVVEADAVLMAIGRTPNTDRLDVDAAGLDV +TEDGVLATDRHQRVLSGGAPVEGVYALGDVANTWQLKHVANHEARVVAHNLEHPEDLRSA +VLAPVAAAVFTRPQVAAVGLTVEQALAEHGADAITVKTQAFGDVAYGWAMEDSEGLCTVV +AEKATGRILGGHILGHDAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGL +DVPDSGLL +>MOLHKGIG_01374 +MSPPPAGRPTGPDATASGPVPILGGMATTAEHHDLLIIGSGSGNSLVSEHWKGRSVVIAD +SGPFGGTCLNVGCIPTKMYAYPASLAALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGI +SRDGLRHRRDDLDYTSVIQEEVRFVGPRRVRTASGREITADQVVVAAGSRPTLPEIPGLD +LPSVHTSDTVMRLDRLPRRLLVVGGGFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSV +STTFTKIAARRWDLRTGWTPAGIEPVEDAERAADGWVRVRLDRAEGQEQTGIVEEAIEAD +AVLIAVGRTPNTDRLDPAAAGLDVTDDGILASDEHQRALSDGAPVEGVYVLGDVANTWQL +KHVANHEARVVAHNLEHPDDLRANTLGPVPAAVFTHPQAASVGLTVEQALADYGADAITV +KTQPFGDVAYGWAMEDTEGVCTVVAEKATGRILGGHILGHEAANLIQPLVTGMAFGIDAH +RLARGQYWPHPALTEVVENALLGLDVPDSGLL +>NAFOICDF_01413 +MSPDPAASSAGDEVDGPDDPHVRAVSYADAMATTERFDLIILGSGSGNSLVTDHWEGRRV +AIVDAGVFGGTCLNVGCIPTKMYAYPAQLAASGAEAERLGVGLDFTGADFEGIRDRIFGR +IDAISEGGLRYRRDQLEHTEVVAEEAWFSGPKELTTASGRVLAGEQVVVAAGSRPTVPDV +PGVGLPSVHTSDTIMRLPRQPKRLVILGGGYIASEFAAIFSGLGTEVVQVNRGARLLKAH +DSSISTRFTALAARQWDVRTGWTLAGVEPVGDQRRADEGWVRVRLDAVEGQEQMVEREET +LEADAVLLAVGRTPNTDRLRPEAAGFDVTAAGVLAVDEHQRVLSSGVPVEGVYALGDVAN +AWQLKHVANHEARVVAHNLEHPEDLRANTLGPVPAAVFTRPQIASVGLTQDEARELLGED +AVTVKEQAFGDVAYGWAMEDAEGVCTIVAERATGRILGAHLMGHDAANLIQPLVTAMSFG +IDAHRLARGQYWPHPALTEVVENALLGLDVPDSGLL +>MHAAABBN_01094 +MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL +AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV +GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG +GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP +VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT +DDGVLASDEHQRALSDGAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT +LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA +EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD +VPDSGLL +>LFPAFLNI_01329 +MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL +AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV +GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG +GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP +VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT +DDGVLASDEHQRALSDAAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT +LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA +EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD +VPDSGLL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001010.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001010.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5c89e624f6f9e40b5c02044078e27c696da47b0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001010.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01519 +MREISEPYHPRLSPESNITDFLERQAEERPDHGLFAVADEQDQWTDVSARDARERVRALA +KGLIAAGVGAGDRVGLIAATRLEWTLVDFAIWYAGAVTVPIYETSSATQVAWIVEDADVC +AVVAGDESLVKTVRDAVHREHLPELRGVWVMDVAGGEPGSGLDELAALGADVSDEDLEAR +RSAANLEDLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGEVVRPDTSTVLFIPL +AHVFARFVSVLTVAAGARCGHVTDLKRLSNSLQTFQPSFVLAVPRVFEKIYNAALLNAQS +GGKDKIFRRGADVAVRWSRALDSGKMTAPLRLQRAFYSALIYRRIRAAMGGRLEYAVSGG +GPLSPDLAHFFRGVGLTILEGYGLTETTAPITVGRPGRLKIGTVGLPLGGNAVRIAEDGE +ILTRGTSLMRGYHDRPEANEEAFEDGWFRTGDLGSLDEDGFLTITGRKKELIVTAGGKNV +APAMLEDAIRSDALISQVMVVGDAKPFIAAIVTLDADTLPSWLAAHGLPKDLDVAAAAKE +ERVRRHVQEIVDKASSAVSRAEGIREFRILDRDFSMEEGHMTPSLKMKRAVIMQDFAAEI +ADIYGEAPAQG +>MOLHKGIG_01373 +MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL +AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSDV +RAVVTGNEDLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGADVTDEELET +RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVREDTSTVLFIP +LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ +SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSG +GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG +EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN +VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR +EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ +IADIYGEPAPQN +>NAFOICDF_01414 +MRQISEPYLPRLSPDAAITDFLRDQAVQHPERALFAVPREDGSWDDVTAAEAWDRVRALA +RGLVAAGVGPGDRVAIVSATRLEWTLADFAIWTAGAVTVPVYETSSASQIAWIFEDAGVG +AAIADTPARAKSVSDAVHREGLPELKGLWVMDEDGGAPGAGLDRLTDAGADVPADELDAR +REGVTLESLATIIYTSGTTGRPKGCELTHGNFAELVNQTLRSSLGEVVDEGASTLLFIPL +AHVFARFVSVLTVAAGARCGHVPDLSRLATSMDTYHPTFLLAVPRVFEKIYNASLLKAQA +GGKEKIFRRGADVAVRWSRALEEGRMTAPLRLQRAFYSALLYRRIREAMGGHLKYAVSGG +GPLSPDLAHFFRGVGVTILEGYGLTETTAPITVGRPGKLKIGRVGQPLGGNEVRIDDDGE +ILTRGTSLFRGYRNRPEANAEAFTEDGWFRTGDLGELDDDGFLKITGRKKEIIVTAGGKN +VAPAQLEDAIRSDALVSQVMVVGEAKPFVAAIVTLDADTLPSWASAHGLDPQISMAEAAR +EPQVIAHVQKAVDRANDTVSRAEGIREFRILDRDFSADEGHMTPSLKMRRTAILKDFQPV +LDEIYGAGPARG +>MHAAABBN_01093 +MHEISEPYHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRALA +KGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHVR +AVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELETR +RSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIPL +AHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQS +GGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSGG +GPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDGE +ILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKNV +APAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAARE +DAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQI +ADIYGEPAPHN +>LFPAFLNI_01328 +MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL +AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHV +RAVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELET +RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIP +LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ +SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALIYRRIRTAMGGRLAYAVSG +GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG +EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN +VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR +EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ +IADIYGEPAPHN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001011.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001011.fa new file mode 100644 index 0000000000000000000000000000000000000000..4dd547005d0b75db6ab4f9f2fd85b090ccc27474 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001011.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01520 +MDRPVPPVEPAPPAVPAPAVDPVHLPLRLAPGSGAGADRCVVVLHGFTSGPDSVRAWAEG +IAAGGSHVSVPLLPGHGTRWQDLAATGADEIRGAVRETVDRELSRHRHVVVAGISMGGAL +ALDAAAHRPVSAAIVVNPALRFASPLAPLAPALAPFVPSVAPIANDIADPDARELAYPRT +PVAGVAAVGRIQRAARRALPRITAPVTVFRSARDAVVPAASHRTLLRGLRRAPVDVVPLP +RSRHVATLDYDLPLLIERSRAAVEAATRA +>MOLHKGIG_01372 +MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL +PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV +LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR +AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP +LLIDHGRSAVAAMTTH +>NAFOICDF_01416 +MTRLRPAAPDRRPAPGVDPAQRPFRLPATSLPGVAVVMLHGFTSGPDSVRAWAEGVAAGG +AAVHVPLLPGHGTRWEDLGTTDADELRAAVRDAVDAALATHRRVVVAGISMGGALALDAA +AHRDVAGVLVVNPALRFGSPLAVAAPLLRHVVPSVPSIAGDIADPDARELAYERAPVAGV +AQVGRIQTAARRGLGRITAPVTVFRSAEDAVVPERSHHTLLRGLTAAPVEVVRLLHSRHV +ATLDRDLPLLVARSRDAVAAAAR +>MHAAABBN_01092 +MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL +PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV +LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAAVGRIQR +AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDHDLP +LLIDHGRSAVAAMTTH +>LFPAFLNI_01327 +MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL +PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV +LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR +AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP +LLIDHGRSAVAAMTTH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001012.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001012.fa new file mode 100644 index 0000000000000000000000000000000000000000..cdd29d2faffd2f2708e3291b7d72ede6ed3b5102 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001012.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01521 +MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGAAILASNHLSVSDSVFMPAMLERQV +HFLAKKDYFTGAGPKGWITRKFFEATNQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQAQPIGRTLPRIRRIGMIFGEPL +DFSDRAEGVTDARVLRAVTDEIMEAIRRLSGQEYVDAYAADVKSGRVPAPPRARD +>MOLHKGIG_01371 +MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV +HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL +DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD +>NAFOICDF_01417 +MSAFYWSAKTFVVAPATRLLFRPWVKGLSHVPAEGPAILASNHLSVSDSVFMPAMLDRQV +HFLAKQEYFTGRGAKGWATKKFFEATNQLPMDRSGGAASLRSLEAGLECLREGKLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGRILPTLRRLGMIFGEPL +DFSHLQGREGDHRALRQVTDEIVEAIRRLSGQDYVDVYAADVKSGRVAVPPRAGRD +>MHAAABBN_01091 +MSTFYWSAKTFAVAPATRLLFRPWVKGLANVPAEGPAILASNHLSVSDSVFMPAMLDRQV +HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLAALREGRLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGVPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL +DFSGRAAAADDRRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRVAAPPRAGD +>LFPAFLNI_01326 +MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV +HFLAKREYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQVQPIGHVLPRIRRLGMIFGEPL +DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001013.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001013.fa new file mode 100644 index 0000000000000000000000000000000000000000..b40285c83921007abe9d141654ebed79565ce1f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001013.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01522 +MTEDPREKILAFGTAISEGAADIPGLDHWRSLPVAQAPSWADEAEHRAAVAELSQVPPLV +FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEEARRHDARRMVQAYHTS +ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA +MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR +NPIGVKLGPTTSAADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE +PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRALGTRPGGMHVELTGDDVAEC +LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERVAPRR +>MOLHKGIG_01370 +MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV +FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS +ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA +MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR +NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE +PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC +LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA +>NAFOICDF_01418 +MHEDPRDQIMAFGTAISEGAAPDPALDAWRELPIKQAPTWADEDDFRAAVAELSQVPPLV +FAGEVDVLRTRLADVARGQAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQYAKPRSSDTETRDGVTLPSFRGEIVNGFEFTEEARRHDARRMVTAYHTA +SSTLNLVRAFTQGGFADLRSVHQWNRGFMENPAYAQYEQIAAEIDRAVRFMDAAGADFEA +MRRTEFYAAHEALLLDYERALTRLDSRTGLPYATSAHFLWIGERTRDVDGAHVDFLSRVR +NPIGVKLGPTTTVDDVRALADRLDPEREPGRLTFITRMGADKVRDVLPGIVAGVRDEGLQ +PVWVTDPMHGNTVTAANGYKTRRFEDVMDELTGFFEVHRELGTHPGGMHVELTGDDVAEC +LGGSDPVDEADFDEHYETLCDPRLNHQQSLELAFKVTDALAHPHQD +>MHAAABBN_01090 +MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV +FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS +ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA +MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR +NPIGVKLGPTTTTADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE +PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC +LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA +>LFPAFLNI_01325 +MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV +FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS +ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA +MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR +NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE +PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC +LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001015.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001015.fa new file mode 100644 index 0000000000000000000000000000000000000000..719f523ad2c777d3c830b8321ad19fe2ada46813 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001015.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01526 +MGRESAAPTRRSLAHVSTSSSDTPVPADAIPAELDALVGDWLTMPDVAERLDQRVTRVHN +LVKDHRLLAVRRPDPAVRAVPALFLTETGLLEPLQGTLVLLADAGYSDEESLRWLFTEDP +SLPGRPIDALRDGRKTEVRRRAQALAW +>MOLHKGIG_01367 +MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP +AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK +TEIRRRAQALAW +>NAFOICDF_01421 +MTTEHPVDRVPSDAVSPELDALVGDWLTLPDVAERLDLRVTRVHNLINDRRLLAVRRPEP +SVRAVPAAFLTERGLLEPLHGTLVLLQDAGFDDEEALRWLFTPDESLPGRPIDALRDGHK +TEVRRRAQALGW +>MHAAABBN_01087 +MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP +AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK +TEIRRRAQALAW +>LFPAFLNI_01322 +MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAERLDQRVTRVHNLVHDRRLLAVRRPEP +AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK +TEIRRRAQALAW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001016.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001016.fa new file mode 100644 index 0000000000000000000000000000000000000000..b94818af808db64491b97759f65fb6af710e6fae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001016.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01527 +MPVDAAVTRPRPADQDRFRAAVAEELTRTLDEHRERARAVHPLTVPLVDAVGDLAAGGKR +LRAVLGWLGWRAAGGDPENPRIARTGAALELFQAAALIHDDILDRSDTRRGMPSVHRRFE +AEHRASGWRHDAGHFGVSAAILAGDVALGMSETAFAAALEGAGRPARARDEFERMRFGVM +VGQYLDVAAEMAPPATDPAEAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDALVAAFA +EVSLPFGLAFQYQDDLLGVFGDPAATGKPAGDDLREGKRTVLIARAVALLSPADAAALDA +DLGDPGLSAERIAHWQRALEECGARQAVTDRVAALSARAAEAVGALEAHGVPADVRAELT +ALIEAATTRRH +>MOLHKGIG_01366 +MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRDLARDVHPLTAPLVDAIADLTAGGKR +LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE +SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM +AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA +RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAALDA +DLGDPDLGADRVAHWQGVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSAELT +QLIDAYTSRRH +>NAFOICDF_01422 +MPTPETASVSDFRAAVAERLTAVLDGHARGAARIHPDADPVVEAVSVLTSGGKRLRAVLC +WLGWRAAGGSPTDPRAAVAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFEARHREH +GWRHEAEHFGVSAAILAGDVALALSDSMFSRAIEGTPRAERARREMERMRFEVMVGQYLD +VAAEMAPPAADPAAAERAARAVVEHKSARYSAVHPLALGALLAGADDDLVAAFEAVSLPF +GMAFQLQDDLLGVFGDPAHTGKPAGDDLREGKRTVLVARAEALLPRGEAAALDAELGDPA +LSAERVAHWQRRLEEVGARTAVADEVDRLSAEARRGLERLAALGVGTDVRGELAELIDAY +TVRTA +>MHAAABBN_01086 +MPADVAVPRPRPRPADQDRFRAAVADALDRLLAEHRELARDIHPLTAPLVDAIADLTAGG +KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR +FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG +VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA +FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAAL +DADLGDPDLGADRVAHWQAVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSTE +LTRLIDAYTPRRH +>LFPAFLNI_01321 +MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRERARDVHPLTAPLVDAIADLTAGGKR +LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE +SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM +AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA +RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEVAALDA +DLGDPDLGADRVAHWQAVLEACGARQAVEERVAVLSHEAAGAVAGLLAHGVPEDVSAELT +RLIDAYTSRRH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001017.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001017.fa new file mode 100644 index 0000000000000000000000000000000000000000..cd58c5e9e0cfc3e5ee7f495228ab6b266801a73a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001017.fa @@ -0,0 +1,44 @@ +>ACLBLIBL_01528 +MSDTAAAQARPEASILHVDMDAFFLSVELRERPDLTGRPAAVAAPSGRSVVLSASYEARA +YGVRSAMPLAHARALCPPLVVVPPRQDVYRSVSADVMALLGQVTPVLEQLSVDEAFLDVA +GARRRLGPPARIGGLIRRRVREELGLPCTVGAAGVKFVAKMASTAAKPDGLLVVPPERTL +EFLHPLPVGRLWGVGPKAAEALRRRGMATIRDLAAADPEQLERAFGAAGRSWAQLSRGID +PRPVAPRPAARSIGADHTFDVDPLDVAGVDLEVLRLCHRVAARLRAEEVAAGAVTVRLKD +PDGRVRSRTARLARPTTTAHGLLGPARRLVAELHAQRPHPVRLVGVRAERLTDADEPAPE +QEALFGGSGFGDDDAAEGGAGDWAGAEAAADAVARRFPTAAVRPASLLRRAAGRPDTRRD +VPGP +>MOLHKGIG_01365 +MSETAPAAPRDEATILHVDMDAFFLSVELRERPDLEGRPAAVAAPSGRSVVLSASYAARA +YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA +GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL +DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID +PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQATAGAVTVRLKA +PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA +QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA +PRPGPGGPDRE +>NAFOICDF_01423 +MSAPDPGPAPSSPPPPRREPSILHVDMDAFFLSVERRERPELRGVPAAVAHPEGRSVVLS +ASYEARAYGVRSAMPLAQARALCPPLRVTPPRQELYRSTSARVMDLFGRVTPVVEQLSVD +EAFLDVAGARRLLGPPERIAALIRERVRAELGLPCTVGGAGVKFVAKMASTAAKPDGMLL +VPPQCTLAFLHPRPVGALWGVGPQAARRLRERGVETIGDLAARDPRWLREAFGAAGAAWA +ELAAGRDPRPVAPREPARSVGADHTFDVDARDPAALDREVLSLCHRVAARLRSGGHTAAA +VTVRVKDPALATRARTVRLPAPTASGRVLHAHAGPAVAGLLTERPHPVRLVGVRAERLSD +AEAHGAVQEALFAPEGHEGPTDDAGWRRAEEAADAVARRFPGAGVRPASLLGPPEGS +>MHAAABBN_01085 +MSESAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA +YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA +GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPQRTL +DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID +PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQVTAGAVTVRLKA +PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA +QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA +PRPGPGGPDRE +>LFPAFLNI_01320 +MSETAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA +YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA +GARRRLGPPEHIGHLIRERVRSELGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL +DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID +PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEGVTAGAVTVRLKA +PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPIRLVGVRAERLGGEADQPPA +QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA +PRPGPGGPDRE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001018.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001018.fa new file mode 100644 index 0000000000000000000000000000000000000000..c9e49ec3c317b4912b454b62b9b36c4a659312c5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001018.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01529 +MPLSEHEQRMLDQLEHQLRTEDPRLATQMADTRRDPVPVKRVVLGAVLAVVGLLVIVMGV +ANQLVPVGVLGALVVGAGIFLVTTRPRGGRAAGADRPGPGRGGRPGGGRPEGGRPGGDFM +GRLERRWDARREQGD +>MOLHKGIG_01364 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW +DERRAGGD +>NAFOICDF_01424 +MPLSDHEQRVLDELERQLHADDPSLASQLSTPRGPAPVRRIVLGAAMMLAGLAVVLVGVS +THLVVVGVLGAVLLGGGILVLTSRRVSASRAPGAPVAGDGGPHAGRRRGGLMDRLDREWD +SRGRADT +>MHAAABBN_01084 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW +DERRAGGD +>LFPAFLNI_01319 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW +DERRAGGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001020.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001020.fa new file mode 100644 index 0000000000000000000000000000000000000000..f26a8abf7c134967da2841f82f40d8f0faaa0d71 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001020.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01531 +MDADQLRPEDRHVPVMRDRVVDLLAPAVQAALDAGRAPVAVDGTLGMGGHTEAMLTRFPE +LTVIGIDRDAHAQALAAERLGPLAERLVPFHGTYDLVPEAMAAAGVEKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEHELRRIIRRDGEERFAGPIAR +AIVRARAEAPIETTGRLVEVIRTAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRIAKRHLSAWAASTAPPGFPVVLEEHEPVVRTLTRGTE +KPTEEEILENRRASSAKVRAVEKIRTSRTPA +>MOLHKGIG_01362 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSARVRAVEKIRTSRTTA +>NAFOICDF_01426 +MDPTQPLPRDRHVPVMRDRVVDLLAPAVEAAAAAGRTPVAVDGTLGMGGHTEVLLRRFPT +LRVVGIDRDPNALAMAQERLGPLAERLVPFHGTYDQVPEALAAAGAERMDAALYDLGVSS +YQLDARERGFAYSYDAPLDMRMDTTAPVTAADLVAELDEQSLRRIIRRDGEDRFAGPIAR +AIVRAREEEPILTTGRLVDVIRAVVPVSAGNKGGHPAKRTFQALRIAVNEELDILDAAVP +AVLDALEVGGRLVVMSYHSLEDRIAKRHLQEWAASTAPPGFPVELPEHRPLVKVLTRGTE +KPTEEEIEENRRASSAKVRAVEKIRTSRTTA +>MHAAABBN_01082 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAAERLGPLADRLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARAEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSAKVRAVEKIRTSRTTA +>LFPAFLNI_01317 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSARVRAVEKIRTSRTTA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001021.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001021.fa new file mode 100644 index 0000000000000000000000000000000000000000..f14bc9b42803b355c6aa18133172312232ec335a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001021.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01532 +MTLHEEMSMAAHARIAEPLRHTGAPARPAPQERTPLSVVPAPLPRSRSGMTVLCVVVLLA +ALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARADALGMVA +PAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRGDIEGPRT +LGAPAAAPGAAASDDRDASDR +>MOLHKGIG_01361 +MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV +VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARADALG +MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT +LGGEDASAAPDQDAADR +>NAFOICDF_01427 +MTAYEETGMSAQAWRDEARTAWPRTGATPEREHRQRTPLSVVPTPLPRSGSGVAVLCGLV +LLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARAGAMG +MVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEAQGQIPGPRTVDP +AAPTAAPSGETAPTPAPTDAPAGR +>MHAAABBN_01081 +MTLHEEMSMAAHARIAESLRPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVLCVLV +VLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARADALG +MVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEGQDEIEGPRT +LGGEDASAAADQDAADR +>LFPAFLNI_01316 +MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV +VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARADALG +MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT +LGGEDASAAPDQDAADR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001023.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001023.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ae45c77ccfd336aff442a7f6154a49c487599e5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001023.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01534 +MSSQPAQPQPLTPAQQDDAFRPSRTPATPWDELTRALQAAGVAARTHGRGPAAGVTGACL +DSRVVRPGDLYVALPGARSHGADFARAAVDAGAAGVLTDAEGRARLAEQGLDGSAVIEVD +SVRTAAGVVAARVYGGGQDAGPRLIGITGTNGKTTTSFLAAALLEALDRRSGVIGTILIR +AGGREVPSTLTTPESTQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL +TRDHLDMHGSMEEYFEAKAGLFDPERTARAVITVDGGEGPRWGLSMARAVRTPVTTLALG +PAAPHPGALAEEDPDFRADWEIAELVPDGLGHRFTLRHGATGRALRASVGLPGRFNAANA +ALAVLLVLYAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGRAPDAVVDFAHNPDGM +VQALRSLADAREAAGRSGRTLIVFGSAGDRDREKRPIMGEIAARAADVVIVTDDTPHTED +PAPIRAQILEGARAEAARLLQAEGRTVLVEEVADRAVAIRRAAELAAPQDGILVAGRGHE +TTMDYDGELVPLDDRQALREALAARAAAASPRASDPGSGAPRGGKVDES +>MOLHKGIG_01359 +MTTPSDPPAPLTPAQQDAAFRPSHTPAAAWPALAQALAEAGIAAHVHGAAPADGVTGVSL +DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLADVPVLEVD +AVRTAAGTVAARVYGGGGDTGPRLLGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR +AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL +TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG +PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA +ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM +VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED +PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE +TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES +>NAFOICDF_01429 +MTDDAPQTTAPLTPAEQDAAFRPAAVTPVAWAEVAAALRAAGQDVRERSAAAAPAVTGAA +LDSRVVRPGDLYVALPGARAHGAAFAAAAREAGAAGVLTDGDGVALLAEQGLDDLPVLEV +ESVRAAAGVAAARIYGGGPDAGPRLLGVTGTNGKTTTSFLAASIVEALGERSGIIGTILT +RAGDRQVPSTLTTPESAQLHALMALMRQEGVDTAVMEVSSHAVEYRRIAGLHYAVAGFTN +LTQDHLDQHGTMEGYFRAKLGLFEADRTDRAVVVLDGGEGPRWGVKTARRAGAPVTTLAL +GAASPTPGALAEEHPDVVPDWQVTDLVADGLGHRFALVHAATGRRLPASVGLPGLFNVAN +AALAALMVLESIGEDRLDELAAVLDVPAGTGPLAAAVPGRMEVVGREPDAVVDFAHNPDG +MVQALRALGDARAAAGRAGRTLIVFGAAGDRDATKRPLMGRIAAEHADVVIVTDDTPHTE +DPAPIRAQLLEGAREEAARAAAAGREVRVEEFADRAAAIRRAAELAAPEDGILVAGRGHE +TEMDYDGTLVPLDDRVALRDALAARRPGDAQEPGVAGGKVAGK +>MHAAABBN_01079 +MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAQSLAGAGIAAHVHGAAPADGVTGVSL +DSRVVRPGDLYVAVPGAHAHGAAFAARALEAGAVGVLTDAAGRALLAEQDLADAPVLEAD +AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGHRSGIVGTILIR +AGEREVPSTLTTPEATQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL +TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG +PAAPTPGALAEHDPGVRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA +ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM +VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVVIVTDDTPHSED +PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRAAAIRRAVELAGPQDGILLAGRGHE +TTMDYDGELVPLDDRVALREALAAGAAVASASVSGPVREGKVIES +>LFPAFLNI_01314 +MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAHALAEAGIAAHVHGAAPADGVTGVSL +DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLVDVPVLEVD +AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR +AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL +TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG +PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA +ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM +VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED +PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE +TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001024.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001024.fa new file mode 100644 index 0000000000000000000000000000000000000000..983564f5566e8c2b6ae9888fc53ddd9cffca74c4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001024.fa @@ -0,0 +1,56 @@ +>ACLBLIBL_01535 +MIALTAAQIAEAVSGTLSPALDPQTVLVHVTPDSREVAAEGTLYVAKPGERADGHDFIDA +ALAAGAVAVLAERPTQAPDGAEHPSIVVEDAVLAMGALAREVVSRIREHSPTTVIGITGS +AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELETRYLVVEMGADHVGNIA +YLCDIVRPDVGVVLMVGTAHAGSFGGVANIAATKGELAEAVGPEGAVILNLDDDRVAAMA +SRAQAPVTWFTADEAGAARAAQDVAAGRAAGLVAARALHADDHERAAFDLQIGADADAPR +HPLTSGLTGLHHAHNVLAAAAAAHAAGMAPADVARVLDGLGPTSRFRMERTDRPDGVTII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA +QLLVVGAGARPLYIGALNEGSWGDEAHFVEDVAQAEEFLAEHLAPGDLVLVKSSNGVGLA +ALGERLATAGASDPAPRPVRLPEGVPTVIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQ +FVRDDGPTTHKTKRGTPTMGGAVIIGAFVLAYLLTHGILALLGVGFGGPTASGLILLFLT +VGMAFVGFVDDFTKITKQQSLGLTPRGKIILQGLIGTAFAVLALNFPDDRGLTPASTAIS +FARDVPWLDLAFAGPVVGLILFVIWSNLITTATTNAVNLTDGLDGLATGATAMITGAYVL +MSIFQSSQACSLVDEPGCYEVRDPMDLALLGAILTGSLLGFLWWNTSPAKIFMGDTGSLG +LGGALAGFAILSRTELLVVLLAGLMVAITVSVIVQVGWFRISGGKRVFLMAPLQHHFELK +GWAEVTVVVRFWLVSLMCVTAGLAVFYGEWIVRQGGLAGVTP +>MOLHKGIG_01358 +MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA +ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVRGHSPTTVIGITGS +AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA +YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPEGVAVLNLDDERVAGMA +ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTEEAAVR +HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA +QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA +ALGERLATADAVAAPSASPKESRP +>NAFOICDF_01430 +MIALTAAQIAEAVSGTLSSTLDPETVLVHVTPDSREVVGEGTLYVAKPGEHADGHDYIDA +ALAAGASAVLAERPTQDADGAAHPAILVADAVLAMGALAREVVRRIREHSPTTVIGITGS +AGKTTTKDLLAALLSTQGPTVAPVGSFNGEVGVPLTVFRAALDTRYLVVEMGADHVGNIA +YLCDVVTPDIGVVLMVGTAHAGSFGGVENIAKTKGELVEALGPDGVAVLNRDDGRVAAMA +SRTQAPVVWFSTEESGAAAAAEDVAAGRASGLSVARALTADAEERPVFDLQLGADLDAPR +HAVRAGLTGLHHAHNMLAAAAAAQAAGMDPADIARGLDGLGPTSRHRMERSERADGVSII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARIREHTLVGESVVRLNIS +QLLVVGAGARPLYIGAMNEGSWGDEAHFVDDVEQAEAFLAEALQPGDIVLVKSSNGVGLA +ALGDRLAAADVTPSTASPSDTTKETRP +>MHAAABBN_01078 +MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA +ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVREHSPTTVIGITGS +AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA +YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA +ARTAAPITWFTADERGVARAAEDVAASRASGLVAARDVRSDDQERPVFDLQVGTDEAAVR +HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA +QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA +ALGERLATADAVAAPSASPKESRP +>LFPAFLNI_01313 +MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA +ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRIRGHSPTTVIGITGS +AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA +YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA +ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTDEAAVR +HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA +QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA +ALGERLATADAVAAPSASPKESRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001026.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001026.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ed986116cd874fde9ea29395aff2fd1e26b4de2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001026.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01537 +MSPTELHPVRTPADEEETEARSRPLQRLWRLVEGRRALDLSVLLIGGSTFLLTALGLVMV +LSSSSVEAIGTGGGSYGLFLRQTMWAVAGLAALLLFSRLPIGWIKALAWPAFGLAVVLLS +LVAFTPLGVTVGGNTNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALVPV +LPGGLLLIGLVMAGSDLGTAIILALVLAAVLFVAGTHHGVFIAFSAVTVVGAIALTLLAP +HRMVRVQAWLGDCSDASDPCFQPDHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT +ILGEELGLVGTLGVLLAYLALAVGMYRVAAGTTSPFIRLATWGIMAWLVGQAFVNIAMVS +GVIPVVGVPLPFISYGGSALTLSLTAVGIVLAFARHERRRAEEPDARPDADDPDTDPLPV +IPAPASQES +>MOLHKGIG_01355 +MSPIELRPVRPRAADDAPEHRERILRRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVLKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLVLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP +HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT +ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS +GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV +IPTPALQEPR +>NAFOICDF_01433 +MPSTATRPEASSRASARTAVRPRLAGFWGALEGRRALDWAALLIGLCTAVLTVLGLVMVL +SASSVEAISSSGGSYGLFLRQGGWALGGAVLLAVLRRLPVDLYRRLAWAAYLFAFLLLAL +VAFTPLGKEVNGNTNWLQLGPVTFQPSEAAKLAMALWAAAVLQRKERLVHLVSHALVPVL +PFGVALILLVLKGRDLGTALILAFILAVILFVAGTPGRVFAVLAGIGVVAALGMTVFAAN +RMERVQAWLFGCEGLQGDPCMQPDHGIYALASGGWWGVGLGQSRQKWNYIPEAENDFIFT +ILGEELGLVGTLLVLACFVGLAVGMYRVAAGASSTFVRLATWGILAWIVGQAAMNIAMVT +GLLPVVGVPLPFISYGGSALTLSLAAVGVVLSFARHERDLLPAAEASAADPASSASPQES +R +>MHAAABBN_01075 +MSPIELRPVRPRADDDAPEHRERLLHRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLGLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP +HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT +ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQASVNIAMVS +GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV +IPTPALQEPR +>LFPAFLNI_01310 +MSPIELRPVRPRADDDAPEHRERLLPRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLILVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSMLGILALTLLAP +HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT +ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS +GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV +IPTPALQEPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001027.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001027.fa new file mode 100644 index 0000000000000000000000000000000000000000..da4d2ae42bf033a742c66471e496882666e784a1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001027.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01538 +MPQTPDPARELRVVLAGGGTAGHISPMLAIARALESDDAGPVRCTMVGTASGMETRLVPE +AGYELDLIERVPMPRRPSMDVVHFPARMRAAVAAAGRILAERRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAQRRAARAALGLDPERTTVVVTGGSSGALAVNRTVRDSLDDLLGAGLQVFHLTGRDKAL +TEADGTPLRREGYVQREYLDGMEQAYAAADLLVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALTVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAEEGARR +>MOLHKGIG_01354 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR +>NAFOICDF_01434 +MTTPNDASRPLRVVLAGGGTAGHISPMLAIARALGRQDPSTVCTMVGTDSGMETRLVPQA +GYELDFVERVPMPRRPSMDVVRFPGRFQASVRQAGEILRRRGADVLVGVGGYVSTPMYLA +ASRAGVPVVVHEANARPGLANRVGALRAARVGTALPDTRLPKAQWVGMPMRPEISGLDRA +AARDAARAELGLDPERTTVVVTGGSSGALNVNRTVRESLDDLLGAGLQVFHLTGRGKELT +DEAGQRVTRPGYVQREYLDGMEKAYAAADLIVARSGAGTVCEIAAVGLPAVFVPLPVGNG +EQALNARPVVDAGGALLVRDETFRADWVRRELIPLATDPQRLAAMGEAAARLGVRDADVR +TADLVREAAREGARR +>MHAAABBN_01074 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR +>LFPAFLNI_01309 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEDDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAAGRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001028.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001028.fa new file mode 100644 index 0000000000000000000000000000000000000000..c9a1ece9130a9f39c9aa464badd8fa4d6a09a67c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001028.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01539 +MSRDESTRPVAEGRFDELGRVHLLGIGGVGVSGVARILQDQGVAVSGSDAKDLPVMRELA +AAGARITVGYDAAHLGEDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR +VLAVAGTHGKTTTSSMAAMAFASAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG +TLVNYPTTIAVVTTVEADHLDHYGTEEAVHQVFRDFAAGLPDAASGGVLVACLDDDGAAG +LAAWAREHAAARVLTYGTGPRDGVAPDLLVADLAVEPGESGVGQRATLRLASGPEATLHL +QVPGRHNALNAAAVALAAVQAGMGFEDAVRGLEAFRGTARRFEFRGAGRGVKVFDDYAHH +PTEVTAAVSAGRAVAGDGRVHVLFQPHLFSRTREFAAEFAAALSAADVVRVLPVYAAREE +PMEGVDSSLIAGRLTTAADADRAVAEDRAVAVRELAAGAESGDVILTMGAGDVTALGADL +VAALGPDAAPGAAGR +>MOLHKGIG_01353 +MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA +AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR +VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGRGEWFIAEADESDG +TLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD +LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPERTLHL +QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH +PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE +PMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGADL +LAELGRDAAPGVAHP +>NAFOICDF_01435 +MTTQQTPEGRARRERVAALGRVHLLGIGGVGVSGVARILQDQGVAISGSDAKDLPVMHDL +AAGGARITVGYDAAHVGDDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMEGH +RVLAVAGTHGKTTTSSMAAMAFTDAGWDPTFAVGAAVAGLGTNARAGAGEWFVAEADESD +GTLVNYPTTIAVVTTVEADHLDHYGTEEAVHEVFRVFAGQLPAAEDGGALVACLDDEGAA +GLAAWAHEHARAAVVTYGTGPRDGVEPDLLVDGVTVEPGESGVGQRARFTLADGTSAEVR +LQVPGRHNALNAAAVALAAVRAGMSLREAVHGLEQFRGTARRFEFRGAERGVRVFDDYAH +HPTEVVAAVSAARAVAGEGRVHVLFQPHLFSRTRDFAAEFAAALSGADRVRVLPVYAARE +EPMEGVDATLITRALTTPDPADRTVAVDRAAAVRELAAGAREGDVILTMGAGDVTALGPD +LVAALAADPSVDA +>MHAAABBN_01073 +MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA +AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR +VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG +TLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD +LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPERTLHL +QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH +PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE +PMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGPDL +LAELGRDAAPGVAHP +>LFPAFLNI_01308 +MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA +AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR +VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG +TLVNYPSTVGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD +LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMADGPERTLHL +QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH +PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE +PMHGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGPDL +LAELGRDAAPGVAHP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001030.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001030.fa new file mode 100644 index 0000000000000000000000000000000000000000..3347f594e2a6c653f479109c4b269b493c31114d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001030.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_01541 +MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD +VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI +ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM +DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA +AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD +ALGDEVRVTVIAAGFDKVDATSAPASPQAGQFQQAPQRPAQQAQPQQQAPAPQQHQAQPA +QQEQPQQVQPQSVRGTVPLAPQQPQQTEQRRQQDLPTVVEPDLGAGSSDLDVPDFLK +>MOLHKGIG_01351 +MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR +ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS +LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF +RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL +AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG +DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPAQPQPAAQPQPAAPAQPQQAE +RPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK +>NAFOICDF_01437 +MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD +VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI +ARSLGALTIGVVTRPFTFEGRRRAGSAENGIDALRDEVDTLIVIPNDRLLSISDRNVSVM +DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA +AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD +ALGDEVRVTVIAAGFDKVDATSAPAAPFQQQAAPQRAAAPQQPAQQAQQAPVSQQAAPQR +PSVPGTMPLNSSSAFGGAPAQPAATQQPAAPQQPAAPQRAQQDLPTVVEPEFGSSDLDVP +DFLK +>MHAAABBN_01071 +MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR +ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS +LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF +RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL +AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG +DEVRVTVIAAGFDKVDVTSAPAAPQAAQQQAAPQRAAAPAQPQPVPAQPQQAERPAVRGT +VPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK +>LFPAFLNI_01306 +MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR +ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS +LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF +RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL +AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG +DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPTQPHPVPAQPQPAPAQPQPAP +AQPQQAERPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001031.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001031.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d726cdcb2805e071ed29908b13a21257873bb31 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001031.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01542 +MTAAEGPVGTVPVPAGPFVHREAVATAGGTVHVAWSGVAAGNLGLHVVADEDAAGRRAVG +EARRGLERAMGVPVGSTLYLDQVHSADAVWADGPGWGEEAGPTADAAVSRDGGRALAVMV +ADCLPVVLVDEATGATAVAHAGRRGLVDGVLEGTVDRLLSLRPADRRDAPGLRAWIGPGV +CGRCYEVPEQMRAEAAERVPATAATTAWGTPGLDLPAGAVAILRGRGADVAVVQACTLED +ERLFSHRRAPGQGRFAGLVWRADEDASTPTRAA +>MOLHKGIG_01350 +MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS +AARRALERVMGVPEGATLYLDQVHSADVVWADGPGRGGASAPVADAAVSRDGSRPLAVMV +ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPEADRTGPGLRAWIGPGV +CGRCYEVPAAMRDEAAARLPATAATTSWGTPALDLPAGAAEVLRARGVATATIDVCTRED +ERLFSHRRAPGEGRFAGLVWRADPDATVPRGDA +>NAFOICDF_01438 +MSLAGGPVGTQPVPSGPFVHREDLRADARGRVAHVAWTSAEAGSLAFHILGAEQEQARAD +VVAARHRVEDAMGVPRGSVFYLEQVHSVDVVTAGPGWEEGFAPTADASVSPDGHTPLAVM +VADCLPVVFVDGLTGATAVAHAGRRGLLDGVLENTVDALLALRPEGSAGAFGLKAWIGPG +ISGESYEVPQAMQDEAVARIPELEATTSWGTPALALASGAQAVLRARGVAVERIALDTFT +DERVFSHRRAPGRGRFAGLVWTTPADVDQDHDAGDARG +>MHAAABBN_01070 +MTAAGGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGPARVS +AARRALERMMGVPEGATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV +ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV +CGRCYEVPAAMRAEAAARLPATAATTSWGTPALDLPAGAAQVLRARGVATATIDVCTRED +ERLFSHRRAPGEGRFAGLVWRADPDATTPRGEA +>LFPAFLNI_01305 +MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS +AARRALERAMGVPEDATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV +ADCLPVVFVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV +CGRCYEVPAAMRTEAAARLPATAATTSWGTPALDLSAGAAQVLRARGVTTATIDVCTRED +ERLFSHRRAPGEGRFAGLVWRTDLDATTPRGEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001032.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001032.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc96ea14b7075ead56d7dac49ba5b22155eb3e73 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001032.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01543 +MSTPEQHPTPHDAAAETRTREIAAGLAAVRERIARAAREAGRADEPALVVVTKTHPAEDV +VRLAGLGVAAVGENRDQEARPKAAAVAEALGDAAPRWHFIGQLQTNKAKHAARYASVVES +VDRTELAEALSRALVLRREREPGVEVPDLECLVQVDVDDRADEDRPEGIGPRGGAAPEDV +PALAAAIAALPGLRLGGLMCVAPRGLDPEASFRRLAALGEELRSAHPDASTLSMGMSADL +ESAVRAGATQVRIGSDVLGARPAVG +>MOLHKGIG_01349 +MTAPATAGPTPTDPRAREIADALAAVHARIADAARDAGREAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALVLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +ADVIAGLPGLRLGGLMCVAPRGLDPEHAFRRLAALGARLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG +>NAFOICDF_01439 +MAEPLQDDPRVAEIAAGLDGVRRRIADAAAAAGRADLPELIVVSKTHPAEDVVALAGLGV +RQVGENRDQEARPKAAAVAEALGGAGVPAPAWHFIGQLQTNKAKHVARYASAVHSVDRLD +LVDALSRAVVLRREREGADAVSALDCLVQVDVDDRADEDRPEGIGPRGGAAPEDVPELAR +AIAAADGLRLRGLMCVAPRAADPAAAFARLAALSARVRAEHPDADALSMGMSGDLEAAVA +AGATHVRVGSDILGARGAVG +>MHAAABBN_01069 +MTAPATAGPTPTDPRTREIADALAAVRARLADAARDAGREAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +TDAIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAHLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG +>LFPAFLNI_01304 +MTAPATAGPTPTDPRAREIADALAAVRARIADAARDTGRAAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +ADVIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAGLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001033.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001033.fa new file mode 100644 index 0000000000000000000000000000000000000000..47b6260290920445030f08847e6aafe44b4d55cc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001033.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01544 +MAGALKKTMIYLGLADGEEYDEQQRAAERDAAERRDVVEARRAAEPDTDPSMEPVRSATV +VRPESIERAESPAPSGSTAAAPAEPAELRRSSRPEPVDPGYRAPVTPIKRAAASSAEGAP +VSTLSTVHPRSYNDAKAIGEAFRSGMPVIMNVTELGENEAKRLVDFAAGLVFGLHGSISR +ITSKVFLLTPANVDVVGAEQGDAEESGDPYDGD +>MOLHKGIG_01348 +MAGALKKTMIYLGLADGDEYDEQPRAAERETAPRHEVVEARRPAEPDTDPHMEAVRPAAV +RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT +LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS +KVFLLTPATVDVVGAEQGESGAADSPFDGD +>NAFOICDF_01440 +MAGGLKKTMIYLGLADGDEYDDDPRHEAVDAAPRREPVEARRVAEPAPRLEPEDEEFDEP +STPSHAGSTAAAAAEPAPRRAASRPETADPGHRAPVTPIKRAAAPSAEGDAVRTLSTVHP +RSYNDAKRIGEAFRTGTPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITSKVFLLT +PSSVEVVGEEPPAGRDGDAPYDND +>MHAAABBN_01068 +MAGALKKTMIYLGLADGDEYDEQPRAAEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV +RDPEPAERPEPVTPSGSTAAEPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT +LSTVHPRSYNDAKAIGESFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS +KVFLLTPATVDVVGAEQGESGVADSPFDGD +>LFPAFLNI_01303 +MAGALKKTMIYLGLADGDEYDEQPRATEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV +RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT +LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS +KVFLLTPATVDVVGAEQGESGAADSPFDGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001034.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001034.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6f78ecc2838fc94e30590d73abe73a77ac44d92 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001034.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01545 +MQLILALVYIVLTVVLAALTVRIVLDVTQSFARHWRPTGAALVAASAVYAVTDPLMRPVR +RAVPPVNLGGIGLDVAFLVVFLGVVLLRVLVLVLAGNL +>MOLHKGIG_01347 +MQLLLALAYIALTVVLAALTVRIVLDVTQSFVRHWRPTGAALMLASGVYGATDPLLRPVR +RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA +>NAFOICDF_01441 +MQLVFALLYFVLTAYMAVLTVRIVLDVTRSFARSWRPSGPVLVAASGVYALTDPPLRALR +RRIPPLTLGGVGLDVAFLVVFLGVVLLRVLVLTLA +>MHAAABBN_01067 +MQLLLALAYIALTVVLAALTVRIVLDVTQSFARHWRPTGAALVLASGVYGATDPLLRPVR +RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA +>LFPAFLNI_01302 +MQLLLALAYIALTVVLAALTVRIVLDVTQSFARHWRPTGAALVLASGVYGATDPLLRPVR +RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001035.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001035.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7ec10f1af2fec1e6e3eee25930f5f6a18cbdf40 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001035.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01546 +MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA +VPDADAAVDAPVADADAAAVVDAGQSPAPAALADAEPGLEVEPTPSSADPASASAAGVLA +MAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQL +RGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA +>MOLHKGIG_01346 +MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA +APAAGPAADTPEAAATPASAEESAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR +STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE +GQLREIRAQKRVEPPTPTA +>NAFOICDF_01442 +MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP +AQAEASAPAAGEAAPALQAPAPVAPVEPSAPGEPVAPTDSATSAAGVLAMAQRLHDEYVA +EGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVERLRAFETDYRSRL +TAYIEGQLREITAQERLEPAKGTV +>MHAAABBN_01066 +MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA +APVADTPEAAETPSPVEEPAPAAAPEAADAAATSAAGVLAMAQRLHDEHVAAGEQRSTEL +VAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQLRSFETDYRSRLTSYIEGQLR +EIRAQKRVEPPTPTA +>LFPAFLNI_01301 +MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA +APAAAPAADTPEAAATPASVEEAAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR +STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE +GQLREIRAQKRVEPPTPTA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001036.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001036.fa new file mode 100644 index 0000000000000000000000000000000000000000..ffd027cb0bede2f304623801214459b2616ca2b1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001036.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_01547 +MSAAVEAPAPAAGPGARRRAVLAALLVAVLAYALDQLTKLWVETTMELGDSVTVVPGLLR +WHYILNPGAAFSIGEDHTWVFTVIQAVVAVAAVVGIVRARSLPWALALGGLAGGVLGNLT +DRLFRPPSFGQGHVVDMISVPRFAVFNVADSFIVCSILAIAFLVMTGRRLDGTREA +>MOLHKGIG_01345 +MLTALIVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV +FTIIQAVVAVAALVGIARVRSTPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV +PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA +>NAFOICDF_01443 +MSPAAPQDALTDHRDAPARPGRGVVGAALGVATLAYALDQGTKLLVERTMELGESIVVIP +GLLRWHYILNPGAAFSIGTDVTWLFTLIQAVVAVVALVALLRSRSRAWSVALGGLLGGVM +GNLTDRLFRPPSFGQGHVVDMVSVPNFAIFNVADSFIVCSILTLCLLLMSGRRLDGTRES +DAAAEA +>MHAAABBN_01065 +MLTALVVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV +FTVIQAVVAVAALVGIARVRSTPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV +PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA +>LFPAFLNI_01300 +MLTALIVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV +FTVIQAAVAVAALVGIARVRSMPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV +PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001037.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001037.fa new file mode 100644 index 0000000000000000000000000000000000000000..46d32953dd49d04dff5569c14730610150cd12d6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001037.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01548 +MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA +KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG +PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK +VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV +TSEHPDDLAHALARLRRDGS +>MOLHKGIG_01344 +MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDED +>NAFOICDF_01444 +MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA +KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG +PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK +VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL +ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI +VSPYPDDLAHALRVLRGEDRGAAPDA +>MHAAABBN_01064 +MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDED +>LFPAFLNI_01299 +MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001038.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001038.fa new file mode 100644 index 0000000000000000000000000000000000000000..776d6a1e2d7021e2023708d9af97443fc17b9142 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001038.fa @@ -0,0 +1,105 @@ +>ACLBLIBL_01549 +MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAERLGMDSLAITDHGYLFG +AYDFWSQAKSAGIRPIIGLEAYVTPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL +SENTAGMHNLFRMSSIASLDSVYAKWPRLDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ +YDEAVAAAAEFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT +LLIAERCDVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF +ERFLNPDRVSMPDFDVDFDDRRRPEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSLGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA +KGLEGLKRQWGVHAAGVIMSSEPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG +LRNLTIISDAIENVKANQGVELDLETLDVDDAASYDLLARGDTLGVFQLDGGPMRSLLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREDKGAYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVSQKRKEDHGEFTFD +LFALGGPQEDESDAADGVAVPDLPEWAKKEKLAYEREMLGLYVSDHPLQGLDGVLAQHAD +TQITRVLDDDGPADGSQVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY +APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRISMPSFKATEQV +VGQLADVLRTHEGSSEVRLSLVGQRGTQEFQLGPQFRVNPNPALFGDLKILLGPACLS +>MOLHKGIG_01343 +MTVSADARPDAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG +AYDFWSKAKAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL +SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ +YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT +LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF +ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA +KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG +LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD +LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD +VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY +APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV +MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG +>NAFOICDF_01445 +MSVQQETTAEATRDGGFVHLHTHTEYSMLDGAAKLDELFAEANRLGMDSLAITDHGYLFG +AFDFWKKATDAGIKPIIGLEAYLTPGQQHRSDKEKIRWGEPHQRGDDVSGGGAYTHMTML +AESTQGMHNLFRMGSIASLDSVYAKWPRIDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ +YKEAVEAAAEFRDIFGRDNFYCEVMQHGLDIEKRVVEDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLAIQSGSKLNEPTYDQGGSRFAFSGTDYYLKSPRQMRELFAELPEACDNT +LLIAERCETSFDTSANYMPRFPTPEGEDETSWLIKEVAKGLAYRYPEGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLRHGLIF +ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPEAKRYAEAGEFRELVAADPVAKQVFETA +KGIEGLKRQWGVHAAGVIMSSHPVIDVIPIMRRLQDGQVITQFDYPTAEGLGLIKMDFLG +LRNLTIISDAIENIRANRGVDLDLEHLDVDDAESYALLARGDTLGVFQLDGGPMRALLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGLQEITPIHPELAEPLKDILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEGAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESFLNFTPVGDDIRFGMGAVRNVGGNVVKGMVQAREEKGLYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVQQKRKEDHGEFTFD +LFALGGAADAADDSDASDGVAVPDLPEWPKKERLAFEREMLGLYVSDHPLQGLDGVLSQF +ADTQITRILDDDGPADGAHVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSLDVMFFGQ +VYAPIAMMLAEDLVVAVKGRVQRRDDGSVVLSAMELAIPELTDATGGPVRITMPAFKATE +RVVGQLGDVLRTHEGSTEVRLSLTGQRGVQEFQLGPQYRVTPNPALFGDLKILLGPSCLG +>MHAAABBN_01063 +MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG +AYDFWSKAKAAGVKPIIGLEAYVAPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL +SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ +YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVVTDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT +LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF +ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA +KGLEGLKRQWGVHAAGVIMSSAPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG +LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGRENEGSYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD +LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD +VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY +APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV +MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG +>LFPAFLNI_01298 +MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG +AYDFWSKATAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL +SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ +YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT +LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF +ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA +KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG +LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD +LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD +VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY +APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV +MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001042.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001042.fa new file mode 100644 index 0000000000000000000000000000000000000000..b78b063d529ba0d6cca67019c69432836d1d5b45 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001042.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_01554 +MLTAYDAMTAALFDEAGIEVLLVGDSVGNTVLGHSSTLPVTLDQMILFSQAVVRGAQRAL +VVADLPFGSYEASPQQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVIAHIG +FTPQSEHVIGGYRVQGRGEGAVEAMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVP +TVGIGAGPGTTGQVLVWQDMLGLREGRTPRFVRQYARLHEVIGAGVRAYRRDVLDGAFPA +PEHGFEA +>MOLHKGIG_01338 +MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV +LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES +AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG +AVERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM +LGLREGRVPRFVRQYARLHEVVGDAVRAYRADVLDGAFPAPEHGFQG +>NAFOICDF_01450 +MDSRTVTPPASSPAASEAAAPYGGAATAAAAAPVEAPARYRTVHLQRAKDEGRRFAMLTT +YDAMTAALFDEAGVEVLLVGDSLGNTVLGHGSTLPVTLEDMIVFSAAVARGARRAFVLAD +LPFGSYEASPEQAVRAGVRLMKEAGVHGVKVEGDERFAPHIAAMVAAGVPVMGHIGFTPQ +SEHVLGGYRVQGRGEGAAERLIASARALEDAGAFAVLMEMVPSDVAAAVDAALRVPTVGI +GAGPKTTGQVLVWQDMLGLGAGRTPRFVKRYADLRAVMGDAVRAYRADVLSGAFPDPAHA +FES +>MHAAABBN_01058 +MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV +LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES +AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG +AAERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM +LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG +>LFPAFLNI_01293 +MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV +LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES +AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG +AAERMTVSARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM +LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001043.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001043.fa new file mode 100644 index 0000000000000000000000000000000000000000..73794b43466653b1916a0c849cec0c721f585e12 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001043.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01555 +MDRQQDYVLRTIEDRDVRFVRLWFTDVVGTLKSVALSPAEVENAFAEGLGFDGSSIDGYT +RISESDMLLQPDPATFQILPWRGDGGQSSRMFCDVLTPDGRPAPADPRHVLRRVLEKASD +MGFSCFMHPEIEFYLLTSDQPGPDGRPVPVDRAGYFDNVPGSDAADFRRDAVTLLESMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG +SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG +GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHDPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>MOLHKGIG_01336 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG +SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG +GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI +EEGYEVPEAAAEDISALTTHERRVLGHVPLPGTLHDALRTAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>NAFOICDF_01451 +MDRQQDFVLRTIEDRDVRFVRLWFTDVIGTLKSVALAPAEVEAAFTEGLGFDGSSIDGYT +RISESDMLLQPDPATFQILPWRGEAGQTSRMFCDVLTPDGRPAPADPRNVLRRVLDKASD +MGFSCYTHPEIEFYLLASDRPGPDGRPVPVDSAGYFDHVPGGAAQDFRRDAVTLLEDMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVQTFRTIMKEVAARQGHYATFMPKPFGDQPG +SGMHTHFSLFEGDSNAFYDPADEFRLSVTGRRFIAGLLKHSVEISLVTHQFVNSYKRLWG +ADEAPAYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGLDASANPYLAYALLLAAGLKGV +EENYDLPEPASEDVGALTPQERRVLGHVSLPGTLHDAVRAAEESEFVADVLGEHVYEALL +RNKRQEWDDYRVEITPYELRRYMTGL +>MHAAABBN_01057 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +QGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG +SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG +GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>LFPAFLNI_01292 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQEQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG +SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG +GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001044.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001044.fa new file mode 100644 index 0000000000000000000000000000000000000000..8a57b57ed96893bdc098140ca30a4a20cd0e2890 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001044.fa @@ -0,0 +1,95 @@ +>ACLBLIBL_01556 +MSALPDAATADAPDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRAL +LLWVRLAEREPRVHRALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATA +PALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPRAGLTGADAAVALRRAYRRQLA +AIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIGM +GKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAA +GIGRVIQAAAPEPGLWEVDANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPI +AGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVLETIAPAEREREIKLGSGGLRD +VEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRIQ +LVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRP +LLSTTAALSDDEVRLSAEAVRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAM +LGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLAASRFVGDLLEH +SPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVALA +DISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYG +SDLDALFVHRPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGR +QGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTAD +AREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTL +PALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSG +VGTAGGELEERYLRVTRLARQVFEARFYGL +>MOLHKGIG_01335 +MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRA +LLLWVRLAEREPRVHHALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAAT +APALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPVAAVTGKDAAVALRRAYRRQL +AAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG +MGKCGAGELNYVSDVDVVFAHAVREAADGADPDAEVPDGPRAAALAAELAAGIGRVIQGA +APEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGER +YIAEIWPRVWESSSRDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQ +LVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRIQLVHLRRTHL +MPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALS +AEDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGAD +PDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVG +DDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLE +AVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVH +RPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLD +SYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKA +RVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARH +GLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELE +ERYLRVTRLARQVFETRFYGL +>NAFOICDF_01452 +MAPTPDSHVPGPRRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLL +YIRLAERDPQVHRVLAEADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPA +LAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPVAGLTGADASVALRRAYRRQLTAI +ALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIGMGK +CGARELNYVSDVDVVFVHDVLEPGAPDAPSAQEAARLAAELAAGISRVLSGPAPEPGLWE +VDANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPR +VWESSAREGFVENVRAMRTRVLDTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADE +SVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRIQLVHLRRTHLMPVKEGPR +RVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSA +DAVQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAF +RRLSESLGSSPWFLRMLRDSTDAARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPR +GLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTALADITGVVGLEEVGHALAD +VDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADE +TAAAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYAR +WAEVWERQALLRARVVAGPAGLAEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLP +RGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGTLPALRALARLDLLPPSEA +ALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVT +RQARQVFEQRFYGL +>MHAAABBN_01056 +MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL +LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA +PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA +AIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIGM +GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA +PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY +IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL +VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM +PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA +EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP +DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD +DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA +VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR +PRPGVDEGRAREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDS +YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAQDLSAADAREIRRIKAR +VEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGTLPALRAIARHD +LLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGGELEE +RYLRVTRLARQVFETRFYGL +>LFPAFLNI_01291 +MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL +LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA +PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA +AIALRDLDSAEPTAAMPSVGRWLADLAGAAVDAALAVSRAVLTEREGPVVDRVDLAVIGM +GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA +PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY +IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL +VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM +PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA +EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP +DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD +DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA +VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR +PRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDS +YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKAR +VEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARHG +LLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELEE +RYLRVTRLARQVFETRFYGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001045.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001045.fa new file mode 100644 index 0000000000000000000000000000000000000000..63dfc162996299c13f0dc8776a04239b3bacac0f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001045.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01558 +MFTSPADVLAYIKEEGIEFVDIRFTDLPGMQHHFNVPASTVDEDFFTTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVAAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>MOLHKGIG_01333 +MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>NAFOICDF_01454 +MFTSVEDVLAYIKDEGVEFVDIRFTDLPGMQHHFNVPASTVDEDFFVTGQLFDGSSIRGF +AGLAESDMQLIPDVTTAFVDPFRVRKTLAMNFSIVNPRTGEDYRRDPRGVAQRAEAYLAS +TGIADTAFFAPEAEFYVFDDVRYESSARSSFYRVDSTEAHWNTSRDEEGGNLGHKTPRQG +GYFPVTPVDKQADLRDEICAVLAEVGLEVERSHHEVGSAGQAEINYRFNTLTHSADDLQK +FKYVVKNVAEMFGKSVTFMPKPVFGEAGSGMHCHQSLWLGGEPLFYDEKGYANLSDTARW +YIGGLLQHASAVLAFTNPTVNSYRRLVPGFEAPVSMVYSQGNRSAGVRIPVTGSNPKAKR +LEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPPEEAADIQKAPTSLE +EALNALEEDHEFLLAGDVFTEELIRTWIDYKREMELTPLAARPNPYEFELYYSC +>MHAAABBN_01054 +MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>LFPAFLNI_01289 +MFTSPQEVLTYIREEGVEFVDVRFTDLPGLQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICAVLAEVGLTVERSHHEVGAPGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001046.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001046.fa new file mode 100644 index 0000000000000000000000000000000000000000..207117209f3afb5d2bddf756dd125c54b236ab30 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001046.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_01559 +MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT +AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR +LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM +>MOLHKGIG_01332 +MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT +AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR +LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM +>NAFOICDF_01455 +MSCVFPACNASSGPDYPGGVAHRASDPAPRDRSERDAAGRAEPLISRADLAGWIDGPGGG +RAGGRWPGDLLGLPEHGPASMATAARRAGALMIDWALALVVSNLAFGGDAIATLLVFAAM +HVVGLTLLATTVGKALCRIQVVREGTGGTAPVHRVLIRTALLCLVLPAVVVGPDGRGMHD +RVAGTVELHM +>MHAAABBN_01053 +MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT +AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR +LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM +>LFPAFLNI_01288 +MVAHYAGGVARRAPDPQDRTETTGRAEPLITRRDLAGWVDGPGGGRAGGRWPGDLLGLPE +RGPASMATAARRMGALVLDWFIALGISWLAFDADAIATLLVFAAMHVIGLTLLATTVGKA +VCRIQVVRVGGRPAGLLRILLRTALLCLVLPAVVVGPDGRGMHDKLADTVEIRM diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001049.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001049.fa new file mode 100644 index 0000000000000000000000000000000000000000..172a0f4d62f0adaa2aca61d2ddabf37b4eb2692e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001049.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01562 +MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>MOLHKGIG_01329 +MPETLLPPLRLLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>NAFOICDF_01458 +MPHALLPPVRVLGLAPDLIDYEEGWALQRTLHADVVAGRSDGEILLLEHEAVYTAGRRTE +DADRPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEEVLIRTAAEF +GVTAVRVDGRAGIWITAREGDPRPDRKLGAIGLSIHDGVSMHGFSFNCSNSLTPYETIIA +CGIADASTTTLSVETGREVTPVDVLPVLVRHLEDLGPEHIALTPTEGTPA +>MHAAABBN_01050 +MPETPLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>LFPAFLNI_01285 +MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001050.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001050.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd6776db441ea487cbe4ad7bdb8ee8bb05ba64db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001050.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01563 +MRDWDEADDGAVGRVGGGPETEPERTSELGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR +GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM +VQRVGPLSPGHAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV +GGASGAGATPGFAAPEALAAVQGAGAEPEASPAVGAPSDVHAWAALGWYALTGRAPGAAG +HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV +AHLLPTVLPGSGPTRRRRRRAGPGRRALVGRRGAAPRRGVLLAAGLATALAVGGGTAGLW +WPAAPGSAAEGAPAEGAPEPAGTEPTGTPVDAARPADGTPESGTPARATDTGAPGEDAAG +ADAVDVGEALAAVGQARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGL +EVTVEQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGED +PEARDGGAAGRTWRVETVDPR +>MOLHKGIG_01328 +MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR +GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM +VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV +GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG +HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV +AHLLPTVLPGSGPTRRRRGRRAAPRRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGL +WWPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAV +DVGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTV +EQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGR +DGGAAGRTWRVETVDPR +>NAFOICDF_01459 +MEAEDAERSGGVPPVGRPATDDWFADGGRDVSAWADPPRGGEGPAAVEPGVGDVGSPAEL +GPADRPPQAPGLRVVSRIGMGGQAEAWLVRREDGTECVLKVPRADGDPDAVAKEAAVYGH +LRHPHLLRVLGTVDTDRGTGVLSERLPAGSLASMVHDAGPLRPGQAVTVLVPVAQALAHL +HEHGVVHGDVSPGNVLFGVDGRPALADLGVARVVGGPRGRGGTPGFTAPEDEAGVGEGGA +AADVYAWGALGWFALTGRAPGPREHRAPLPVLVPDVPVELALLLSAALDPDPAGRPGAAE +AAVAAYDAAPPEPVPLHESAPAEVAHLLPTVVPPARPGGSGDARRSRPRAGGRRDAGRGR +GGRKRRNRSPRSRGWHPVMLVGAAVLAGTVVSAAVGGLTDRPEDQGEGAGSRAVAAPPTS +PTAAPANPRASVTPTGAADPKDAITPTRDGGVPSAAGTGPAAVLPAEDAAAALAAVAEGR +TAALTDPDPARVDAYAVPDGPAWRRDRAIQDQLREGGSAFSGLVVTLEAVGRPRPAEAGG +SGGAEAGWVVVPAVLRMSAHTVLDDAGSVVGEVPASEEDVSVTLVPGGEGRWRAAAVDPR +>MHAAABBN_01049 +MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR +GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM +VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV +GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG +HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV +AHLLPTVLPGSGPTRRRRRRAAPRRRALALRRGAAPRRGVLVAAGLATALAVGGGTAGLW +WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAVD +VGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE +QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD +GGAAGRTWRVETVDPR +>LFPAFLNI_01284 +MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR +GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM +VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV +GGASGAGATPGFAAPEALAAVQGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG +HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV +AHLLPTVLPGSGPTRRRRRRAGPGRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGLW +WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTRESGAPARVPDTGAPGEDAAGEDAVD +VGETLAAVGHARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE +QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD +GGAAGRTWRVETVDPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001051.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001051.fa new file mode 100644 index 0000000000000000000000000000000000000000..31cf19c5d1d9b0a1d089cbe0f79135ae7ac0c799 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001051.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01564 +MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN +HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ +>MOLHKGIG_01327 +MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN +HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ +>NAFOICDF_01460 +MEILHNVVVAIHIVSAAAIVGGWFAHFKNPTVTVSQWWGALGMILSGVVLFGWAMTGEPN +HMKLGIKFLIGVIVFIAALLGRRKANRGEVVPKGLAHAVGGMGLVNILVAVLWS +>MHAAABBN_01048 +MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN +HMKLGVKFLIGVIVFVAALTGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ +>LFPAFLNI_01283 +MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN +HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGMAHAVGGLGLVNILVAVLWQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001053.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001053.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7632283415159a544db7713203ed643cb0bfa7f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001053.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01566 +MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKLGGTCLHWGCIPTKAYLH +AAEVADETRNSAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLTGLLKMRKVQVIEGEGK +LVSKNEVEVDGTRYKAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVEVTIIEGLETLVPNEDPAIIKVLAREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGITMDRGFVITDERLHTGVGSI +YAVGDIVPGLQLAHRGYQQGIFVAEEIAGNSPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEKFGKDNVEVVEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHG +>MOLHKGIG_01325 +MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH +AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK +LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI +YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEEFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS +>NAFOICDF_01462 +MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH +AAEVADETRNAAKVGVNATLESVDMAKVRDYKDGIVSGKHKGLAGLLKMRKVQVIEGAGK +LVSKNEVEVDGTRYTAENIVLASGSVSKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKVFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI +YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS +>MHAAABBN_01046 +MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH +AAEVADETRNAAKFGINATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK +LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGSI +YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS +>LFPAFLNI_01281 +MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH +AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK +LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI +YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001055.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001055.fa new file mode 100644 index 0000000000000000000000000000000000000000..02336ddcc05bbc9bfe0b72dcd562078352f617b2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001055.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01568 +MQDAAPIYTRHDAEAVPPGLALLVTLTGHMDAGRVSRQVRTALREHLEHRTVASFDVDSM +FDYRARRPRMRFDRDRYRDLRLPTLEVQLVEDLIGHPFLLLAGPEPDFRWQAVVEAVLGL +AEEWQVDSLTFLDAAPLPVPHTRRIGVTTHGTRAEAVEGLSTWSPEAEIVSGLLQMLELR +ADEAGIPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASREIEAELE +RQVSGSEEVQQMIAGLERNFDQNAEDQERSLLETEEGLPDGDELASAVEAYLAGRAGPDG +SAPAQEDGPPRPSTDDER +>MOLHKGIG_01323 +MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM +FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL +AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR +AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE +RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG +SAPAQEDGPGRPSTGDGD +>NAFOICDF_01464 +MQDPTQLYTRHDAAPGDAVPDGLGVLVTLTGHLDAGHVGRQVGAGLRERLAHRTVARFDV +DQLHDYRARRPRIRFDRERYTDLRMPALDVELMEDLLGHPFLLVAGPEPDMQWGRFTAAL +LGLLQEWEASSATFLDAAPLPVPHTRRIGVTTHGSRADALEGLSTWSPEADVVAGLVQVL +ELRAEEAGLPTAGYTVHVPHYVAEAGYPQAAVAALEYAGASLDLMLPTDELRDAAREVDA +ELERQVAGSPEVQTMITGLEKNYDQNSEGQERSLLESHGELPDGDELASAVEAYLAERDE +SVQPRPTTPAQDDEGPAPSPDPQV +>MHAAABBN_01044 +MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM +FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL +AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPEADIVAGLLQMLELR +AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE +RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG +SAPAQEDGPGRPSTDDGD +>LFPAFLNI_01279 +MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM +FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL +AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR +AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE +RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG +SAPAQEDGPGRPSTGDGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001056.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001056.fa new file mode 100644 index 0000000000000000000000000000000000000000..8873d0ade8e2a45fc685dc4895b3c5e7a34f6141 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001056.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_01569 +MWLSQWESVLAGERGAAGPVTAEGTAPVSGTEEHPSADAAVLGAPLTLPSWRDALVLHAA +VRPGDPPPEPAERERFLIAGSEQAPPWERLDRLRAGLRRLVPAAPPPAAAQALALAGWVG +WARGQGSDAAAHLAAAAELAPDDPFVTLMRRVVDTGCVAGWAAHPDTAWRPGA +>MOLHKGIG_01322 +MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD +VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC +ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR +WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGDPGDEERILTAASGRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALSPDDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP +>NAFOICDF_01465 +MRPRTLEGMDHPPAVPSAVPAGVTPPHLPVLRARGVDDLLGYAFHVLGTEPRESILLVTL +ARARLRAVVRVDRPGRETPPAARHWAEAVAAVARRDAAADAVVCVSLTGRAGGLEPPGWW +PPLVRALRDRGIPAREGWGVVAGHAARWPVEPGAGPGPLEEVDPRHSDLSLHLIGAGSVW +GLRAGHRSVPTPAALDPAAPDRPHWTAARARPEAPGPWLAAWERVLDGGGLPERPAGRAR +LGAGLEHPARRDALLIAAAGAAADELPAAERAALLTGTRDPGPDWRRLDRLWDALRALAA +DAPAPCAAPALALAAWICWARGEGTAAGAHLDVARRLAPRDPLVGVLRRILDAGAVCAWA +ADPRRAWTPWDPQDPASGMRG +>MHAAABBN_01043 +MEAPTSLDAPVLPARGPEDLLAYVGHALGRLPEDSLVLLTLHDGRLRAVVRVDLPPEEVD +VDAWACAVAEVCRRDAAADATLCLALPDGARATLTRPGWAAALDDALASAGRPLAAAWTC +AHGRARPWWGSSIAEEGTLDPRAAPLSLHLMTRGSVWDRAAVSDPVPRRGPAAARPDDAR +WRPPEQDAPPARRAWLAQWEPVLTGTARGRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGDPGDEERILTAASRRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALSPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP +>LFPAFLNI_01278 +MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD +VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC +ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR +WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGEPGDEERILTAATGRAPAWDRLDALRAGLCALVPAATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALNPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGGP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001057.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001057.fa new file mode 100644 index 0000000000000000000000000000000000000000..784fd3632a17d25459f1ec1a789b2c23f0989d0a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001057.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01570 +MTTSTTNGAQDAPETTDSGAATTRSRSTAAKKTTAAKSTTAKGTAARKTASSTTAAKSTA +KSAAAKGAATKAAAKTAAADGEAPAKTTTRRTAASKTTAAKSTPTKPAAKTTTRKKAAPA +ATAKGKKATASAAAQAEQDEELADAVERTDAADAVDPDVADVVDGEAKAATEDSDDEDAD +GSDAPDAPAMDQEAVTGTKAGSGQAVAQTKGAFVMDDSEDDAPVQQVVVAGATADPVKDY +LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQAEASDDYRERRDIQLIIADGRKAKNHL +LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI +TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK +YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADVVSFTLLQEQLHSVLDTLSEREAGVV +AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD +>MOLHKGIG_01321 +MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAATKSATTKG +ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAAKTTAAVKTTAT +KKTATTRGKKATASAASAEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDEDAD +GSDAPERPAMDAEAVTGTKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDY +LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHL +LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI +TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK +YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVV +AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD +>NAFOICDF_01466 +MTAGTPTERPRVTTSTTSGKQDGKETAASTTTAAAAKKTTTAAKKKTTAAAAKKPAAAKT +ASGASTAAKKTTAKSTAAQATTTRGATTKKAAADAETEAAPAAAPRKRTSTATSTAKAAP +KKTTRAPKKTASKAVAEEELVEEEDLELDADDVAEQASQDGDDADADGSDAPAAEDLVAT +TEKPAETAAKGAFVMDNSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLAM +RIEAGLYAEHHFAENPPEDYRLRRDVELIIADGRRAKNHLLEANLRLVVSLAKRYTGRGM +LFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV +INKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEF +GDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKV +YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD +>MHAAABBN_01042 +MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAAKKSAATKS +ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAKKTATTGGKKAT +ASAASAEQAEDDEELVQARERTEAADAVEEDVVADETATEDSDDEDADGSDAPERPAMDA +EAVTGTTAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNA +EQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLA +KRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIR +IPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPL +GEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPK +TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD +>LFPAFLNI_01277 +MDCKDPRVAADETERPRVTTSTTSGAQDGKETTASGATTTRTRSTAAKKSTATKSATTKG +ATTRTTATKSAATKTAATPTAKKKAARKPAAAKTTATAKTTATKKTATTRGKKATASAGS +AEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDADADGSDAPERPAMDAEAVTG +TKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVD +LAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLAKRYTG +RGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHM +VEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGD +SEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEI +GKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001059.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001059.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5100245adb45efea70a28209b2a868b16aaabb1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001059.fa @@ -0,0 +1,66 @@ +>ACLBLIBL_01572 +MPANSEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGYGQSI +EITLHPDGSVEVEDSGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG +ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK +AKRGQTGTRVRYWADEQIFIKDAAFSADDLHARARQTAYLIPGLRITVKDLRRRPGTPGA +EGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGSFKERVPVLGEDGRTAMQDVQRT +CEVDLALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRTQVESNARRLKAGSD +KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVAQVVEKELTARLTATARAQ +KQQVHVLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE +GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVFAAVPPLHRIEAVTKGVK +EREVIYTYSEQELYATLARLEKEGRSYKEPIQRYKGLGEMDADQLAETTMDPRHRTLRRV +NIAEVEAAERVFDLLMGSSVAPRKDFIVSHADELDRERIDA +>MOLHKGIG_01319 +MSGPRSRLDRPLSSTERPAPVPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHC +LWEIIDNSVDEALAGFGQSIEITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLH +AGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRP +SPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL +IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFK +ERVPVLGEDGRTSMQDVQRTCEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAAL +LKVFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRI +VSQVVEKQLTARLTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP +AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILAN +AECAALIQVVGGGAGRSFDLDAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAG +RVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEM +DADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRARID +A +>NAFOICDF_01468 +MPANTEYSARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +DVTLHPDGSVEVADNGRGIPVDVEPRTGLTGVEVVFTKLHAGGKFGGGSYAASGGLHGVG +ASVVNALSSRLDVQVVRGGKVHQLSFRRGEPGRFQDGSRPTPDAPFEPAADAAPLDVVGK +AKRGQTGTRVRYWADEQIFTPDATFSMEDLQARARQTAYLIPGLRIAVTDLRRLTGTAGE +AGPVQEVYQYDGGIAEFVDHLTPAKPVTDVWRIQGSGTFTERVPVLGEDGRTQMQDVQRT +CEVDVALRWDVGYETVFRSFVNIIATPKGGTHQSGFESALLKVFRAQVEAGARRLKAGSD +RPDKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTPAVRRIVARVVEKELTALLTSTARGQ +KQQVGALLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVAASELFIVE +GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILSNAECAALIQVVGGGAGRGFDL +DAARYGKVILMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGKK +EREVIYTYSEAELHEVLARLEAEGRTYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV +TISEVEAAERVFELLMGSSVAPRKAFIVSNADELDRERIDA +>MHAAABBN_01040 +MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG +ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPAAPFEPSTDASPLDVVGK +AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA +DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT +CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKVFRAQVEANARRLKAGSD +KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARLTSTARAQ +KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE +GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK +EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV +NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA +>LFPAFLNI_01275 +MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG +ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK +AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA +DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT +CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRAQVEANARRLKAGSD +KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARFTSTARAQ +KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE +GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK +EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV +NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001063.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001063.fa new file mode 100644 index 0000000000000000000000000000000000000000..4fc0dc89f5f3d8413400995fd1840d03e4dfbf12 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001063.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01579 +MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI +NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV +PRRLHLAAIWCAVIGAHLSAYFILTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH +FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTDSKARDRLDHRVWI +TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG +DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA +PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA +ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL +LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY +>MOLHKGIG_01313 +MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI +NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV +PRRLHLAAIWCAVIGAHLSAYFIMTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH +FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTGSKARDRLDHRVWI +TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG +DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA +PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA +ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL +LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY +>NAFOICDF_01475 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVRTGREHYLRMTKFWGKLFLI +NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGMWIFGWDRL +PRRLHLAAIWCAVIGAHLSAYFIMAANAFMQHPVGYEVVDGRPVLNDIVAVLTNPIVLTH +FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDAEGRVVVGTTGSKARDALDHRVWI +TSLRAGAAVVIVGFLGTAFTGHAQAQQMIHYQPTKMASAEAACHDGTAFSVLTLGDVNTP +GATTCDDVTGVIEIPGLLSFLAYSDFTTPVPGITTLLPQFEARYGTQLPDDPMYGERAGQ +EISYLPLMEVTYWGFRLMITFGGLAALAGALTLWMTRKGTVPDSKPWMITAVASIGASFA +ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSGEEVLTSLIVFVVLYAVL +LVVEVALLARYVRGGVPAGMPELTADEHRDPDDDRHDRDDVLAFAY +>MHAAABBN_01036 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI +NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI +PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH +YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL +TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG +GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS +EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA +ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL +LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY +>LFPAFLNI_01271 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI +NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI +PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH +YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL +TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG +GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS +EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA +ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL +LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001065.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001065.fa new file mode 100644 index 0000000000000000000000000000000000000000..51848751bf10a41e956cfc1cc88e3fcd68d4338e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001065.fa @@ -0,0 +1,107 @@ +>ACLBLIBL_01581 +MTDDGAPRGPGREHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT +RMADTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR +RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV +PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR +GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL +RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD +ALADPTAAPARAADPAAAPRRAVVLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG +KSTLLHLLAGLLRTTDARVQGSVSGVDPERTVWVGQHPRLLEPTVGEELDAAAGRALADS +ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL +DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD +GAADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS +GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL +DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV +PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL +LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA +LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLLGEDEP +GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD +LRVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV +AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLERVGLGPWLAAAPEGLDTPVGAG +GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH +DERLAAEADVRLRLGVSPPRPSRGRPRPAAR +>MOLHKGIG_01311 +MTDDGAPRGPGRGHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT +RMAGTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR +RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV +PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR +GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL +RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD +ALADPTAAPARAAGPAAAPPGAVHLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG +KSTLLHLLAGLLRTTDARVQGSVSGVDPDRTVWVGQHPRLLEPTVGEELDAAAGRALADS +ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL +DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD +GPADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS +GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL +DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV +PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL +LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA +LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLMGEDEP +GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD +LCVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV +AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLGRVGLGPWLAAAPEGLDTPVGAG +GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH +DERLAAEADVRLRLGVSPPRPSRGRPRPAAR +>NAFOICDF_01477 +MTDRPPRRRGRVRAGRGPGPGLDRRARRAVGVMALLAGVRALGWILLAESLARLLTSLAM +TLDPEASAQLFQLLFMPPAPVGPVGPVADVAGVVVLGAAGVVLRALADQGQHVAGRRAAL +GAQVGIRRELVAHRLAATDGTRPRSGADAVLVTHGLAGLDDYYTEVLPALASAAVVPPML +GVWILTRDGVSAAVVLLTVPLIPFFMVLIGRHTQERIAAAQDGLDRISGQLLELARGLPV +LVGLRRAGVQRRALEKASERYHAATLGTLRTAFVSGLALELIASLSVAIMAVFIGVRLVY +GQMDLYSGLVVLVLAAEVYLPLREVGSAYHSSEDGRAAAERAAAAVAEPVPTPALASLAW +PGPETGQDHGTDGGMDDGMDDRTPAAGTVLLRDVSVSRGPRPVVRGADLTLRPGGLTVLG +SASGAGKSTLLHLLAGVLRTPDVAVSGTVAGVDSDRTLWVGQHPRFLEATVDAELDAAAG +GALAAPVRREVLRAAALADFGARAPHELSPGEQRRVALARAMSRLAADRTAVETRPWLVL +LDEPTAHLDDASAAVVRATVGALARGAVPGLPTPPAAVLAASHDPVLQRAADALVDVEGR +PLAPGADAAPYADPDAAGPPLAAGAPDDAGPGDAPDAPRGEGSEGRPSLRAVLAVLPWGA +PRLWAGVGWATLTHLAAALLAGLSGWLIVTAAGRPPILYLLSVIVLVRGFGLFRAVFRYA +DRLATHDAVLRWASELRLRLWDAMGRRPALWSRLSRADGALSVLLSDVDALRDAAPRVLV +PVPAAVLAWAVTALLIGGLAPELAVTALVPGAVGLLVIPVVVAALDRRDTLLTARRRAAL +LDRVSAVLGAAPDLHGLGRTREAAAALTAWDEDLQRPQRRAAWVAGLGRALAVLASGGAA +LAAALTATQTGTSTPVAAFVVFLALSWAEPLGALAQAAQQTGTLVDQARQAAGLLGVEDE +AASGATSAAPDEAAASAAGSSAPAGRITGVRLEDAAYAYPGSTRVLWSGLDVALESGQTA +AVTGPSGAGKSTLLAVLLGFLTPTAGRHLLTVERDGVSREAPADPAALARVAWTPQDALV +FDSTVRGNLALARDADDAPTDAELADTLRLVGLGRWLDAAPDGLDTPVGPGGDRLSGGER +QRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRRALAGRIAVVATHDPRVAAAAD +VRVRLGGDAAGHP +>MHAAABBN_01034 +MTPAALRALPALLALAVLRALGWILLAESLARLITGLAMTLDPEDSARLLDLLFHPPAPV +GPVPAAQTLSGPVLLGAAGVALRALAEAGQRVVGRRAALGAQQQVRAAVVAQRLAAADGG +RPRSGADAVVVTHGLKSLDDHYTEALPALAATAVVPAALGVWILTHDLVSAVVAAITLPL +VPLFMILVGRHTQERIDAAQDGLDRLAGHLLELARGLPVLVGLHRAGVQRRALQEVSQRH +HAATMVTLRTAFLSGLALELIASLSVAVMAVFIGLRLVNGQMALLDGLVVLILAAELYLP +LREVGAAFHASEDGREAESRARAAADAPVPAPVLDTLGPASGPDRDGGVLVQDLSVRMAG +RQVLEGLDLTAPPGHLTALAGPSGTGKSTVLRLLAGLLRQDAAEATGRVAGVDTERTLWI +GQHPVLTERTVAGELDLAAGGALPGPVRSAVLAAVALEGLQERDPADLSPGECRRVAVAR +LLARLHAADGTGPWLVLLDEPTAHLDGAVAAVVVETLAALPSGAVPGLSTPQCTVLAASH +DPTLLTAADAIVRLAPGAGPTAGSPATAMPVAAAQGRARPEPVTPRQVSLRAGLRLLPWR +QPKLWAGIGWAAGTHVSAALLAALSGWLIVTASTRPPVLYLLAVIVLVRGFGLSRAVFRY +LDRLTTHDAVFGWATELRLRLWDALGRQPRLWGRVGRTDGALSLLVSDVDAFRDAVPRVL +VPAPAALLAWLATAALTWALAPELAVVALVPGAVALVVIPALVAVLDRRQTAAQVRGQGA +LVDRVAAVLNAAGDLRGLGLTEPALRGLAVLDDRLQRPRRRAAWAAGGGRALAVAASGGI +AVAAAAAAAHTGTSAPVAALVVLLALSWAEPYGALAAAAQHWGTLADRARATGELLGPEE +GGAAAAPPEPAEAAEPEARVCRLRLVEAAFAHPGAPPLWTDLELDLAPGDVAVVTGPSGS +GKSTLLAVLLGFLPLTAGRYTLETVPPTPQPDPVRPDATALARVAWTPQDALIFDSTARG +NLALARGVADAPSDAELTAALELVGLGPWLAAAPQGLDTRVGPGGQRLSGGQRQRLAVAR +ALVARADVVLLDEPTAHVDADEARALITDLRRALADRIVVIVTHDGRLLEDGDVPVRVGC +>LFPAFLNI_01269 +MSPSRPAAPAVERSASAAGPHPGRTRRARPPMTPAARRALPALLALAVLRALGWILLAES +LARLITGLAMTLDPEDSARLLELLFHPPAPVGPVPAAQTLSGPVLLGAAGVALRALAEAG +QRVVGRRAALGAQQQVRAAVVAQRLAAADGGRPRSGADAVLVTHGLKSLDDHYTEALPAL +AATAVVPAALGVWILTHDLVSAVVAAITLPLVPLFMILVGRHTQERIDAAQDGLDRLAGH +LLELARGLPVLVGLHRAGVQRRALQEVSQRHHAATMVTLRTAFLSGLALELIASLSVAVM +AVFIGLRLVNGQMTLLDGLVVLILAAEVYLPLREVGAAYHASEDGREAESRARAAADAPV +PAPVLETLAPASGPDRDGGVVIRDLSVRLAGRQVLGGLDLSALPGRLTALAGPSGTGKST +VLRLLAGLLRQDAAEATGRVAGVDTERTLWIGQHPVLTERTVAGELDLAAGGALPGPVRS +AVLAAVALEGLQERDPADLSPGECRRVAVARLLARLHAADGTGPWLVLLDEPTAHLDGAV +AAVVVETLAALPSGAVPGLSTPQCTVLAASHDPTLLTAADAIVRLAPGAGPTAGSPATAM +PVAAAQGRARPEPVTPRQVSLRAGLRLLPWRQPKLWAGIGWAAGTHVSAALLAALSGWLI +VTASTRPPVLYLLAVIVLVRGFGLSRAVFRYLDRLTTHDAVFGWATELRLRLWDALGRQP +RLWGRVGRTDGALSLLVSDVDAFRDAVPRVLVPAPAALLAWLATAALTWALAPELAVVAL +VPGAVALVVIPALVAVLDRRQTAAQVRGQGALVDRVAAVLNAAGDLRGLGLTEPALRGLA +VLDDRLQRPRRRAAWAAGGGRALAVAASGGIAVAAAAAAAHTGTSAPVAALVVLLALSWA +EPYGALAAAAQHWGTLADRARATGELLGPEEGGAAAAPPEPAEAAEPEARVCRLRLVEAA +FAHPGAPPLWTDLELDLAPGDVAVVTGPSGSGKSTLLAVLLGFLPLTAGRYTLETVPPTP +QPDPVRPDATALARVAWTPQDALIFDSTARGNLALARGVADAPSDAELTAALELVGLGPW +LAAAPQGLDTRVGPGGQGLSGGQRQRLAVARALVARADVVLLDEPTAHVDADEARALITD +LRRALADRIVVIVTHDGRLLEDGDVPVRVGC diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001066.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001066.fa new file mode 100644 index 0000000000000000000000000000000000000000..0e631ed14d546c04ef3e061c394f53f5165b2c68 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001066.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_01582 +MSRSSRSRPSEQDVARPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLKP +VQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPVV +DGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAYP +NLLVNGTTGIAVGMATNMAPHNLREVVAAARHLLADPEADLEAIMAHIPGPDLPSGGRIV +GLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYAVGPEKVIERIKAGVDAKK +LSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQT +LGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDTA +AARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEARL +REVVSAELQAVADEFGDDRRTVLLEAETVAAPAASTVGGPTPAGAAQAGADLMVPDTACW +AVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDLP +AAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNRE +VAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVAA +DDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPAK +GRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRIE +AVGAGASPELLSAPPVADDPVTVSAD +>MOLHKGIG_01310 +MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK +PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV +VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY +PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI +VGLDGVRDAYATGRGTFRMRAAVDVEQVTARRTGLIVTELPYGVGPEKVIERIKAGVDAK +KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ +TLGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDT +AAARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEAR +LREVVSAELQAVADEFGDDRRTVLLEAETVAAPAASNAGGPTPAGAAQAGADLMVPDTAC +WAVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDL +PAAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNR +EVAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVA +ADDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPA +KGRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRI +EAVGAGASPELLSAPPVADDPVTVSAD +>NAFOICDF_01478 +MTTRSSRSRTAEADAPAPLPVEQENIVDVDVSQEMEASFLEYAYSVIYSRALPDARDGLK +PVQRRILFMMSQMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV +VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAY +PNLLVNGAAGIAVGMATNMAPHNLREVVAAARHLLAHPDADLEALMAHVPGPDLPSGGRI +VGLDGIRDAYATGRGTFRMRATASIEQVSSRRTGIVVTELPYAVGPEKVIEKIKDGVRGG +RLQGISDVVDLTDRKHGLRLVVELKSGFNAQAVLAALYRHTPMEESFGINNVALVDGRPR +TLGLRELLQVYVDHRMDVVRRRTVHRLGERRDRLHLVEGLLLALVDIDEVIEIIRSSDDT +AAARTRLMQVFDLSQVQAEHILELRLRQLTKFSRIELEAERDELAAAIAELEAILASDAR +LREVVSAELQAVADEFGDDRRTELVTADAAASVVSAPGEPALPAGTGPSDGGELMIPDTA +CWALLTTTGRLLRTVDRTPLAPQGRRRKHDAFVSVVPTTARGEVGALTSTGRVLRLQAVE +LPAAEESSPAPALTAARPAKDLVPLAKGESLVALVPLDAVLALGTAHGVVKRVRPEWPLN +RDELTAIALKDGDSVVGAAPAPDDGDHLVFVTRAGQLLHFAASQVRPQGPAGGGVAGLRV +GAEDAVIAFGVAPAASMTAEGEDPAAHPRPAVVVTVTDGDADLLGSAGGSVKVTPLGEYP +VKGRGTGGVRAHRLLKGETHLTLAWVGASPALAASKAGVARALPVEYGRRDGSGVPVDQR +VEAVGAGASPELVAAAPVDDSGVEVSAD +>MHAAABBN_01033 +MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK +PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV +VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY +PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI +VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK +KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ +TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT +TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR +LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA +CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD +LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN +RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL +AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP +AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR +IEAVGAGASPDLVSAPPAEDDAVAVSAD +>LFPAFLNI_01268 +MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK +PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV +VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY +PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI +VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK +KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ +TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT +TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR +LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA +CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD +LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN +RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL +AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP +AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR +IEAVGAGASPDLVSAPPAEDDAVAVSAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001067.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001067.fa new file mode 100644 index 0000000000000000000000000000000000000000..22802c2c43617f9b8b90b36a9566680ff1eba59d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001067.fa @@ -0,0 +1,85 @@ +>ACLBLIBL_01583 +MGDTEPVRDYPSHWEADVVLRDGATARLRPITPEDADELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHKDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAAREHGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAEARSVAELVAPESVAVVGASRDPQAVGSMVLRHILEGGFAGPVHAVN +RAAGEVQGLTAHASLAEIGEEVELVVVAVPVDQVEALVPEAAAAGAAGLLVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAVRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGAKRRGVGVSTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFT +RITRRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGAVDSMLDQTGVLEVHTHEAMLD +LLMAVASQPLPTGRRVVLVADSLAVDRLARDAAAEAGLDVVATVGLAGSEQGVAPPAETL +VASVREAVAHEQADAVVVVGRLGLHQEDDDPETVARALAEATAGARMPVLVCLTDVVSPR +YAGATLGASGPVADDAEPGSLQPGVPFYPSPQQAMSVLGALADYVRWRGEEAGEPLEPAD +VRLHAAEDLVEAAAARAEGTELVRLSAAETEELLGHYGIAVLPSARFETADEAVAAAERL +GFPVAVKAVDPHLRHRLDLGGVRLNVVDAASLRRNVEQMRRVLAPFGVTELEVQAMAPAG +QACMVTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAAKLEGR +GGVPAVDLAALEDLVGRVSVLKDDLPQVARLRFSPVLASPEGVTVLQAEVDVANAAGRTD +SARRALRGS +>MOLHKGIG_01309 +MGETEADRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAAAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGTVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASTGLVRTDPAIRLNASPSPGLAQRGPVSLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPADTL +VSAVRDAVCHEQADAVVVLARLGLHQADDEPERLAHALADATREARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMAVLGALADYVHWRHQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSVRFETAEEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPPVDLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPERVTVLQAEVHVANAARRTD +SARRALRGR +>NAFOICDF_01479 +MAEPDTETAYPSQWEADVVLRDGATARLRPIREDDVDGLRALHAGQSESSIYLRYFTFKS +ELSAKELERFTHVDHRDRVALVIERGGRILGVGRYDRYGDSDAAEVAFNISDAAQGQGLG +SILMEHLAVAAREQGIRRFTAEVLPENRKMLSVFQDSGFEVARHFEDGVVAVEFPIDPTA +RWRAVVESREHRAEARSVAELVEPESVAVVGASRDPHAVGSIVLRHILEAGFTGRVHAVN +RAAEDVQGLTAHASLKDIGEPVDLVVVAVPVAEVDAVVAEAAEAGAQGLLVLTSGYADAG +EDGLRAQRRLVARARARGMRVIGPASAGLVRTAPDVRLNASPSPGLASRGPVGVFSQSGA +VGAMITAGMKRRGVGMSTSLSAGNRADVSGNDAMQFFEDDPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRALPPGHETRTTQAPEGAVDSMLEQTGVLEAATHEDMLD +LLMAVATQPLPTGRRVTLVADSLALDRLGRDAAAVAGLEVVATHGLGGSEQGIAPTADDV +VASVEAALAAGDTDAVVVVTRLGLHQDEDAAHEVAQALARVAEGATVPVLGCLTDVVSAR +YGGARVGGAAAPAADAEPGALQPGLPLYPSPRKAMTVLGRLCDYVAWRREDAGEPIELTD +VDVRAAEALVDRALERALGTELIRLTGAETEELLRIYGIGVLRSRRFTTPDEAVAAAEEL +GFPVAVKAVDPYLRHRLDLGGVRLNLEDAESLRQNVRQMRAVLAPFGVTELEVQSMAPSG +QPCMVTALEDPLLGPVVSFGMAGDATDLLGDWVHRVPPLTDQDVRRMVRSPRAAVKLDGV +GGVPAVDLDALEDLLARVSCLKDDLPAVARLRFAPVLAAPTGTTVLSAEVDVANAAGRTD +SARRALRAS +>MHAAABBN_01032 +MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL +VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD +SARRALRGR +>LFPAFLNI_01267 +MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL +VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD +SARRALRGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001068.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001068.fa new file mode 100644 index 0000000000000000000000000000000000000000..51578fdbd77e5173a1bcc2ce3b4183fc721b3cda --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001068.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01584 +MEPMSPFRRSHESGRPEHRPGAPASGEHRHEARTLEGAGGLGASLARAGFYPELVAHAIA +VELGERTPDAHLVHVDTHFDYEEIHRHITVLVLAQDALLAVHLDDHAADAAGQAVLAQVS +TEMVPVRALGSVVLTTGHADPARFSPADPVAEMTLALIWAGGQRLDLQPAGCADPQCDLD +HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATA +>MOLHKGIG_01308 +MGDMSPFRRSHEPGRPDHRSGTPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA +VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS +TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD +HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT +>NAFOICDF_01480 +MEGMTPLRWNNHDDSASDGRRPAGEVRRTRQTVDATGTLEQALARAGYYPELVSHAVALE +LEGRTVHAHLVHVDTHFDYEEIHRHITVLVVADDVMLAVHLDDHAADPAGHSVLAQVATE +MVPLRAIESVLITTGHATPERYRPTDPVAEVTLGVQWAGGQRLDLQPAGCADPQCDADHG +YTGTSVREDLVIRVAADAEGQGAVDAALAFARTLRRVHLAAVA +>MHAAABBN_01031 +MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA +VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS +TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD +HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT +>LFPAFLNI_01266 +MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA +VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS +TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD +HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001069.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001069.fa new file mode 100644 index 0000000000000000000000000000000000000000..a408968b63ed23aeeb2cf03dfece16bbdaaa4e1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001069.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01585 +MSGPAVPVGVVPPERALRSVLTSAAAALGVPGCENALGVPASRRVVVALVDGLGRSVLKR +FGGHAPTLRAAMADGGRVLQAAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPERDAVVN +QLGGWDEATDPVAWQPRPTVFERAGAAGVDAVTVSLPAFEHSGLTRAGLRGGRFVAGRGL +LARAQAAERVLKDAREPTLVYFYVNELDKAGHRDGVGSDRWLHALEEIDGALRRLVDRVP +AGTVVLATGDHGMVDVPPTRRVDYAAADESGALADPALLEGIAHTAGEPRLVQLHFRPDA +DADVRARVRRAWEDRFGAHAWVLTRDEAVAAGWFGTVVEERVRGRIGELLVAVHGDLALY +DGRRVAPHAFEMVGQHGSPTRAEREVPLLTWRR +>MOLHKGIG_01307 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERALKDARVPTLVYFYVNELDRAGHRDGVGSDRWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADAALLEGVAHTAGEPRLVQLHFRSDA +GPDVRARVRRAWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR +>NAFOICDF_01481 +MTGPDAAAPAGPGLPPGPVPPERALRSVLTSAAAALGVPGCANALGVPVTRRVVVALVDG +LGRGVLKRFSGHAPTLRAAMADGGRVLTAATPTTTAASLTSLGTGLDVGEHGVAGYDVLD +PDRGVVVNMLGGWDEATDPLAWQPHPTVFERAVEAGVDAVTVSLPEFEHSALTRAGLRGG +RFVGGRGLLARAGHAERVLADACVPTLVYFYVNELDKAGHRDGVGSRSWLHALEEVDAAL +RRLVSRVPAGTVVLATGDHGMVDVAESRRVDYAALGDDGAPVRPGLLAGVAHTAGEPRLV +QLHFAPTATPAEREGTRRAWEDAYGDQAWILTRDEAVAAGWFGERVADRVLPRIGDLLVA +CHGELALYDGRRVSPRAFAMVGQHGSPTRAEREVPLLTWRR +>MHAAABBN_01030 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLVQLHFRSDA +GPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR +>LFPAFLNI_01265 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLVQLHFRSDA +GPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001070.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001070.fa new file mode 100644 index 0000000000000000000000000000000000000000..efc8df023d2cad92c24ec14e643f355be75b350f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001070.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01587 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDETEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREKNGMTYCTDCEG +>MOLHKGIG_01305 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG +>NAFOICDF_01483 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDETEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREEGGLVYCTDCEG +>MHAAABBN_01028 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG +>LFPAFLNI_01263 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001071.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001071.fa new file mode 100644 index 0000000000000000000000000000000000000000..f07a3dc92f52b29f55d6dd62d5f2f479d0ef4b0b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001071.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01588 +MREPQQHPVSDAPVDRPQDPAQGSDRVLFEERLTPSAGVWVVALMLASLTILVFAPIDLW +FGVAAAVVFFGLEALLLLTTTPRIVVRERTLQVGRASIERRHVGEVTGHRGEDARRQRGP +LLHGLAYVVVRGWISPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMVQEDPADEDR +>MOLHKGIG_01304 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR +>NAFOICDF_01484 +MQDASATPDHHAPRTVAASADPVQYEERLSPSVGVWLVALLLAGLCIFVLAPVALWAGFL +AAAVFFVVEAVVLLASTPRIVVRERTLQVGRAQIERRHLGAVTGHRGEAARAQRGPLLHG +LAYVCVRGWISPVVRIQIEDERDATPYWLASTRHPEDLVAALGGRMAGEG +>MHAAABBN_01027 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR +>LFPAFLNI_01262 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001072.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001072.fa new file mode 100644 index 0000000000000000000000000000000000000000..fb77876b871544a4c1ae0df8a7465791538a2e2f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001072.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01589 +MTDSAELPVPLHALDPDLAPPAYAQPGDAGADLRAAVDVTLAPGERALVPTGVALAIPEG +FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTDAVELRRGDRIAQLVI +QPVVRARFAPVDALPGSERGAAGFGSTGGFGTENAPGRTS +>MOLHKGIG_01303 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS +>NAFOICDF_01485 +MNGPREIDVPLRALDPQLPPPEYARPDDAGADLRAAEDVTLAPGERALVPTGVALAIPAG +FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPVVLRRGDRIAQLVV +QPVVQARFMAVDRLADSERGEAGFGSTGGFTPAAHDDAPGRTA +>MHAAABBN_01026 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS +>LFPAFLNI_01261 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001074.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001074.fa new file mode 100644 index 0000000000000000000000000000000000000000..2e68db4159156309c50dc5c98a0369ade5cc0ccb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001074.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01591 +MSPAAGERADAGPGDLIERRGVVASVTLPGADDATVFRAALADRLPEPGSVTPAESLQLV +WHGRRRVPGVMPGQWLAVRGRLTRPDGVLTLHNPAFDLIDAPEAALRARPPREESP +>MOLHKGIG_01301 +MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW +HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR +>NAFOICDF_01487 +MSPRRTPAPAGERPAGERVGVVVAVTFPGADDATVFRAALADDLPAPGRPEPQEVLHLVW +HGRHRVAGVMPGAWMRVLGHPVAVAGEPTLFNPEFHLIDDEGGPA +>MHAAABBN_01024 +MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW +HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR +>LFPAFLNI_01259 +MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW +HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001076.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001076.fa new file mode 100644 index 0000000000000000000000000000000000000000..e1a77e7c006fc0c95786cd87d58082bfd82ca668 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001076.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_01593 +MRAVIAGAGAVGASVARELHAHGHEVVVVEIRPDAAHKADVGGAKLVLGDACDLALLERC +GAMEADVLVAATGDDRANLVCSLLGRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVETGDLVRLLRLEAGGAVLSEFRVPAEHWLAGRRVGTVSWPQDAPLVAVV +RDGVPRHATADEMLEAGDELFFLAAAAADAALRRLLVGEDRAQARPGAGSSSAAGRRPSS +SPGAGALTDQASQSPRA +>MOLHKGIG_01299 +MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC +GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV +RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS +>NAFOICDF_01489 +MRVVIAGAGAVGSSIARELHAHGHEVSVVESRADAAARSDLAGARTVLGDATDLGVLGRA +GALGADVLVAATGDDRANLVASLLARSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVESGDLVRLLRLEAGGAALTEFRIPSGHWLRGRRVGTVSWPAAAPLVAIV +RDGAPRSSTPDEVLEESDELFFLADAEAEGALRRLLVG +>MHAAABBN_01022 +MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC +GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV +RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS +>LFPAFLNI_01257 +MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC +GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV +RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001080.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001080.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7b1970b6ef5f8db1cc2f4a7fd533e8913dc9ab3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001080.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_01597 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAEKLPYSLKVLLENLLRTEDGANVTAEQIK +ALASWNPDAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE +LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPAGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG +NMSPEFGSTAAMFPIDEVTLDYLRLTGRTAEQVDLVEAYTKEQGMWHDPSSEVKYSEYLE +LDLSTVVPSISGPKRPQDRIELSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVSMEDGRQ +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDSEGNDVFLKDIWPDPTEVQKIID +ESIDTEMFTSQYGTIFDGDERWQSLETPSGSTFEWDEQSTYVRKPPYFEGMTMQPDAVSD +ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGKYLLENGVERKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGSGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS +GITALNEGTTPKTVKVTATGGDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA +>MOLHKGIG_01295 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK +ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE +LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG +NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE +LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID +ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD +ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS +GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA +>NAFOICDF_01493 +MTTVDSFGSKGVLDVNGSEYEIFRLNAVEGAQKLPYALKVLLENLLRTEDGANVTAEQIK +ALASWDPTAEPDTEIQFTPARVIMQDFTGVPCIVDLATMREAIADLGGDPSRVNPLSPAE +LVIDHSVQIDSFGNDAAVERNMDIEYQRNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARAVMVRDVDGVKRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGQIPAGATATDVVLTITEQLREHGVVGKFVEFYGEGVGAVPLANRATIG +NMSPEFGSTAAMFPIDDVTLDYLRLTGRSEEQVALVEAYTKEQGLWHDPSAEVQYSEYLE +LDLSTVVPSISGPKRPQDRIVLSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVHMEDGRE +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLTAKPWVKTSVAPGSRVVTDY +YEKSGLNASLDALGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDCDFENEALGTDQDGNDVFLKDIWPDPAEVQRIID +ESIDTEMFTSQYGTIFDGDERWQSLETPTGKTFEWDEASTYVRKPPYFEGMPAQPEPVQD +IAGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGTGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPAGESADSLGLTGTETFAIS +GIAELNEGRTPKTVKVTATAEDGKVTEFDAVVRIDTPGEADYYRNGGILQYVLRQIAAKA +>MHAAABBN_01018 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK +ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE +LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG +NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE +LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID +ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD +ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS +GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA +>LFPAFLNI_01253 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK +ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE +LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG +NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE +LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMADGRQ +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID +ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD +ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS +GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001082.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001082.fa new file mode 100644 index 0000000000000000000000000000000000000000..10e4d3b7e8ccde22dbf4d648b4544e83cab99802 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001082.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_01599 +MSIVRLYRETTNEDGSRLFEYREAWADVEGGEFVVHHGRVGHPGTVGEQPLADEAEGEEL +LAAFLAQGAEEGFAEADPAGFALLPVAFRLRGREASDIERRNVEHLRVEVTHQLAWRGLG +EVEDVTEEPGALVLAVRTPHARKAAAEIPVAARRADGVQPNKVEVRSAVQED +>MOLHKGIG_01286 +MSIVRLYRESVGDDGARLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQAEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATAIERRTVERLRVEMTHQLAWRGLG +EVEDVVEEVGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG +>NAFOICDF_01495 +MSISRLYRDRTEEDGRRSFEYREAWIDPSGELFTVHHGRVGHPGTVGDQPLTSEAEGAEL +MDAFLAQGEADGFAPADEDAFDVLEVAYRLRGRAITEIERRHGRTLREEVTHQLAWRGLG +EVTDVVDGDGELVLVVRTPHAPKAAAEVPAAAKRAHGIQPNKVEVRRVDAPRTPAGAAPD +ADGEG +>MHAAABBN_01005 +MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG +EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG +>LFPAFLNI_01244 +MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG +EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001087.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001087.fa new file mode 100644 index 0000000000000000000000000000000000000000..3bff0ecb59a7e5b118bcd06890531183bc861470 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001087.fa @@ -0,0 +1,69 @@ +>ACLBLIBL_01605 +MTFTPAPLAPFESLLPLVPDEVLTHVAATDHVLPGGAGTLVLLTLDNGQGPRRPATLGPA +SLLELGRAVDAQAERARAGEVQALALTGVEGTFAAGADLSLIAGIEDRTVGRDLARLGHA +VHDRIDAFPAPTLALVNGTALGGGLELALAADHRVVAADARGFGLPEVRLGLIPGWSGVW +RVPHLIGPEAAVEVVLKNPLDNNRMLDARTAHGLGLMDEVAEGDLLEAGLAFAARIVAGD +DAALAAVRDHRDRDVSDAAWDRALEAMEALQAGRPGRDLPARRALQELFAGARTRTREES +AEAEAEALHGLIGSDEFRRTVYAFLDLLQRRAKRPVGDPGKELAREVTKVGVVGAGLMAG +QLALVFAQHLRVPVVMTDMDQERVDRGLAGVRGQVEKMVSRGRITAEQGEALAGLITAST +DKSVYADADVVIEAVFEELEVKRTVFRELEPIVREDAVLMTNTSSLSVAAMAEVLEHPER +LVGFHFFNPVAQMPLIEVVRVAETSDEAVATAFELSRRLRKTGVLVHDAAAFVVNRVLLR +MMGEVQASFDEGTDAHTADHALDPLALPMTPFTLLAMVGIPVAQHVSESLQAAFGAERFP +VSANLQRLIDAGKTAIWAKDVRRDKVEEEAAGATGETIPAGTAALIERGSSPQTAEELRR +RVEDALAEEIGLLLAEGVVAAPEDVDLCMILGAGWPLHLGGITPYLDDCGAAERVNGTRF +HG +>MOLHKGIG_01281 +MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL +LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIASITDDVGRDLALLGHAVYD +RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP +HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVTGDESV +AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEALFTGARTRTRAESAQA +EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA +LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGQALAGLITADTDKA +VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLERPERLVG +FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG +EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA +NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE +DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA +AQA +>NAFOICDF_01500 +MSHTPAPLDQFEHLSTIAPDEILTRATATDHALPDGAGTLALITLDNGQGPRRPATLGSA +SLLELARAVDEQAARASAGEIQALGITGVEGVFAAGADLALVASLPADAETGRALGRLGH +AVYDRIDAFPVPTVALVNGTALGGGLELALACDRRVIAPEVKALGLPEVRLGLIPGWSGV +WRAPHLVGPEAAVALLLTNPLDNGRMIGAADAVRLGLMDSLAEGDLLAAGLTAAADAVAG +RTVQRTADVSDAAWDRALQAFGAAQSARPGRDLPARRHLEELFAGARTRTRAESAEAEAD +ALADLIGSAEFRRTVYAFLGLVQGRAKRPAGDPGVEQAHTVHRVGVVGAGLMAGQLALLF +ATALRVPVVMTDLDQERVDRGLAYVRSQLERSVTKGRMKAEDAEAVAGLITGATDVSAHA +EAEFVIEAVFEELEVKRTVFRQLEQVVSPTAILATNTSSLSVAGMAEVLEHPERLVGFHF +FNPVAQMPLVEIVRVAETTDAAVATAFELARRLRKTAVLVNDAAAFVVNRVLLRMMGEIQ +NSFDQGTDAHTADHALDPLAFPMTPFTLAAMVGLPVAQHVSESLQAAFGAERFPVSENLQ +RLIEAKKTAIWAKDVKSPEEAGGATGETIPADTAALIEQGDTPQTADELRVRVEDALAEE +IGLLLDEGVVAAPDDVDLCMILGAGWPLHLGGITPYLDDCGASERVRGARFHQA +>MHAAABBN_01000 +MTSVSLASFDHLPALAPDEVVTTVTVTDHALPDGAGTLALLTLDNGQGPRRPATLGPATL +LGLGRVLDEQAARAAAGAIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD +RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP +HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV +AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA +EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA +LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA +VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG +FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG +EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA +NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE +DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA +AQA +>LFPAFLNI_01239 +MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL +LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD +RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP +HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV +AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA +EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA +LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA +VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG +FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG +EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA +NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE +DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA +AQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001088.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001088.fa new file mode 100644 index 0000000000000000000000000000000000000000..b93d68ee1cfefac9dce4a352d4f68ea29c89c575 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001088.fa @@ -0,0 +1,42 @@ +>ACLBLIBL_01606 +MTDVPEPAEPDATPRLIAEPADGVPRVTDTPAGLEACAAALAAGTGPVAVDAERASGIRY +GQRAMLVQLKREGAGIWLVDPEALDGLEPLQEALSGVEWILHAASQDLPCLAEQGLRPDR +LFDTELAARVAGLPRVGLAAVLESMLGVTLAKEHSAADWSVRPLPEAMLAYAALDVELLV +PLRAAMLELLEAEGKREWAEQEFEHVRTAPAPGPRADPWRRTSGSQTLRRPVQRAVLKRL +WEAREDLARHRDVAPGRLIPDRSLIAAAESQPRTVPALRQTSGFHGRAASREAPPLDHRD +PRRRRGRRARRRPARPGARRGRPAPAPGVEGPRPARRPPPEDRQGARGPARRAAGPAHGE +PAHPGHPAPALLGAAAAADARGRGRVPPRARGPALAGGPGGRGGHRGPAGPGPRRGLSRG +GRRADAAVGRGPTHR +>MOLHKGIG_01280 +MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY +GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR +LFDTELAARVAGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV +PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL +WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI +RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN +LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA +>NAFOICDF_01501 +MTSPTSPAVATSPDPSDRPGGEQAAPTLVAEPAGGVPVVTDTPAGLAACAAALAAGTGPV +AVDAERASGIRYGQRAFLVQLKRAGAGIWLVDPEAFEDLAPLDEALRGVEWVLHAASQDL +PCLADCGMRPDLLFDTELAARLAGLPRVGLAAVLESQLGLTLAKEHSMADWSTRPLPVDW +LNYAALDVELLVELRDALAVLLEEQGKLAWAEQEFEHVRTTPPAAPRQDPWRRTSGMAAL +KRPVQLAVLRRLWQAREDLAQHRDLAPGRLLPDSALVAAASTLPRTVPELRATRGFHGRS +AAREAPRWITAIRAGIEDAAAGQAPPRHGPGSDAPPPPRAWRDRDPLADRRLTTAKPRIA +RAAEALGMPPENLLTPDTLRRVCWTPPETITPETVAAALAERGARPWQVEQTSAIITVAL +LDPDPARDR +>MHAAABBN_00999 +MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAIDAERASGIRY +GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR +LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV +PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL +WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI +RAGVEDAERDDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN +LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA +>LFPAFLNI_01238 +MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY +GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR +LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV +PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL +WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI +RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN +LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001089.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001089.fa new file mode 100644 index 0000000000000000000000000000000000000000..e90e76a90e4967dea10ffdffb4c9691796ea7a0c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001089.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01607 +MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH +AVALAAEVCGSPGADDVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLAG +AVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLGA +HLEAWSDMIGAFAGLPPR +>MOLHKGIG_01279 +MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA +ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW +TWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA +WSDMICAFAGLPPEHAADVHTAGP +>NAFOICDF_01502 +MTESGPRAPAPAAGGASGAFADALADLRAAHPRPEVRLRPIPDPPGLAPFAVTLAADVLD +PHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLAGAVAWDWLAE +ALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLGAHLEAWSDMI +CAFAGLPPLADDDVPAAVPLRP +>MHAAABBN_00998 +MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA +ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW +TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA +WSDMICAFAGLPPEHAADVHTAGP +>LFPAFLNI_01237 +MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA +ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW +TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA +WSDMICAFAGLPPEHAADVHTAGP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001091.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001091.fa new file mode 100644 index 0000000000000000000000000000000000000000..f77fdbf591cf2009f377ac5bb1242d78a0ff7f17 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001091.fa @@ -0,0 +1,44 @@ +>ACLBLIBL_01610 +MRTGVKAASPLARWTPPVLSVLASSAFVLAGASSALAGVFARTVVTPVRRHTETTAVLAV +VDTPTGPEVILKADEYTTVPGVYSLTFDGGAGCARIGRISSFDPRDGTVQRVVEEVYFGD +LAAATRGRLTGFVYPTPADAGLDAEEVLVPVPGGHAPAWLVGPDPDDDGAARPAAGIWAI +MVHGRGARRNEGIRTVPTAQRLGMTSLLISYRNDGDAPDAADSRYGLGTTEWEDVEAAIR +YALDNGASDVVLFGWSMGGAVVLQAVDRSDLAPQVRGVVLTGPVVDWVDVLQHQARLNRI +PEAVGVLGQWLLSNRAGRFITGLAAPVDLKSLDWVTRAEHVRVPTLIIHSEDDEYVPVGP +SQDLAERNPGLVRFVRFHQARHTREQNVDPKRWDTTVRGWLRAVLNADRPGAAER +>MOLHKGIG_01277 +MAARPRRPRPHPADLPPALAAAVTVAARRAGSRESRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAAYAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIAPYPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSALAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTAVRGWLRAVLSAPRPGGRGR +>NAFOICDF_01505 +MACPRRHSPRLRARPDLRDALLGSLRGSAAVARPAARLAPAAASVAASAAFVLAGASAGL +AGVFARTVVTPVRSRPEHTAVLAVLDTGDGMDVILPADEHTTVPGTYSLTFHGGEGCARI +GAIRSYDPRDGTVQRVVEEVYSGDLRSAVRGRFTAFIWPGPAEAGLEAADVEVPVPGGAA +PAWRIDPPPAEDGEERAGEGMWAVMVHGRGAVRNEGLRAVPTAARLGMTSLLVSYRNDGD +APDAEDARYGLGTTEWEDVEAAVRYALDHGARDVVLFGWSMGGAVVLQTADRSDLTSRVR +GIVLTGPVVDWMDVLRHQARLNRIPEGIGLLGQWLLSNRAGRLVTGLAAPVDLKALDWVT +RADHVRVPTLILHSEDDEYVPVGPSQDLAERNPALVRFVRFHQARHTREQNVDPVKWDRS +VRGFLRAVLTAPRPGAVSPPGAPQAPSGSSPRRRSSGSSSASRPRNAR +>MHAAABBN_00996 +MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR +>LFPAFLNI_01235 +MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001093.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001093.fa new file mode 100644 index 0000000000000000000000000000000000000000..2fce2f6caebd594a95cad0db25b4a69be62805d8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001093.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01612 +MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGADLAGNPALDLAVSKAKKAS +VPNDNIDRAVKRGAGLTGEVVDYAEIMYEVRGPQGSAVLVECLTDNKNRAAAEVRTAVTR +NGGTMADSGSVSFLFTRQGVVRLPAEGRTEDELLEAVIEAGAEEVVLSGDEFEILSDPSD +LRAVAEALDAAGIDYESDETEFVPTMKVELEDAKGAGTFLKLADALEELDDVQNVYSNVD +ISPEVLAELDQD +>MOLHKGIG_01275 +MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS +VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR +NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP +SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV +DIAPEVLAELDED +>NAFOICDF_01507 +MSGHSKWATTKHKKAVIDQRRAKAFAKYIKGIEVAARAGGADLSGNPALDLAVSKAKKNS +VPNDNIDRAIKRGAGLTGEVIDYTEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR +NGGTMADSGSVSFLFHRKGVVRLPAAGNTEDSLLEAVLEGGADAEEVVLSGDDFEIVSEP +GDLRAVAEALDAAGIDYETDEMEHLPTMKVELDAKGARTFLKLADALEDLDDVQNVFSNV +DIAPEVMDELEQD +>MHAAABBN_00994 +MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS +VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR +NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP +SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV +DIAPEVLAELDED +>LFPAFLNI_01233 +MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS +VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR +NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP +SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV +DIAPEVLAELDED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001095.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001095.fa new file mode 100644 index 0000000000000000000000000000000000000000..863f13bd68669dbfb1a6f89cf04c51f4688b4cf4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001095.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01614 +MIASLSGTVEHVALDRAVIAVGGFGVQFSATPQTLATLHEGRTGSVQTHLVVKEDALTLF +GFADRHEREVFEVLITANGVGPRLALAVLSVHHPEAVRRAVTEEDENALTRVPGVGPKLA +RKIIVELSGRLTPTGEQVPAPEEPAAPETPEAAWHADVVQAMTGLGWSEKEALKAVEATV +AARPELDEARDVAALLRATLRDVGTAGTVRGGR +>MOLHKGIG_01273 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLSTLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR +>NAFOICDF_01509 +MIASLSGTVEHVGLDHAVIAVGGVGLSFSATPQTLSHLHEGRDGAVQTHLVVKEDSLTLF +GFADRAEREVFEVLLGANGVGPRLALAILAVHRPEAVRRAVTDEDEKALTLVPGIGPKMA +RKIIVDLAGRLAPTGEVEPEAAVVEPEAAADAWHADVVQAMTGLGWSEKEAAKAVAATVA +THPDVDASGDVAALLRATLRDVGAAAAVRGGRRA +>MHAAABBN_00992 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR +>LFPAFLNI_01231 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001097.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001097.fa new file mode 100644 index 0000000000000000000000000000000000000000..3de700e442b08e29ade655858ff0d0c936122d3b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001097.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01617 +MAKRTPTGSARRTLAWLAALTVALTAILGWGVASGAASWAPKLALDLEGGTQMVLAPETA +TGESVTSEQLDQAVEIIRQRVDGSGVAEAEVATQGAENVVVSLPGVPDEETRRLIQASAD +MQFRPVLQSGSGEATPEDQRLPEDQLPQPEGEPADAYDPNWVTPALLTQYQALDCAAPRD +PAAPPPPSDQAIVACERPADLGEGVQTPARKYILGPVVIPGTQIEGATNGLAQAQSGVST +NQWVVNIDFDEEGAKTFSEVTQKLTPYPDGDPRKQFAILLDGDVISAPQSNAVITAGSAQ +ISGPTLNEETTAQLAEQLNYGSLPISFSIESEQQISATLGQDQLFWGLIAGLIGLALVAV +YQFFQYRALGLLTFASIVVAGILTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRAGHSVPMAVHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLIVVFMFTHPIMVLLAQTRFVGGGHRMSGLDPSLLDRQALYQGAGRLREPGGAR +RTGSTAAPAADVAADDGARVPVPVGAAPADEASGEEGTATRGLRRPRPAQPMTIAERRRA +ERRRQEEDQ +>MOLHKGIG_01270 +MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS +TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD +MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD +PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST +NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ +ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV +YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP +RTGLPAEASDEPADADDAAAADAPRPLAATGAPRAGSSARGGRRSRTAPPMTIAERRRAE +RRRQEEDQ +>NAFOICDF_01512 +MAKTSPTRAAGRTLAWLAALIVALTAILGLGVASGQASWAPKLALDLEGGTQMVLAPTTA +SGEQATPEQLQQAVEIIRQRVDGSGVAEAVVATQGDQNVVVSMPGVPDEETRRLIQASAD +MQFRPVLQAVPGGQPTPQDQLVPKDQFPTPSAEPTDAYDPNWITPELADEFQRTDCTLPR +DPNAAPPATDRAVVVCEPQQETPAGTMPATKYIVGPVVIPGTMIEKASNATAQSQTGVTT +NEWVVNIDFDGEGTKRFTEVTQKLTPFAEGDPRKQFAIMLDGQVIAAPQSNVVITGGQAQ +ISGPGFTEESTAQLAEQLNYGSLPISFTIESEQQISATLGRDQLFWGLIAGLIGLALVAV +YQFFQYRALGLLTFASIVVAGALTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRSGHTLDAALHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLLVVFMFTHPLMVLLSRTDFVGGGHPMSGLDPRVLGVEPALYQGAGRFREPAAA +RAARGGSHAADDDDAGSSAARRGRRSEQPMTIAERRRAERAGAAQTPAAQTPAGSAPAAD +TEEDAL +>MHAAABBN_00989 +MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS +TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD +MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD +PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST +NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ +ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV +YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP +RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR +RQEEDQ +>LFPAFLNI_01228 +MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS +TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD +MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD +PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST +NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ +ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV +YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP +RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR +RQEEDQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001098.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001098.fa new file mode 100644 index 0000000000000000000000000000000000000000..5579d0045d2f3733953ecc9558d537a004bc88e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001098.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01618 +MNRFADWGNALYSGRVSYPFVQRWRLWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTAATDIAAGERAVTDVLAGGHATVTNIAPGTVRVQTEQLDDAQTRQVAANLQDAYG +VGQDQVTSTFVGPTWGAAVSQQALLGLVIFVVLVTLFMAFYFRTWKMSLAAVIGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGQEEDPERTFEQNVNL +AVNQTLVRSITTSIVGILPVGSILFIGAGLLGAGTLRDIALAIFVGIIVGTLSTLFIQAP +LYALLRRGDEDVRDHDARAAARAARENRGDTVTDPDVAPWEDGARL +>MOLHKGIG_01269 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL +>NAFOICDF_01513 +MNRFADWGNALYSGRISYPFVRKWKTWFLIAAALLAVAFGLTALRGGFNLGIDFRGGSEF +TVSDAASSELDPGRAAVTDVVAGAEPTVTQVAPGTMRVQTEQLDDAQTRQVAQNLQQAYG +VTGDHVTSTFVGPTWGQAVSQQAVIGLVIFVVLVTLFMALYFRTWKMSLAAVVGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTRGVEEDPDRTFDGSVNL +AVNQTLVRSITTSIVGLLPVGSILFIGAGLLGAGTLRDISLAIFVGIIVGTLSTLFIQAP +LYALLRRGDADVVAHDARVGADHDEREQEEDLADARGAVL +>MHAAABBN_00988 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL +>LFPAFLNI_01227 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001099.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001099.fa new file mode 100644 index 0000000000000000000000000000000000000000..40c19f976dd5da79ddb66bc5a24c0918852ac07d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001099.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_01619 +MSEHDPTHAPARVAAVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKAELADLIRAF +EVARAAHEGQMRRSGDPYITHPVAVATILAEIGVSGPTLLAALLHDTVEDTDYSLERLRA +DFGPEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRY +VSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPER +EKHIAALRTVIEDHLREHRIRAEVTGRPKHYYSIYQKMVMRGKDFDEIHDLTGIRVLVDS +VRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPGGRPVEIQIRTHEMHR +QAEYGVAAHWRYKAQAAAESSSSSSGTPAWLRSVMDWQKDTRDPDEFLDSLRTQIGADEV +YVFTPSGEIRSLPAGSTPVDFAYAIHTDVGHRTIGAKVNGKLVPLSTPLNHGDTVEAFTS +RAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQAERGRESLTRQLRRAGLAVQSVLG +GEELAQVASDMGYADLDGLLVALGDGHVSAQAVQERVSERLAPPPPARTEPQGELTVGEV +DLAELVPAQARRTPARATNDAGVLVDGDGGVMAKLARCCNPLPPDAIDGFVTRGSGVSVH +RLDCPNLATLLEQEPERRTPVGWAPSRHTVYLVEIQVEALDRKSLLSDVTRVLSENHVNI +LSASVNTTRDRVAMSRFVFEMGDPRFLGHVIAAVRRIDGVFDVHRT +>MOLHKGIG_01268 +MSEQDPTPVPVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKTELADIVRAFEVARA +AHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSLERLRADFGSD +VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES +SARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPEREKHIA +ALRTVIEDHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIRVLVDSVRDCY +AVLGAIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRTQEMHRQAEYG +VAAHWRYKAQAAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGADEVYVFTPKG +EIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNGKLVPLSTPLSHGDTVEVFTSRAEDAGP +SRDWLGFVVSPRARSKIRHHFATQRRGEQADRGRESLTRQLRKAGMTVQHVLGGEELVQL +ATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTPTQAEPEGELTVGEVDLQELVP +AQARRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGVSVHRVDCPNL +ATLLAQEPERHTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENHVNILSASVNT +TRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT +>NAFOICDF_01514 +MTEQDRRPAAPPRRGRIARLTGRRATEYSPLLEPLMRTVRQSATHAEQEDIVRAFEVAER +AHRGQMRRSGDPYITHPVAVATILAELGVTGPTLLAALLHDTVEDTDYSLEQLTADFGPQ +VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES +SAKKARETLDIYAPLAHRLGMNTVKWELEDLSFAALQPKVYAEIVRLVGERNPEREKQLA +ALRGVLEEQLREQRVRATVTGRPKHYYSVYQKMVTQKKDFAQIYDLTGIRVLVDSVQDCY +AVLGVVHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPEGKPVEIQIRTWEMHRQAEYG +VAAHWRYKAGARGELEAGRSQQTPGWLRSVMDWQEDTRDPDEFLAALRTQIGADEVYVFT +PKGEIRSLPADSTPVDFAYAIHTDVGHRTVGARVNGRLVPLSTVLRHGDTVEVFTSKAED +AGPSRDWLNFVVSPRAKSKIRHHFATRRRDEQIERGREAFTRQLRKAGLSVQRVLGGEDL +GVVAGELGYHDPDTLFAAMADGHVSPQAVTERLEARLAPPPAPTAPDAELRVGEVDLAGL +VPEKARRAPTRSTNEAGVLVNGDGGVLAKLARCCNPVPPDEVVGFVTRGSGVSVHRGDCR +NLATMLENEPERRVDVAWAPSRDAVYLVEIQVQALDRTSLLSDVTRVLSENHVNILSASV +NTTRDRVAMSRFVFEMGDPKFLEHVVNAVRRIDGVFDVRRT +>MHAAABBN_00987 +MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE +IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL +ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA +RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE +RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR +VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT +QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA +DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV +FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ +VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV +GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV +SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH +VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT +>LFPAFLNI_01226 +MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE +IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL +ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA +RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE +RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR +VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT +QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA +DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV +FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ +VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV +GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV +SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH +VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001101.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001101.fa new file mode 100644 index 0000000000000000000000000000000000000000..b896bf66cef654e3b2aa25d7083892d81af1d972 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001101.fa @@ -0,0 +1,49 @@ +>ACLBLIBL_01621 +MPDASSEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGKALGQMTSAVNERHMVGDM +DALRTRLAALETLLGDYRGAEQEARQAAQAQQLATREAIVAEAEEFAATPAERMPWKTAS +TRMTALFEEWKAAQKAGPRLSKSVEDGLWKRFRGARTAFDKTRRAHFSQLDAKSAEAKQV +KERLIARAEELSSSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFDAR +KAVNQEIDREYGANLKVKEQILADGKKLLPFKDVKAGRRALNELRGRWEDAGRVPRGDVR +RMEEGFRSLEDALKQAENEHWRRTDPETKARTSSALTQLEETIAGLEADLAKAQASGDER +AVKKAQEALDARLQWKQALEASASELS +>MOLHKGIG_01266 +MQPDDQQSPATEATPASAEAAETTVPAEARPVPEIVPDAPAHGDSAQPAEAPAVPSPAAM +KKASPAAVRPATPAAASAVPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG +QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGRALGQMTTAVNERHMVGD +MDALRTRLAALETLLADYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA +SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTTFDKTRRAHFSRLDAASAEAKQ +VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA +RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV +RRMEEGFRRLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQAQGDQ +RAVKKAQEALDARLKWKQALEASASELR +>NAFOICDF_01516 +MTHQPQSDDQQTPDAEQATPAAAPQQTSPAQDAPEQVVQDQTPAAQADLADALGSIESVE +APAPAQGEEPADAAETDAEKTPEAAPSPAVPAAPSPAALKRSAAPRSAAPRPATAAVPVA +PAPSVEPTPLGEAAAFARVSEDGHVTLLDGADEVAVGQVPDATEQDALAYFVRKYDDVRA +QMALFEQRIAAGAPSSELGKALGQMTAAVTERHMVGDMPALRTRLAALETLLGDYRAAEA +ERRQAAQAEQLATREAIVTEAEKFAATPAERMPWKQASARMTELFDEWKTAQKAGPRLSK +SVEDGLWKRFRGARTQFDKTRRAHFSQLDARSAEAKQVKERLIARAEELSSSTDWGVTAG +KYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAARKAENAAVDREFGENLKVKEQIL +ADGQKLLPFTDLKAGRKALNELRGRWEDAGKVPRGDIRRMEDGFRKLEDALKQAENEHWR +RTDPETKARTNSALTQLEETIAGLEADLAEAQAAGDQKRIATAQEALDARLQWKQALEAS +ASELR +>MHAAABBN_00985 +MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM +KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG +QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD +MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA +SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ +VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA +RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV +RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ +RAVKKAQEALDARLQWKQALEASASELR +>LFPAFLNI_01224 +MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM +KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG +QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD +MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA +SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ +VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA +RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV +RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ +RAVKKAQEALDARLQWKQALEASASELR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001102.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001102.fa new file mode 100644 index 0000000000000000000000000000000000000000..62b7b4e7e18319c19560460cd444a4f362b46ca9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001102.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01622 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGRREAKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGELSPRHDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLTDAAGVLRSIDKLEKIGADEVARLLQEEVGASPEQARQALALAAIRTE +DVSFVEQVRALGVSDPLLEEGLAELADVVETLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQEMAQASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFLGRDDAG +ARVHEVKDIRSGDQHPADPADWTPPSEDLLPQVTRTESTEG +>MOLHKGIG_01265 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGRREPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAVDPADWTPPTEDLLPQITRTQD +>NAFOICDF_01517 +MSRKQSLSGFHEWLPAERIVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDQEVAEGVREAKDPSDPKRLALHFDLTVPFARYVTENAGHLAFPFRRHQIQ +KVWRGERPQEGRAREFTQADIDVVGDGELSPRYDADVALVMAEALGALPIGDFRIRVNNR +KLAEGFYRGIGLEDAAGVLRSIDKLEKVGAEEVARLLQEEVGATAEQAAQALKLAEIRTP +DTAFVEQVRALGVEDPLLEEGLAELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALATKGNRAFPGVGLSIGVTRLVMRMLSQEMAVASRAVPTVV +YVALTHDDDWSRAQDVAAGLRGRGIAAEVAVSAEKFGKQIKYADRRGIPFVWFLGAEGAS +DEVKDIRSGEQVPADAATWAPPAEDLVPQVTESPRAED +>MHAAABBN_00984 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD +>LFPAFLNI_01223 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001104.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001104.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b9be559f071fa53f8b7a414d15a5d5c0b82bea2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001104.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01624 +MNPTISSGRSPDGEDAFVLRTHQLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDAS +GFAQVVVRDEADFDPLRNEWVLQVSGVVERRPEGNENPNLPSGEIELIAETVTVLNTAAA +LPFQVDEHVEVGEEARLRHRYLDLRRPEPSRIMRLRSEVNRTAREMLHGEGFTEVETPTL +TRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR +QPEFTQLDIEASFVEQDDVIALGEKIVKAVWALVGVDVPTPIRRMTYAEAMEKYGSDKPD +LRFGLELTDLTAYFKDTPFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAY +VLIQEDGSLTGPVSKNISDEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGR +RCELFTDAGNGVEAKDADWAFVWVVDAPMFEPAADAVASGDVAVGSGAWTAVHHAFTSPK +PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDMQERVFSVMGLSQEDAQEKFG +FLLEGFKYGAPPHGGIAFGWDRVVALLAGTESIREVIAFPKTGGGFDPLTAAPAPITAQQ +RKEAGVDAKPEPKKAEGEKAEAAGQPQA +>MOLHKGIG_01263 +MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR +NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL +RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL +APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD +DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT +PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI +SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA +DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY +AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA +FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA +EPEA +>NAFOICDF_01521 +MLRTHHLGELNASLIGQTVTVTGWVAKRRDHGGVAFVDLRDASGRAQVVVRDEADFDPLR +NEWVLQVTGTVERRPEGNENPNLPTGEVELIADDVVVLNTAAALPFQIDEHVEVGEEARL +RHRYLDLRRPQPARIMRLRSEANRVARELLNEQGFVEVETPTLTRSTPEGARDFLVPARL +APGSWYALPQSPQLFKQLLQVGGLEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD +DVIALGEQIVKALWGLVGVEVQTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT +PFRVFQNEYVGAVVMPGGASQPRRTLDAWQEWAKQRGAKGLAHVLIQEDGTLTGPVSKNI +TDEEKAGLAAAVGANPGDCVFFAAGKAKESRALLGAARVEIGRRCELFTDAGDGVEAKDA +DWAFVWVVDAPLFEPAADAVASGDVAVGAGQWTAVHHAFTSPKPEFMDTFDTDPGSALAY +AYDIVCNGNEIGGGSIRIHRQDVQKRVFSVMGLSEEDANEKFGFLLEGFKYGAPPHGGIA +FGWDRVVALLAGTESIREVIAFPKTGGGYDPLTAAPAPITPQQRKEAGVDAKPEAKKAEG +AASEGAEAQAKANDEKTAADEAQLR +>MHAAABBN_00982 +MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVREEADFDPLR +NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL +RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL +APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD +DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKHT +PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI +SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA +DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY +AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA +FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA +EPEA +>LFPAFLNI_01221 +MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR +NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL +RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL +APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD +DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT +PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI +SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA +DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGSALAY +AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA +FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA +EPGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001106.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001106.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ad0e25ff2644f54aba8d5419c648e8cc10cf916 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001106.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01627 +MRTLSRLAAATSMVALSAAVVAPLTVAAPAANPSGRSIELTAAGTHATGVFDASAAEIPA +FDKTTGRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVA +GAVMAATVEAEDKTGHGWLVFFDTRTLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPA +DDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAALPEGVRVFGPDVAVPS +GHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTE +GVLDVSDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVK +DLELCGDVFPHAKALQKNEALGRLNVLTDLGYDAERGCHTELHALGGRGFSIYTADGQRL +FDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVEPESVVVGEVQGRQYA +FVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSP +SGTALLIVATEVSGSTTVYEVDPVKGGKRT +>MOLHKGIG_01261 +MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET +GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT +DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG +AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG +VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED +LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR +EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR +SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES +VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA +EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ +>NAFOICDF_01524 +MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAAAANPSGKTVELSLAGTHETGVF +GESAAEIPAFDAATGRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGG +ATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTTTLSYLGGVRVGALPDSIAFSPDGAYA +VVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTALPEGVRV +FGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWA +LQLTDWSKEGVLDASNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWG +DFVDAARVKDLELCTAEYPDAKALQKKPALGRLNVVTDLGYDADRDCFSQLHAFGGRSFS +IYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPEPEAVVV +GRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGL +TFVPANESPSGTALLVVANEVSGSTTVYEVNPVRR +>MHAAABBN_00980 +MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET +GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT +DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG +AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG +VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED +LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR +EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR +SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES +VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA +EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ +>LFPAFLNI_01219 +MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET +GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT +DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG +AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG +VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED +LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR +EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR +SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES +VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA +EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001108.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001108.fa new file mode 100644 index 0000000000000000000000000000000000000000..a37175293d886610113d5c656c31d9df6066e8b4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001108.fa @@ -0,0 +1,23 @@ +>ACLBLIBL_01629 +MSQHQPYAQDPRSTVPATTADAAYAGGPLGAADHRVLESVPDYARAQAIVDQLSDAGFPV +EHVRIVGTGLRTVEQVLGRMTTGKAAGRGAVQGLWFGLLLGLLFSIFSPGFGFLWILLIS +LGLGALWGAVFGAIGHAATRGRRDFSSLQTMDAASYEVQVEAAHLDRARQTLGAGPAAPR +A +>MOLHKGIG_01258 +MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG +FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL +LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG +TAATPRA +>NAFOICDF_01527 +MSASAAHYAVLSTVPDYAHAQSTVDRLSDSGFPVEHVRVAGTGLRSVEQVTGRLTTGAVG +VC +>MHAAABBN_00977 +MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG +FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL +LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG +TAATPRA +>LFPAFLNI_01216 +MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG +FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL +LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG +TAATPRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001109.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001109.fa new file mode 100644 index 0000000000000000000000000000000000000000..6fff494d1e26f8864a8a5b976e525d3a6eb11fc4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001109.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01630 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>MOLHKGIG_01257 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>NAFOICDF_01528 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIEKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>MHAAABBN_00976 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>LFPAFLNI_01215 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001110.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001110.fa new file mode 100644 index 0000000000000000000000000000000000000000..848f235d16c9e85820ded2ad42c209975a4efeb3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001110.fa @@ -0,0 +1,19 @@ +>ACLBLIBL_01632 +MLRSLLLVTAGAASGWLAHRALGDRAAADAAPGRSDAGPQARPGRARLDPEHLARQAGQA +VGDAAAAALNEGARRLADRVRAEAPWAAQFLPHTGPIIEGETVEPPSPSGPGGPRPQTTI +PTTTTQKDTHA +>MOLHKGIG_01256 +MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR +QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT +TTTQKDTPA +>NAFOICDF_01529 +MSRITSLLLVGAGTAAGWIAHRAVESGRRAVDQEAGRRLQETLDPTRLGRSAGQAVGDAA +AEALAQSAQAFTERLRADAPPWVSQLIGPPRDTIEGEALDTPDTTATPSSARKDPHA +>MHAAABBN_00975 +MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR +QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT +TTTQKDTPA +>LFPAFLNI_01214 +MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR +QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT +TTTQKDTPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001112.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001112.fa new file mode 100644 index 0000000000000000000000000000000000000000..04c29360e530b2b743b0aa4d56a74014bb7dd488 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001112.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01634 +MSAGQDGAATATDAVRRGRTLGVDVGRARVGLATADPDGLIATPVATLARDARRGRDVGE +LVAHALELDVVAVYVGLPVNLRGEHTPSTQDALDYARSVARAPAAAGHAVPVRLVDERLS +TVSAQAGLRAAGRTVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDPEEIA +>MOLHKGIG_01254 +MSAGQDGANAATDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDE +LVAHARELDVVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALAEAGHPVPVRLVDERLS +TVSAQAGLRAAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREPIR +>NAFOICDF_01531 +MSAQAAVRGRVLGVDVGRARVGLAASDPDGLIATPVETLRRDARQRRDHAELLDRARELD +AVAVYVGLPRNLRGEHTPSTQDAVEYAAAIEALVAEAGTPIPVRLVDERLSTVSAQAALH +RAGRTVKDSRGVIDQAAAVELLQDALEVQRRRGAWAGITVAEARA +>MHAAABBN_00973 +MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD +VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR +AAGRSVKYSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR +>LFPAFLNI_01212 +MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD +VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR +AAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001122.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001122.fa new file mode 100644 index 0000000000000000000000000000000000000000..9af4602d3150b90db3a82d6020f7d0aef807c3a0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001122.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01646 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDTDRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVYSGEHAGRPEAELLAEVREQPSMAGARLAETVTTEQPYVIEPAA +HGWEGEPLAEIAALDLGIKAATPRHLASRGIRVHVLPATAGLEEIRAVSPDGVFLSNGPG +DPATADAQVALLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVMDNATG +RVAITSQNHGFAVDAPLGEPVEAPETRYGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVRMLTEHRDAAAPAATEGA +>MOLHKGIG_01242 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA +>NAFOICDF_01543 +MSTPTPETALLVLEDGTVHRGRAYGARGSTLGEAVFTTGMTGYQETLTDPSYARQIVVQT +APHIGNTGVNDEDAESRAIWVAGYVVRDAARRPSNWRSQRTLDEELAAHGVVGIQDVDTR +AITRALRTEGSMKAGIFSGEAAQRPEAELLAEVREQPSMAGARLAETVSAPSAYVVEPSD +HGWDGEPIADVAALDLGIKAATPHHLAARGIRVHVLPADSDFAAIQAVRPDGVFMSNGPG +DPATADAQVAVLREVLDAGLPYFGICFGNQIFGRALGFGTYKLPFGHRGPNQPVMDKATG +RVEITSQNHGFAVDAPIGEVVEAPEARYGRVEVSHWSLNDDVVEGLRLLDRPAFSVQFHP +EAAAGPHDSLGLFDRFAHTLTERRAAAPSATPEGA +>MHAAABBN_00961 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELETFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVDAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA +>LFPAFLNI_01200 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001125.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001125.fa new file mode 100644 index 0000000000000000000000000000000000000000..fa5d6a6ec0e3d2220ba1efa86f44042265b65c32 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001125.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01649 +MALRQLSVEERAEARSKALAARQERAALKADFAAGQVSLAEVFSRADAEDAIGRLRTVDL +LQALPGVGEVRAREAMAGCGISPRRRLRGLGRRQREALIAYIGR +>MOLHKGIG_01239 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL +LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR +>NAFOICDF_01546 +MALRQLSVEERAEARAKALRARQERATLKTSFANRDLSLQEVFARADVDPAIGRLRTVDL +LQAMPGVGEVRASAVMEACEISPARRLKGLGRRQREALIAYIGR +>MHAAABBN_00958 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGAVGLADVFARADTEDAVARLRTVDL +LLALPGVGEVRARETMAGCGISPRRRLGGLGRRQREALIAYIGR +>LFPAFLNI_01197 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL +LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001127.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001127.fa new file mode 100644 index 0000000000000000000000000000000000000000..f8a285035005dda72cd55c57e1ed46b8edcd3ae7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001127.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_01651 +MTEQYDGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL +NEKPLSIALREIETDLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLEPSDAGQPV +GDPEAIEEAAEAVRAEEGTSEDAPEA +>MOLHKGIG_01237 +MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL +NEKPLSIALREIEAGLLESHEAVEATPEAELAAEDFGDFSLPGEDDPFATLESSDAHQPT +GDPAAIEEAAETVRAEEGISEDAPEA +>NAFOICDF_01548 +MTPPPPPDGPPPAAPCVPTHGQKTTREQTLETYVTDQYEGIVNPPIDSLLERVDSKYALV +LFAAKRARQINAYYSQLHEGLFEYVGPLVDTQLNEKPLSIAMREIESDMLVMAETAAVEP +AIELAEEEFGDFALPGDDDPFVAEPTAEGVSPEEYGAPVTTGDDDAVEDILSGADVADED +A +>MHAAABBN_00956 +MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL +NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM +GDPAAIEEAAETVRAEEGTSEDATEA +>LFPAFLNI_01195 +MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL +NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM +GDPAAIEEAAETVRAEEGTSEDATEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001129.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001129.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a13f89df88bd84e50864bdc83db7ca114d298a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001129.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01653 +MTDAAQPSPARHADPYTGVGGGELRLFTSESVTEGHPDKICDQISDAILDAILAADPAAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVTRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRQENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHDWVGQEQLRKDVEEH +VIRPVIERSGLDTSGMRVIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTAVVPEER +IIQAVNEVFDLRPAAIVKELNLLRPIYRKTAANGHFGRDDADFTWERTDRVERLRAAAGL +>MOLHKGIG_01235 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPKIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLETREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL +>NAFOICDF_01550 +MSDTPTPTPSAAAQPYRGVGGGDLRLFTSESVTSGHPDKMCDQISDAILDAILAADPSAK +VAVETLSTTGLVQVAGEVNTSAYVEIPHIVRETILDIGYDSSANGFDGAQCGVNVSIGQQ +SSDIFAGVSRSLEAREQGSADEVDEQGAGDQGIMFGYATNETPSYMPTPIYLAHRLSERL +TAVRRQENTPMPYLLPDGKTQVTVGYDADHRPRTVETVVVSTQHHDVVTQEQLRADVAEH +VIRPVIERSGLDVSNARFIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYALRWVAKNVVAAGLAGRAEFQVAYAIGSARPVGLYVDTFGTNAVPEET +IIAAVNEVFDLRPAAIVKSLNLLRPIYRKTAAHGHFGRDDADFTWERTDKVEELRRAAGV +>MHAAABBN_00954 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL +>LFPAFLNI_01193 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEKH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001130.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001130.fa new file mode 100644 index 0000000000000000000000000000000000000000..0da452c60c6c44d921370254b8bc9c05d4cf9cef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001130.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_01654 +MARVLLDSPVPHLDREFDYLIPVTLDERARPGSRVAVRFGGRPMTGWLVSREDEPATGAQ +LTELTAVLTSVPPLTEEVLASARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAGAA +ADHPVALAVEEAPEGEPVGAGDGIAPTVWESLEGGRAFVAAVLAGDGPRAAAVVPSRLLE +WDEAAAMAHLARAVAAGGGGVLLLVPDHRDLDRLCAALDDAVGEEAYARIGSEDGNTPRY +RAHLAALRGTRRIVAGTRAAAWAPVRDLRLTVLWDDGDDAWAEPRAPYFHAREVVLERTR +RTGSALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQREIGPRIVSTADAWETARDPFAQR +ARLPQAAWGAARAALLGERPGPVLVQVARAGFIPALVCDRCRTPARCRRCAGPLGFRDAR +AARLGEVACRWCGTRERGFRCTECGAGALRAGARGVDRTAEELGRAFPRIPVHSSSAQHR +LGTIPPGPSLVVATVGAEPVAEDGYAAALLLDGDAQLQREGLDVPGRVLARWLAAACLVR +PAADGGVVVVTADAGEAVNALVRRDPDGFAAHQVAERRELHLPPAGRLAEVTGEASAVRE +YLDLVEAARRERPEEDVHEDPHSAPLDGGPARLPWIGPVPDAADETRSRALLLFPYAAAD +ATVAALRAARSAASARRETSPVRVRLDPAGVL +>MOLHKGIG_01234 +MPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT +VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAEAAADHPVTLTG +TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA +LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG +TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA +GPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTADAWETARDPFAQRARLPQAAWA +AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC +RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS +LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV +VTADASEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVSGDAAAVAEYLELVEAAR +RERPDEDIHEDPHSAPLDGGPARLPWIGPVPDPADETRSRALLIFPYAAAEATVGALRAA +RSAASARRETAPVRVRLDPAGVL +>NAFOICDF_01551 +MARVLLDSPVPHLDREFDYLVPPALDERAVPGSRVSVRFGGRETTGWLVERVAAPATHAR +LTELAGVLTAVPPLTEHVLAVARAVAARQAGVVSDVLRSAVPPRVVSVEKEVLAELASGP +EVDHPVQGVVADPHARLVWEELTGGTAFVASAVAGDPVRAAAVVPSRVGDWDESSALAAL +ATAVSRAGGGVLLLVPDHRDLDRLSAALAREVGEDGFVRVGSEDGNTPRYRAHLRALTGL +ARVVAGTRAAAWAPVQDLRLVVVWDDGDDAHAEPRAPYFHVREVALERARQSGSALLFAG +PSRSVPVQRLVEHGWLLEVSADRASQRAASPRIVASADSWESARDPFARRARLPHAAWAA +AGEALSGPTPGPVLVQVARAGFIPAVVCGRCRTPARCRVCAGPLAFRDRRSAERGELACR +WCGTRERDFHCAECGFTGLRAGVRGVDRTAEELGRAFPQVPVHSSSADHRLGEVGEGPAL +VVATVGAEPHARGGYAAALLLDGDAQLQREGLDVPVRVLTRWLAAASLVRPAAEGGTVVV +TAEHDAAVGALVRRDPQGFAGHLLAERRELHLPPAGRLAEVTGEAGAVAEYLALVEAARR +ERRRVGPDADPSLDLDVEARPGDATPLPWIGPVPDVADESRSRALLLFPWAASAATVDAL +RVARSAASARRERSAVRVRLDPPGVL +>MHAAABBN_00953 +MPHLDREFDYLVPVALDDRAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT +VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAETAADHPVTLTG +TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA +LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG +TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA +GPSRSVPVQRLVESGWLLHLGPSRATQRELGPRVVSTADAWETARDPFAQRARLPQAAWA +AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC +RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS +LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV +VTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVTGEAAAVAEYLELVEAAR +RERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADEIRSRALLIFPYAAAEATVGALRAA +RSAASARRETAPVRVRLDPAGVL +>LFPAFLNI_01192 +MPERAEGWPERPIARVLLDSPVPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWL +VSREQEPATGAQLTELTGVLTAIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQV +EKAALAEDAEAAADHPVTLTGTDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAA +RAAALVPSRLFEWDEAGALAALARTVAASGGGVLLLVPDHRDLDRLCAALDEHVGEDAYA +RIGSEDGNTPRYRVHLAALRGTRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPY +FHAREVVLERARATGAALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTAD +AWETARDPFARRARLPQAAWAAARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCR +VCAGPLGFRDARAARHGEVACRWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFP +RVPVHASSAQHMLGSVPPGPSLVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRV +LARWLAAACLVRPASDGGVVVVTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRL +AEVTGEAPAVAEYLELVEAARRERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADETRS +RALLIFPYAAAEATVGALRAARSAASARRETAPVRVRLDPAGVL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001134.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001134.fa new file mode 100644 index 0000000000000000000000000000000000000000..9deb5294b2824367c7b55f10e4a9cc61c647d882 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001134.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01658 +MATIEQWRDDALVRLRSRRSQLVGRARYGLKPPRRDRTAVVTDSAAALPAAALGHSLAAG +IRQVPLPVMVGDQIHAEGTDDLALELPLALAAGTAVRTSRPSPGAFRSVYAQLAREGYAR +ILSVHLSGELSGTAEAARLAAVDAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMTVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLIGTLLHVRPVLAVDDGAISLVDRPR +SAARAVDRLVELATERAGDVPVRIAVHEYGDPETAAALAERLTPVSTTPVPVVELPAVLA +AHLGLGALGVVVCPLESPTGGSGD +>MOLHKGIG_01230 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTVYAELARAGYAR +ILSVHLSGELSGTVEAARLAAADAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELAVERAGEDPVRIAVHEYGDPETAMQLAERLQPISTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD +>NAFOICDF_01555 +MASTSQWLEDAVERLRARRGQLVGRARYGLKPARRDRTGIVTDSAAALPVEVFAHPFAAG +IRQVALPVMVGEQIHVEGDADLDLELQLALAAGTPVRTSRPAPGAFRAAYADLAQAGCAR +ILSVHLSGELSGTVEAARLAAADAPVPVVVLDSRTAGLALGHAVLDAAVEAGFGRPLDQV +AAIAQACADQSSVLFTVPHLEQLRRGGRIGAVPSLLGALLQVRPVLGLQDGSVHLVDRAR +TSPRALERMVDLARERAAGGPARIAVHEYGDPAGATALAERLQSASATPVPVVPLPAVLA +AHLGLGTLAVVLSPLEPVPSTSSSPAQAN +>MHAAABBN_00949 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR +ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD +>LFPAFLNI_01188 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR +ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001135.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001135.fa new file mode 100644 index 0000000000000000000000000000000000000000..5677bce890435be3e6bc524e840cd8261400114a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001135.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_01659 +MSHPHRLAPDAALSDDPRRGRPASDLVPVPPALAARGPSAWERVPPRGRVLRWRPALLAV +TVLLVAAAAWWAVAWLTSPAPPSPAPAASAVEARVEPETEDGPDAADAAPPSDGAGPAAE +PSGGSGPVATLLRVHVVGEVERPGVVSLAPGARVADAVRAAGGATREARTERINLAAPLA +DGRQVLVPSARTPEEDLARVAGGQDGPGGPEGGAAGTAPDAAASAPAGPARAGGSGGAGA +GPVDLNAADAVALQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGVGPAALERLRDR +VTW +>MOLHKGIG_01229 +MSPSHRLCDDPPAFAPDPAAVPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLLVA +AAAWWAVAWLTTPAPPAAVPAAAAGAGIPQTGAPSAASTAAGTDARTPEAGPSGEASGSA +GSTPLRVHVVGEVARPGVVSLAPGSRVADAVRAAGGPTRHARAERINLAAPLDDGQQVLV +PSAHTPQDALDRVAGAAQAQPTPTTGGAGATGEPGGAEPRGTVDLNTADAAGLQTLPGVG +PATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDLVSW +>NAFOICDF_01556 +MDTKTLTPAVDEPDWEDPPPRGPLLRWRTAGAGLTLVAILGLTWWLVAWLTAPAPPDAVP +AGAVGSASAAGSAAHEASAAPLRATAATPEGQDGGGRSAAAANPSGRVRVHVVGQVRRPG +VVELPAGARVADAVAAAGGARELARTDRINLAAPVVDGQQVVVPDAQTAVEPAAVAGEAP +DGGPTPRTGSGASAADGSGGGPATVDLNTADLAALQTLPGVGPATAEKIIAQRESVGPFS +GLQDLDAVPGIGPATLDRLKDHVTW +>MHAAABBN_00948 +MRDAPDSATGPQTARMSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGP +VLRWRPALLAVTVLLVAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGT +DARTSEAGPSGEASGPAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARA +ERINLAAPLDDGQQVLVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTV +DLNTADATELQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW +>LFPAFLNI_01187 +MSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLL +VAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGTDARTSEAGPSGEASG +PAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARAERINLAAPLDDGQQV +LVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTVDLNTADATELQTLPG +VGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001138.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001138.fa new file mode 100644 index 0000000000000000000000000000000000000000..16a9a7f6c6b1db30535a0eb856fed55c596357a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001138.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01662 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>MOLHKGIG_01226 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>NAFOICDF_01559 +MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>MHAAABBN_00945 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>LFPAFLNI_01184 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001139.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001139.fa new file mode 100644 index 0000000000000000000000000000000000000000..71c3e020c03c0d16142460f98fa824fbb0761dd7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001139.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01663 +MAFDLNRALALGRRAIRLIGSLRDDDARRSWTGDAAGRGSGAAPFPGPPGPAGRAWDPKE +PTDSWPFPDRGHDGRPRGGQDRTRPASGATDPQGRALLADFTGMGRVEYAPVPGPAAGPG +EVVWTWVPYEEMDGRGKDRPVLLVGRDGDLLLGLMLTSRDRNNARVRDEDYVDVGSGPWD +RAGRPSEAKLDRVLRVDPAAVRREGGVLDPAAFERVGDALARAQGWRR +>MOLHKGIG_01225 +MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD +PTEPTDSWPMPGPGQERRPRRQDAGRHVSLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP +YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNALARDEDYVDVGAGAWDRSGRASEV +KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR +>NAFOICDF_01560 +MAFDFQRALTLGRTALRLVEQVRSMSGAGTTRGAAPSSPASRAGRRRRADAEETRGARSG +GAGSDHALLPDFTGRARVEYAPVPGATPDPGEVVWTWVPFEEMDGRGKDRPVLLVGRDGD +LLLALMLTSKDHTNAARRDADYVDVGTGPWDRGGRASEAKLDRILRVDPAAVRREGGVLE +RSRFDAVAEALARAQGWDR +>MHAAABBN_00944 +MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGERSGPSPFPGPPGPPGPAWD +PTEPTDSWPMPGPGQERRPRRQDTDRHVSLPDFTGTVRVEYAPAPGPTAGPGEVVWTWVP +YEEMDGRGKDRPVLLIGRDGALLLGLMLTSRDRNNALTRDEDYVDVGAGAWDRSGRASEV +KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRVR +>LFPAFLNI_01183 +MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD +PTEPTDSWPMPGPGQERRPRRQDTGRHASLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP +YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNARARDEDYVDVGAGAWDRSGRASEA +KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001140.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001140.fa new file mode 100644 index 0000000000000000000000000000000000000000..c10b409f503598c88c687b8c4b77eb533eb24d86 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001140.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01664 +MSPLASNPPVPAATEPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD +IERERGITIKSQAVRMPWELDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ +GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELATLIGCEPEDVLRVSGKTG +VGVEDLLDRVVRSIPAPEGEADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKIRMM +STGATHELLEIGVSSPEPTPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAKPAAEELG +GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL +HLEIVRERLEREFNLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKIHEVREPMASAT +IIVPAEFIGAVMELCQAKRGNLRGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA +SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHKDNAYSYGVMMTGKLKELIPRQQFEV +PIQAAIGSRVIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE +AFIAALSSDGAGADSAAKK +>MOLHKGIG_01224 +MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD +IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ +GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCDPEDVLRVSGKTG +VGVEELLDRVVRAVPSPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM +STGTTYELLEIGVSSPEPVPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG +GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL +HLEIVRERLEREFGLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT +IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA +SLDWKADGDQAADLVKVDILLQGEQVDAFSSITHKDNAYTYGVMMTGKLKELIPRQQYEV +PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE +AFIAALSSDGAGADQAAKK +>NAFOICDF_01561 +MSEAPEPIKDVPVSPLASKPPVPAATDPAVIRNFCIIAHIDHGKSTLADRMLQATGVVQP +REMKAQYLDRMDIERERGITIKSQAVRMPWEVDGVNYALNMIDTPGHVDFTYEVSRSLAA +CEGAILLVDAAQGIEAQTLANLYLAMENELEIIPVLNKIDLPAADPDRYAAELATLIGCE +PDDVLRVSGKTGQGVEALLDRVVERLPAPQGVADAPARAMIFDSVYDTYRGVVTYVRVVD +GMLSPREKIRMMSTGATHELLEIGVSSPEPMPTKGLSVGEVGYLITGVKDVRQSKVGDTV +TNSSRPATEQIGGYEDPKPMVFSGLYPIDGSDYPNLRDALDKLKLNDAALVYEPETSVAL +GFGFRVGFLGLLHLEIVRERLEREFDLDLISTAPNVVYEVKREDKTVVTVTNPSEFPEGK +VLEVKEPMASATVIVPAEYIGAVMELCQTKRGHLKGMDYLSEERVEIRYWIPLAEIVFDF +FDQLKSRTKGYASLDWKADGDQVADLVKVDILLQGEQVDAFSAITHRDNAYSYGVMMTGK +LKELIPRQQFEVPIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKR +MKMVGRVEVPQEAFIAALSSDGAEPAKK +>MHAAABBN_00943 +MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD +IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ +GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG +VGVEDLLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM +STGTTYELLEIGVSSPEPVPTNGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG +GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL +HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT +IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA +SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV +PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE +AFIAALSSDGAGADQAAKK +>LFPAFLNI_01182 +MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD +IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ +GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG +VGVEELLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM +STGTTYELLEIGVSSPEPVPTKGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG +GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL +HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT +IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA +SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV +PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE +AFIAALSSDGAGADQAAKK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001141.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001141.fa new file mode 100644 index 0000000000000000000000000000000000000000..bbecf6fd58a7999c5934abd066569e2538c7b92c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001141.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01666 +MNPSAQPDAGRPGHEPPAWLASAGGRATPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESKEALNFSGPPTLITTLFFFLALLPVIGAIFAILGALSWAVMAVYGVMGA +SNVSKGRPFRYPFNLRILR +>MOLHKGIG_01222 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA +SHVSKGRPFRYPFNLRILR +>NAFOICDF_01563 +MATTPSTTPAGETATPRRAAGGSAAHEAPAWLRDAAGGRAPLTAKQDRDRAALSHLSLAC +GLPGPLVMWLLYRDRGPFTAQESREALNFSLAPTLLIVLLFLLGGVPLLGGLLAILGALL +WIALALYGVMGASQVAKGRPFRYPFSPRLLR +>MHAAABBN_00941 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA +SHVSKGRPFRYPFNLRILR +>LFPAFLNI_01180 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAAYGVMGA +SHVSKGRPFRYPFNLRILR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001144.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001144.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d972cb1d24f4b75a2e68e6a2b38fe73e1cd34bf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001144.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01669 +MTDHYATLGVSRDASTEEIRRAYRKLARTHHPDVNPDPESAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQSGFPGGFGGGGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT +APIDLEDAVFGGEQTITLDTAVRCKRCEGSCCEPGTEPETCQTCQGHGMIQRPMRSLLGT +VMATEACPACQGFGTVIPDPCHECAGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP +GGGPNGDLYVEIAVRPHETFRREGDHLATTVTVPMAAAALGTTVTLATLDGEQTVRLEPG +VQSGHVETLAGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRELLERLAELRGEEVVHGT +PPARGMFARLRENLRNL +>MOLHKGIG_01219 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT +ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT +VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP +GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG +VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA +PQAKGMFARLRENLRNL +>NAFOICDF_01566 +MADHYATLGVSRDASAEEIKRAYRKLARQHHPDVNPSEEAAEEFKRISHAYEVLSDEDKR +RVYDQTGNENGTAGGFGGGGFGGAGFGGFADIFETFMNAAGTPGGGRGPMPRARRGQDAL +VTARIELRDAVFGGEATLQLDTAVTCERCSGTCCEPGTHPETCSTCQGQGMTQRPVRSML +GTIMAAETCPVCRGFGTVIPHPCTECSGQGRVRVQQPLTIRIPAGVDDGTRIHLAGRGEA +GPGGGPNGDLYVEVQVRPDEVFRREGDHLATTVTVPMAAAALGTSVTLETLDGPQEVDIE +PGTQSGHVETLRGLGVGRLRGAGRGDLKVDVVVTTPTDVTDEQRALLEQLAGLRGEEVVH +GAPPQSKGMFARLRENLKNL +>MHAAABBN_00938 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT +ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT +VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP +GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG +VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA +PQAKGMFARLRENLRNL +>LFPAFLNI_01177 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPGPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT +ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT +VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP +GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG +VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA +PQAKGMFARLRENLRNL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001147.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001147.fa new file mode 100644 index 0000000000000000000000000000000000000000..ffe89e7451eb991321a1ebc84250a7c7485a185e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001147.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01672 +MAVEILNESGIEVPEDELLRMARHVYASLHVHERTETAVTVVDAARMAELHEEWMDLPGP +TDVMSLPMDELTPGTAEAPAEGMLGDVVLCPEVAAEQAARGGHGRDDELMLLLTHGMLHL +LGYDHMDDADRLEMFALQDRLVSEVLGRPAPAPTIED +>MOLHKGIG_01216 +MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP +TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL +LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED +>NAFOICDF_01569 +MAVEIVNESGVEVPEEALLGMARHVYAALHVHPLAETAVTVVDAQRMAELHVEWMDLEGP +TDVMSLPMDELTPGTEKSPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL +LGYDHMEEDERAEMFALQDRLVSEVLGRPAPAPTVED +>MHAAABBN_00935 +MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP +TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL +LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED +>LFPAFLNI_01173 +MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP +TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL +LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001148.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001148.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb6e494f302361ac9b288e84ff47714c8426ad19 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001148.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01673 +MLTPAVLFALFLVFLALVWTLSLAESAFTYLSRRDAEDIVRRRPGSRVLDVTAERDSHLG +ALRVWRFVAEALSAVCLTAAADAVVDNTWFAVLIAAAVLVGVAALLGVWSPRPFGSRNEA +AVARRLGGLVWGLRRALGPLADRLGRDRRRREDELEEEDDFQERHLREVVARAHDADVLA +DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD +DIRGMLHLKDVTRALHQDGAAQSGPVTAAMRDVRFVPESKSVAALLQELQRESTHVAVVV +DEYGGTAGLVTLEDLIEEIVGEIYDEDDLPDRAEVEMIEPGVYSVDARMGLHHFREEFEL +PEEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGLELLADTLEPRRNRVARLRVSETPD +RPARLRRRDEEPHGSSAAETAA +>MOLHKGIG_01215 +MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG +ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA +AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA +DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD +DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV +DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL +PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR +PVRLRRREEQAHGAAPADPVA +>NAFOICDF_01570 +MATAVSLVLLFLACLACTWVLALAESAFTYLPRKDAEDVARTRPGSRILDVTADLDGHLG +ALRVWRFLSEAFAAMFLTAGLHALTDSVWAALAVTAVLLVGTAAVLGVWSPRPIGSRNEA +AVAARTAGLVHGLKQALGPVGDRLGRDRRRTEAEAADEDDFHERHLREVVARAHDAEVLE +DSEAELIASVFSMGDTLVRSVMVPRTDVVTIDADHTLGQALDLFLRSGCSRVPVIGEDSD +DVRGMLYLKDAVRALHHEGHASQDAVTAVMREVRFVPESKPVSVLLEELQRESTHVAIVV +DEYGGTAGLVTLEDLIEEIVGEIWDEDDRPDRPEIEELAPGVYSVDARMGIGDFREEFEL +PEDEDEDDDVDTVGGLLAKELGRVPIRGSRVVVHGLELTADTLEPRRNRVARLKVVETED +RPARLRRQHDPTDPD +>MHAAABBN_00934 +MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVREQPGSKVLEIARERESHLG +ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA +AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA +DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGDDAD +DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV +DEYGGTAGLVTLEDLIEEIVGEIYDEDDRPDRPEVEFVAPGVYSVDARMGIHDFREEFEL +PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR +PVRLRRREEQAHGAEPADPVA +>LFPAFLNI_01172 +MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG +ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA +AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA +DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD +DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV +DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL +PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR +PVRLRRREEQAHGAAPADPVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001150.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001150.fa new file mode 100644 index 0000000000000000000000000000000000000000..c4835c643d352207e7b9c925fa681308568cce37 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001150.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01675 +MSAHLQKPSGMKFHKYVPYQDQIQVSLPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG +PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI +ERTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI +TYEYSPESYTGTELEFARRISDEVAQVLEASTDRKMILNLPATVEMATPNVYADSIEWMH +RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL +FSQGVDPMIDFSDMDHIKRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME +ADAKAAGKTVDEIDWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR +RAQIEFSHVIQEMADAQGGEVSGADLWTAFQDEYLPAEAKDEQWGRYRLRSVTSASGEDG +AFRMEAELEVDGVTQTRTAQGNGPIDAFLRMLGEDDMDVRVLDYTEHALSEGGAAMAAAY +VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRAVRA +>MOLHKGIG_01213 +MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG +PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI +ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI +TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH +RNLEHRDSLLLSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL +YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME +VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR +RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG +AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY +VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA +>NAFOICDF_01572 +MRNLQKPSGMKHGKYVPYHEQIEVHLPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMGP +ERKLRMFQLLVQMGYKEIEVGFPSASQTDFDFVRQLIEGDHIPDDVSIQVLTQAREHLIE +RTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLTGTEIT +YEYSPESYTGTELEFARRISDEVATVLEASTDRQMILNLPATVEMATPNVYADSIEWMHR +NLEHRDSIILSLHPHNDRGTGVAAAELGYLAGGDRIEGCLFGNGERTGNVDLVTLGMNLF +SQGIDPMIDFSDMDHIRRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAMEA +DAAAAGKHVDEIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHKLDLPRR +AQIEFSHVIQELADAHGGEVSGADLWTAFQDEYLPAENKEEAWGRYRVRSVSSESGENGA +FRMTAEIFVDHEPQTRTAEGNGPIDAFLKILGEDGQDVRVLDYTEHALSEGGSAMAAAYV +EAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRSLRA +>MHAAABBN_00932 +MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMG +PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI +ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI +TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH +RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL +YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME +VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR +RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG +AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY +VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA +>LFPAFLNI_01170 +MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG +PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI +ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI +TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH +RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL +YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME +VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR +RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG +AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY +VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001151.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001151.fa new file mode 100644 index 0000000000000000000000000000000000000000..c5f91bc28a99c1c4e6e0c44b7d8669acbdf21dc2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001151.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01676 +MSGSGPSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIVEALTPEHGLVRAVAKGVRKT +SSRLGSTVEPFMHTTLQLARGRGELLTVTQAQLLHPYATMLAADYDAYAVAGALAEAVER +IPAVDEAGRRAQYRLLHGALAALARRRHDPRLILHSFLLRTLAQAGWAPTFDRCARCGAP +GPHSAVHVALGGAVCPECRPPGAAHPAPQTLALLAALAAGDWATADSSDAAARREAAGIV +AAYLQFHAERRLVSPVRPGPGPRPPRPARREETMRADRAPQSPPPHPSGAVAPRIDPRFV +PRHVAIVMDGNGRWANQRGLPRTEGHRAGEAALLDVVAGAVELGVGHVSAYAFSTENWRR +SAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWNGRAPRLWTPVIRELQEAEELTRHNTGT +TLHMCVNYGSRAEIQDGVQALAEEVRAGRMRPADITEDVITRYLDRGFRAGQDVDVVPDV +DLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWPDVDRRTLWEAVETYARRDRRYGGAVDT +AQPAPSSGAPDSASDADGGA +>MOLHKGIG_01211 +MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL +LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN +GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG +EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP +DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA +>NAFOICDF_01574 +MSDVPKVSPPPHPSGAVPPKLDPRFVPRHVAVVMDGNGRWANQRGLPRTEGHRAGEAALL +DVVAGAVELGVGHVSAYAFSTENWSRSAEEVRFLMGFSKDVLRRQRDTLDSWNVRIRWNG +RAPRLWTPVIRELREAEDLTRDNTGTTLHMCVNYGSRAEIVDGVQALAEEVAAGRMRPRD +LTEDVITRWLDRGFRAGDRDVDVTPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDELWP +DVDRRTLYAAVLEYAHRDRRFGGAVDAPAAD +>MHAAABBN_00930 +MSADRAPQSPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL +LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN +GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG +EISEDVITRYLDRGFRTGQDIDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP +DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPASDADGGA +>LFPAFLNI_01168 +MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL +LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN +GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG +EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP +DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001153.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001153.fa new file mode 100644 index 0000000000000000000000000000000000000000..114c59077e820d598b1831ef461f04a1730274c7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001153.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01678 +MQLPDPKAAVDGVLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLAERTGASAALRA +AFRPDPLLARTVMGLRFPTPFGLAAGFDKEGRGTAALADLGFGHIEVGTITAQAQPGNPQ +PRLFRLVEDRALVNRMGFNNDGAAAVAPRLARTRAVLERRFGAVRPVLGVNIGKTKVVAL +EDAAEDYRASTRLLTPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRVVTGR +RVPLTVKIAPDLTDEDVRAVAALAERLGLDGVIATNTTISREGLATPRADVDALGAGGLS +GAPLKERSTEVLRVLRAALPVGTAVISVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF +WAGRISAGLACALRG +>MOLHKGIG_01209 +MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLVERTGASAALRA +AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ +PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPTRPVLGVNIGKTKVVPL +EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR +RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS +GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLAQGYTAFLYEGPF +WAGRITAGLARSLRG +>NAFOICDF_01576 +MQLPDPRFRVQSVLRSSAPRIYPPFFRAVFAGMDPERAHHVGFAGIRAAEASGASRALRS +TMAPDLGLARTVMGLRFPSPFGLAAGFDKTGVGTTALAELGFGHIEVGTITAQAQPGNPA +PRLFRLPEDRALINRMGFNNDGAAAVAPRLAATRRTLEERFGAVRPVLGVNIGKTKVVPL +DGAVEDYRASARLLAPHADYLTVNVSSPNTPGLRQLQEISSLEPILAAVREEADRAVPDR +RVPLTVKIAPDLADEDVRAVAELAGRIGLDGVIATNTTIGRGGLSTPASEVEAMGAGGLS +GAPLAARSLEVLRTLRAALPAGVALIAVGGVTDGDDVLQRLDAGADLVQGYTAFLYEGPF +WAGRINAGLDAAQRAR +>MHAAABBN_00928 +MQLPDPKSAVDGILTSRAPRLYPPFFRAVFGGMDAERAHHRGFDAIRLAERTGASAALRA +AFRPDPMLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ +PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL +EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR +RVPLTVKIAPDLADADVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS +GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF +WAGRTTAGLARSLRG +>LFPAFLNI_01166 +MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIWLVERTGASAALRA +AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ +PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL +EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPDR +RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS +GAPLQERSMRVLEVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF +WAGRITAGLARSLRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001154.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001154.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed3d46aaf36882775b958912b82042b7cd7c75b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001154.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_01679 +MVPEDRKAARKAAREAAAQDRMRQRVALETGDERGLPLRDRGPQKRWVRDYVDARTGIGE +WLMPVVFAYVLLMFLPGREVQLFLMISLYALVALVVIESLIVARRIKKGLTERFGEPESG +TGFYGVMRALQFRRLRLPKPQVKRGQFPA +>MOLHKGIG_01208 +MFKRDKTPETAPAPSTHGSSAAPAEGAAVAEAGPRDRSQGKKGPTPRRRDQEAARRRTLV +PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL +MPVVFAYVLLMFIPGREAQLILMISLYVLVALVLIESFLVSRHIKKGLTERFGTPEPGTG +FYGIMRALQFRRLRLPKPQVKRGEYPA +>NAFOICDF_01577 +MLNRRKKTENDAPASHGSTALGAGNTPAAQPAPRDRSQGKTGPTPRRRDQEAARRRTLVP +EDRKAARKAERDAATAERMRQRQALETGDERNLPARDKGPQKRYVRDYIDARTGLGEWLM +PIVLVYVIAMFIPGTRAQVILMVTLYVIVGLVIAESFYISAQIKKRLTATFGTPEPGSRF +YGVMRALQFRRLRLPKPQVRRGEFPA +>MHAAABBN_00927 +MFKRDKTPETAPAPSTHGSSAAPAEGAVSGAAPRDRSQGKKGPTPRRRDQEAARRRTLVP +EDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWLM +PVVFAYVVLMFIPGREAQLILMISLYALVALVLIESFLVSRHIKKGLTERFGTPEPGTGF +YGIMRALQFRRMRLPKPQVKRGEYPA +>LFPAFLNI_01165 +MFKRDKTPETAPAPSTHGSSAAPAEGAAVAEAGPRDRSQGKKGPTPRRRDQEAARRRTLV +PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL +MPVVFAYVLLMFIPGREAQLILMISLYVLVALVLIESFLVSRHIKKGLTERFGTPEPGTG +FYGIMRALQFRRLRLPKPQVKRGEYPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001155.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001155.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c44b13acc39c7f830e262c463bf242d478a3079 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001155.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01680 +MTETTPPVRDDAALVAAVRDAVDARFPQTLQTLTDLVAIPGIAWDSADRAQLERSSEAVA +ALLRQAGLQGVEIVTETREDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEALWDT +EPLVATEKGGRLYGRGAADDKAGIMVHLAALAALKDVLPDAGVGVRVFIEGEEEAGSPTF +RTFLENHRARLEADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP +VLDAVVLLSRLIATLHDADGAVAVPGLEPRRSASLDYPEDVFRADAGVLDSVTLAGRGPV +ADRLWNAPALSVIGIDVPSVAESSNTIQPQARAKFSLRLGPGMDPAEAFEALKAHLEAQS +AAVLGAEITVEAGEFGQPFDTDTSDPLAAAMMGALGDAWGVAPKEAGMGGSIPFTADLAE +VFPDATILITGVEDPDSRAHSANESLHIEDFRRAVVAEALWFARLAG +>MOLHKGIG_01207 +MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRAQLERSAEAVA +GLLREAGLQDVEIVSEIRDDGRPGGPAVIGEKPGTSDKPTVLFYAHHDVQPIGDEDLWDT +PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF +RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP +VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV +ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSMRLGPGMEPAEAFEALRTHLEAQS +AAVLGAEITVTAGEFGQPFTTDTSAPAAAAMMAALEDAWGVEPRAIGMGGSIPFTADLAE +VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA +>NAFOICDF_01578 +MTQSTQNTPVGAAPDPELVSAIRAAVDRRFPETLQSLKDLVSIPGIAWDSMDREPLERSA +AAVADLLRTAGLEGVETAVEERADGRPGGPAVIGGRPAVGDKPTVLLYAHHDVQPLGEEG +LWDTPPLVATERDGRLYGRGAADDKAGIMVHLAALAALDEVCPDAGVGVRVFIEGEEEAG +SPTFRPFLERHRDRLAADAIVVADSSNWAVGEPALTTSLRGVVSATVTVRALDHAVHSGM +FGGPVLDAVVLMSRLIATLHDADGAVAVPGLEPRHHADVDYPEDAFRADSGILPGTRLAG +RGALADRLWNGPALSVIGLDAPSVDTSSNTIQPAARAKISLRLGPGMDPAASLDALRAHL +EAQSDAVLGAEITVEPGELGQPFSTDTSAPAAAAMMGALGAAFATPARETGLGGSIPFTA +DLKELFPEATILITGVEDPDSRAHSANESLHLEDFRRAIVAEALWLAAMGA +>MHAAABBN_00926 +MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA +GLLRAAGLQHVEIVTETRDDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT +PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF +RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP +VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV +ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMDPAEAFEALRTHLEAQS +AAVLGAEITVTAGEFGQPFTTDTSATAAAAMMAALEDAWDVEPRAIGMGGSIPFTADLAQ +VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA +>LFPAFLNI_01164 +MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA +GLLREAGLQEVEIVTETRDDDRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT +PPLEATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF +RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP +VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV +ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMEPAEAFEALRTHLEAQS +AAVLGAEITVTAGEFGQPFTTDTSAPAAAGMMAALEDAWGVEPRAIGMGGSIPFTADLAE +VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001156.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001156.fa new file mode 100644 index 0000000000000000000000000000000000000000..44bb65cc3e05ff11fb03d0f08bed33eefcac2c61 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001156.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01681 +MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV +GSCACGDSFH +>MOLHKGIG_01206 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH +>NAFOICDF_01579 +MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV +GSCACGDSFH +>MHAAABBN_00925 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH +>LFPAFLNI_01163 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001157.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001157.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8ff68e6e3d090299adf33107b84637afc623e66 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001157.fa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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001161.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001161.fa new file mode 100644 index 0000000000000000000000000000000000000000..4282fe4fee1ad5545d8864419210ef7641e17617 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001161.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01687 +MGEKGFEGTEHGSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL +ISIVGTLLFFVGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD +HETVEDRHEIRSEADRVAATGMISEILDESQIKRRPLLRNTLIGAAVLAPLPFIAVFRDL +DDSDNFSDEETHNFGPERLRHTMWSEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL +GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG +>MOLHKGIG_01200 +MGEKGLEGTERRSGSLEHAGEDAPRYAIDDPGLPPHRPRLADEDPKAAKRAERQVSVMFL +ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD +HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL +DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL +GPDKLNQKAKAVVLLMRLDPAKVRITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG +>NAFOICDF_01584 +MGEKGYEGAERHSDALEHAGEESPRYAIDNPGLPPHRPRLADEDPRAAKRAERQVSVFFL +ISVIGTVLFFIGYFGVGQVGNGESTSVLYLQNLLLGLGVALAMFGIGIGVVHWAKTLMPD +HEVVEERHEIRTEADRAAAQGMIADILDESQIKRRPLLRNTLIGAAVLAPLPFIAAFRDL +DNTDNFSDEAAKNFGPERLRHTMWHEGVRLVRDPTGSPIKASDVTLGSALHVIPDGLNDL +EHGKLNEKAKAVVLVMRLDPSKVKISPGRENWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLAQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG +>MHAAABBN_00920 +MGEKGFEGTEHRSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL +ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD +HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL +DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL +GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG +>LFPAFLNI_01154 +MGEKGFEGTEHRSDSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL +ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD +HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL +DDSDNFSDEEIHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL +GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001162.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001162.fa new file mode 100644 index 0000000000000000000000000000000000000000..e374325db17d4e941671180db01e38898974a7f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001162.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01688 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF +NANCATCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA +QLAAYVASLGAGPAIPEDEYLDINNEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKFA +PSLQGVEEKYIYEAMETGPQNMPVFSDANIKPEDKRDIIAYLKTIENQGSPGGLSLGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>MOLHKGIG_01199 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF +NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA +QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>NAFOICDF_01585 +MKALSQNRRHPLVGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAAAADDITAGEKLF +NANCASCHNMGATGTADGPSLVGVGAAAVDFQVGTGRMPMQMNGPQAQRKPNQFSEEQTA +QLAAYVASLGAGPAVPADEDLDPNAEGVNIAKGGDLFRINCAMCHNAAAAGGALTRGKFA +PSLEGVSEKHIYEAMETGPQNMPVFSDANLKPEDKRDIIAYLKTIEANGSPGGLQLGSLG +PVAEGLFIWTAGLALIVGFMVWLTSRSS +>MHAAABBN_00919 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF +NANCASCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA +QLAAYVASLGAGPAIPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVDEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLTLGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>LFPAFLNI_01153 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF +NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA +QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001163.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001163.fa new file mode 100644 index 0000000000000000000000000000000000000000..e2c8b42885cc402dbe01304b4061493c1e27900c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001163.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01689 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAENTAILNVPLAAANTLILVLSSVT +AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTIA +ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK +>MOLHKGIG_01198 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT +AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA +ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK +>NAFOICDF_01586 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTVILVLSSFT +AQFGVLAAERLQPRRTGGLFSVKSWGMVEWFILTFIMGSIFVAVQAFEYATLVSEGVTIA +ANAYGSAFYITTGFHALHVTGGLIAFLFIIGRAFLARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK +>MHAAABBN_00918 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT +AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA +ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK +>LFPAFLNI_01152 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT +AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA +ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001165.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001165.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d34e1d1c8782fc4f8bd3376fc37113ce48fd61f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001165.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01691 +MVTAIVMIKTDKSSIPETAETLAALEGIGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVEGIQDTETMLAFRTYSSEDLGEGWALGFED +>MOLHKGIG_01196 +MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRAYSSEDLGEGWALGFDS +>NAFOICDF_01589 +MVTAIVMITTDKSTIPETAQAIASLEGVSSVYSVTGAWDLVAMVKLKRYEDLADVIADQL +SKVDGIEDTETMLAFRTYSTEDLEEGWALGFDG +>MHAAABBN_00916 +MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS +>LFPAFLNI_01150 +MVTAIVLIKTDKSSIPETAEALAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001166.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001166.fa new file mode 100644 index 0000000000000000000000000000000000000000..d18710ae06e347f4ac95b7c2714e8d4fd84ddc50 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001166.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01692 +MADTLSENRSETMAQTGGMTDSPTRRHSPASPPSPLWAATALAVDAVLVVVFVALGQDQH +TTDRGLGGLLATALPFLLGLVAATVLTAGHRTWHRVWPHGVAVWLGTVAVGMALRVLWDQ +GGAPLSFVLVALGVLGVFLLGRRAVTAWVIRRRARV +>MOLHKGIG_01195 +MTSSPTARRAAPAEHRDPRGALPALAVDLLLTLLFVALGQGQHSTERGPLGLLVTAAPFL +AGLLLMTGVTAGHRTWARAWPHGVIVWLGTVAVGMLLRVAFGLGGAPVSFVLVALGVLGV +LLLGRRAVTAWLVRRTRR +>NAFOICDF_01590 +MSTTPLPQDSSPAAHPSDRRRGSAPWVAFALDAALVVLFVALGQREHATDRGGLALVTAA +APFLLAWVAGTALAGGPRTWARVWPQGVVVWAVTVAAGMGLRVLWGLGGAPVPFVLVASA +VLAVFLLGRRWASTLLAHRATDRASRAS +>MHAAABBN_00915 +MTSSPTARRAVPAEHRDPRGAQPALAVDLLLTLLFVALGQGQHATERGPLGLLVTAAPFL +AGLLVMTGLTAGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV +LLLGRRAVTAWLVRRTRR +>LFPAFLNI_01149 +MTSSPTARRVVPAEHRAPRGALPALAVDLLLTVLFVALGQGQHSTERGPVGLLVTAAPFL +AGLLLMTGLTSGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV +LLLGRRAVTAWLVRRTRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001167.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001167.fa new file mode 100644 index 0000000000000000000000000000000000000000..7bc687be4c8756bb7508154064f4c780b078c7de --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001167.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_01693 +MIVLHLLPLTAPDAADAAWTRVGDELNRPGAVSSLVMPFDRQGEGSEARLVGGMDSGVEA +VGILLSLVRSGAWAVVVEVAEGRAAGESLLQREAERARRANGHCAVLGPSGPSAAWIEPA +LQLLGALERRRSEPQQDAGRRVEAGASQREVAAELQVSQQAVHARLRGGLWNETRALAGA +TADALDVLARRGDRVSDGGASPSTSERG +>MOLHKGIG_01194 +MVSVHLVPIRPTAATADDAQRLSAALLDDPRPGAAVISAAWHIDETDAAPGDGELAVTLD +GMAAGVGLALWAVRSGSWAVLLDTEGNYDKQSALSHITAGERRRARRAPGRLVLPHGRRP +GRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGISQQAV +HSRLRHGLWHESRTAVAAVLPLLERLSADPGE +>NAFOICDF_01591 +MVPVAVRCGSAGAAGRWAASIPGARRLGREGGRDLIVHADDAAAAVALMLAVRRAGAGAV +GAGVAIEQVEGALRRARRRPGGIAVSRVPGSTGTEEERGLLEAGLGVLLTLESRRSAPQQ +AAGVLIEAGRSQREAAADLGVSQQAVQQRLRAGLWEETRTLLDALLPMARRVLEA +>MHAAABBN_00914 +MVFVHLVPIRPTAATADDARRLAAVLLDDPHPDASVAAAVWRGDEGNPDADAAPGDGELA +VVVESMAAAVGLALWAVRTGSWAVLLDPEDALDKDSLLSYLTPAERRRARRAPGRLVLPH +GRRPGRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGIS +QQAVHSRLRHGLWHESRTAVAAVLPLLERLSADPGE +>LFPAFLNI_01148 +MVSVHLVLIRPTTATAEDARRLATALRDDPRPDAAVTAAMWLGDESDPVDDDAAPHDGEL +AVVLDDAAAAVGLALWAVRTGSWAVMLDPEGGSDKDSALSYLTPAELRRARRAPGRLVLP +AGGRPGRASESGREADLRCAEATLQLVAAVERRRSADQHAAGRLVEAGASQREAAAELGI +SQQAVHSRLRHGLWHVSRTAVAAVLPLLERLSTDPGE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001168.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001168.fa new file mode 100644 index 0000000000000000000000000000000000000000..c213ae0fa37f1a8a509f45cfcb1ae99e01d28397 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001168.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01695 +MALIYTAQLDPDKPEWIRRRLVAHGLPEDVDAEKVGSYRFDDPAGEVGVESMIVRVGDRL +YQTAFAYRGEAPTEGDIVAEADHSVLGRRWVMDAATDPDARRILTAGLRGEIPQAVMDFH +DESGAYLETRQPDVTLRLVGEGDGGELELPVELADAAEESGDGPRRLVAEGEGFTAVVAR +LA +>MOLHKGIG_01193 +MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL +YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH +DESGTYLETRAPDLTLRVIGADATGELEVPVELSETGEADVDGPRCLIAEGDGVRAVVAR +LT +>NAFOICDF_01594 +MSFIYSAQLDPDKNEWIRRALVAHGEDPDVPFTRAGSYRFDDPAGELGLEVMLVRVGGAD +DGRLVQTPLSYRSAARDGATVLLTAEHSVLGTRWIHDALTDPEAREVLRRGVAGELAQEV +LEVHDEHGVRTGTRQPDMTVTAVGTGPAAGELDMPYELDPADTADGGRALVAEGDGFSGL +VVARLV +>MHAAABBN_00912 +MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRLDDPAGEIGVESMVVRVGDRL +YQTPFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH +DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR +LS +>LFPAFLNI_01143 +MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL +YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH +DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR +LS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001169.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001169.fa new file mode 100644 index 0000000000000000000000000000000000000000..1f1c3609ec260ca603dd8dbd0d72651d765f6c69 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001169.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_01696 +MTVAPAITSPLLEPITLGPLTLPNRVVMASMHLGLEDRHEDLPRLAAFYAERARSGVGLI +VTGGVGVVPEGTVAPGGGLLATAEDARAHRVVTDAVHAEGGRILVQLLHTGRYARGEDLV +CASAVRAPISAHTPREMDEADLERTVAAFARAAALALEAGYDGVEVMASEGYLLNAFLAP +VTNRRQDAYGGSAQARRRFPVRVVEAVRAALGERGVLSVRTSAADLVPGGQTREEVADTA +RAFEAAGADVLMTGIGWHESRVPTIVTSVPRATFLPATAALSAAVDIPVIAANRLTTPAE +AEEAIASGAAALVGLARPLLADPDWMAGIGVDDAAALTPCIACNQACLDHVYTGAPVSCL +MNPRAGRETDPAYARPVPVAIGRRRRVAVVGAGPAGLTAAERAARFGHEVTLFDRHDEPG +GQFRLARRIPGKEEFGPALEHLAARARASGVTVLTGEEVTVQTLLTPEGGPAFDEVLLTT +GVRPRRIALPGAGEPGAPAVHAYDDVVLGHAQLGPRVAVIGAGGVGVDVAEALTAGAHRP +DGTPESAEQWRARWGVALDSPTPGQLGEPTGEPPAREVHLLQRSPEPIGARLRPTTGWVH +RAELRRHGVRLHSGVAYEGLSAAGLHVTVPDPERPEERTPLTLDVTDVVVCAGQESEDGL +AGDLVAAGYPAEAVRLVGGAAEARELDAYRAMDHAVRAIQG +>MOLHKGIG_01192 +MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI +VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSPDLV +SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP +ATNRRADEYGGDAERRRRFPVAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA +RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE +AEEALTSGAAALVGLARPLLADPDWMAAIGDPRARTLTPCIACNQACLDHVFTGAKVSCL +MNPRAGRETEPEYAAPVPVALGRRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG +GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT +GVRPRPVALPGTGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP +DGTPETQEHWRARWGVALTSQTPGQLAKPAAADPGREVHLLQRSPGPIGVRLRPTTGWVH +RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPEARVALTLDVTDVVVCAGQESETDL +VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG +>NAFOICDF_01595 +MTHMTDAPASHRLLEPLTVRRTVLRNRVVMGSMHLGLEDSHADLPALAAFYAERAAGGVG +LIVTGGVGVTPEGAVSPGGGLLADAADAAAHRTLTDAVHAEGGRILVQLLHAGRYARGAD +LVSASATRAPISRHTAHALTEAEVEELVAAYARSARLALEAGYDGVEVMASEGYLLNQFL +APSTNLREDRYGGSAENRRRFPVAVVAAVREALGETGLLSVRTSLTDLVPGGQTSAEALD +TARAFEAAGADLIMTGIGWHESRVPTVVTSVPRAAWAEASARVRAAVGIPVIAANRLTTP +DDAEALLRGGAADLVAVARPLLADPDWVRTVGRAGAEHLTPCIACNQACLDHVMAGRPVS +CLMNPRAGRETDPRYARPVPVEIGRRRRVAVVGAGPAGLTAAHRAAGFGHDVTLFEATEE +VGGQFRLARRIPGKEEFEPALRHLEARAVAAGVHLRRETRVTPRTLLTEDGRPAFDRVII +ATGVRPRDVDLPGVGEPGAPAVHRYDDVVAGRVRCGAAVAVIGAGGVGVDVAELLASPEG +GAALGEPEPLEHWRARWGVADDDPTAPGGLTRPEPAERARRVFLLQRSPEPVGSRLRPTT +GWVHRLELRALGVEMLSGVSYERVDRDGLHVTAPAVGGDGDPGRRRLVLPVTDVVVCAGQ +ESEDGLAGDLLAAGWDPEAVTVIGGARVAAEVDAYRAMDDAVLAVQD +>MHAAABBN_00911 +MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI +VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSPDLV +SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP +ATNRRADEYGGDAERRRRFPAAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA +RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE +AEEALTSGAAALVGLARPLLADPEWMAAISDPRARTLTPCIACNQACLDHVFTGAKVSCL +MNPRAGRETEPEYAAPVPVALARRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG +GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT +GVRPRPVALPGAGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP +DGTPETQEHWRARWGVALTAETPGQLAKPAAAHPGREVHLLQRSPGPIGVRLRPTTGWVH +RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPETRVPLTLDVTDVVVCAGQESETDL +VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG +>LFPAFLNI_01142 +MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI +VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSADLV +SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP +ATNRRADEYGGDAERRRRFPAAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA +RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE +AEEALTSGAAALVGLARPLLADPEWMAAISDPRARTLTPCIACNQACLDHVFTGAKVSCL +MNPRAGRETEPEYAAPVPVALGRRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG +GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT +GVRPRPVDLPGTGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP +DGTPETQEHWRARWGVALTSQTPGQLAKPAAADPGREVHLLQRSPGPIGVRLRPTTGWVH +RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPEARVALTLDVTDVVVCAGQESETDL +VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001172.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001172.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed336d10f9540250310cb1c5e926fad3a180e8d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001172.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01699 +MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK +EAFLVSGEKPAEAEGKPVRTHWDMLRERRSLEELQETYALQLNKLRASRGEDVDA +>MOLHKGIG_01189 +MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK +EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA +>NAFOICDF_01598 +MSDRSLRGMRLGAQSLESEAGVEPAPRQRVEYRTEDGEQVFVTFAQEAEVPTTWTSKTGK +EALRVDGEKPEENPGKPVRTHWDMLLERRSMEELEETFQIQLKKLHASRGEAV +>MHAAABBN_00908 +MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK +EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEDVDA +>LFPAFLNI_01139 +MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK +EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001174.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001174.fa new file mode 100644 index 0000000000000000000000000000000000000000..82b1caafa048df040de0b9b224f97ad02c62e27c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001174.fa @@ -0,0 +1,39 @@ +>ACLBLIBL_01701 +MGRVTAHLLTTGIIHSVTDPYAQALLVRDGVIAWLGADDSAERVADPADARTDLDGAVVV +PAFVEPLARPEDARDALSRGTAVVTVLAGPAGDVAPAEGVQAVVYRHAEGPAEGAVGVWL +PVAADADAADLAAALAEATRAGEQAYLVPAADAAGHGDAEAPAAAQAAAIAALRRVAEEL +GAPALGRVRHRLVVTSPVTAEDRAFLASVAVSATVVPAADGTLRAPVASLLADAVPVALG +AGPGRDPWAAVRAALSHPEEAERISARSAFAAATRTPLRALPDAADADLVAAPRLAVSAP +GVFGVWEAEAVAVQSPDGRVAAWSTDTRAGTPLLPALDDQTPLPRWRATWVGGRIAAEAA +DGDARGTGDHA +>MOLHKGIG_01187 +MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF +VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP +VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR +VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP +WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD +ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA +ATPA +>NAFOICDF_01600 +MSSTLFLNGIVHSASDPYATAALVSDGVVAWLGDDSSADRVADPDVPRVDLAGAVLAPAF +VEPGGPSVDPAQALRHGVAIVTVLAEPGQTAQALQAAADPALQTVVYRAADTVDAEAAGV +WLPAEGEALAALVVASTRAGEQVHLVPPAGGDPSEGQAAALAALRSAAEELGAPALGRVR +HRVVLTAPITAEDRALLAAISASVTVGPEADGLLRAPLGTLLAEGVPVCLSTAGEAGPWA +AVRAALSHPDEAERISARSAFTAATRTPLRVLPDAPGATVQAAPRLTVSAPATFAVWEAD +AVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRPAAVEVADA +>MHAAABBN_00906 +MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF +VEPLARPADARDALSRGTAVVTVLAGPEDTGAVPADEDVQTVVYRHADRVDAEAAGVWLP +VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR +VRHRLVVTHSVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVSVCLGAGPAGDP +WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAAGLSVAPRLSVSAPAVFGVWD +ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA +ATPA +>LFPAFLNI_01137 +MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF +VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP +VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR +VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP +WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD +ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA +ATPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001181.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001181.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c66b9c90b86b187e55452e2385c822b68c1648c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001181.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01710 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>MOLHKGIG_01179 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>NAFOICDF_01608 +MAQEQIRPRPAGGPEDEGAAAQAQAKAAPQDTGLDGLLDEIDSVLESNAEEFVKGFVQKG +GQ +>MHAAABBN_00898 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>LFPAFLNI_01129 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLVSNAEEFVKGFVQK +GGQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001183.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001183.fa new file mode 100644 index 0000000000000000000000000000000000000000..b04b07d705fcd7851bf6878f4e4f86e568f4113e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001183.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01712 +MIRDESIEAYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEVLIAA +CLGLADGDERGFGAVAEAFGLPRDTPVARSRRSAAIQAALAEAVRPPRGIVDAAARALDL +AERVLDAANPNVLSDVGAALGCIRGGLTAATVTLETNLGPLRDEGVEGILRTDVDRADRL +VARADALLGRVRAAITG +>MOLHKGIG_01177 +MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA +CLGLADGDERGFGAVAEAFGLPRDTLEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL +AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGIVRTDVDRADRL +VARADALLGRVRAAVTG +>NAFOICDF_01610 +MIRHETVEDHLTRLASGEPTPGGGATGALVVAQGAGLVAMAARFSGREEVAVECERVIRD +SLAISDEDEEGFAAVADAYTLPKDGDAARARRSAAVQAALDQAVRPPRAIVDAVDRTVGL +AERVLDDANPHVLSDVGAALGCARAGAGAAVVTLLTNLSPLHDEQLGAELRAEIARADEL +TSRIDALAARVRERIAR +>MHAAABBN_00896 +MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA +CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL +AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL +VARADALLGRVRAAVAG +>LFPAFLNI_01127 +MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA +CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVRPPRGIVDAAARALDL +AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL +VARADALLGRVRAAVTG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001185.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001185.fa new file mode 100644 index 0000000000000000000000000000000000000000..0067a35cf2c0ca8d6b198be05a7746a7c0458f31 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001185.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01714 +MDQDAQGGPEQLERRLGEARELLRQSQAEAERLRHQLDSAQRHAARLSERRREAEAQTQT +AARNNRRMVELLETTRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG +GADVVQNGRRLRVTVSPLLDAARLVPGAQVLLDESSAIVGVAPGTGSGQLLRVKEALPDG +GLVLAGTADEERVVRRAPALEGVELRHGDAVTVDSRVEWALRRVELSEVDEVLLEEVPDV +TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA +LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL +FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR +VDRPDAAGAAEIMAKHLTADVPLHADDVATAGSADAARATLIARTVAALYDRGTGTALAE +LTDVSGTTRALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVVA +VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA +>MOLHKGIG_01175 +MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT +AARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG +GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG +GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV +TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA +LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL +FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR +VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGADTALAE +LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA +VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA +>NAFOICDF_01612 +MTEDDTQDRAGVLPAGDDARRLAEARELLRQSQAEAERLRHQLASAQRHGAQLSERRRAA +QAQLDVAARNNRRMVELLEATRTEMTSLKEALDDTTKAPFTFARLEAVHAARAPREGVET +GAVVRAGADVVQNGRRLRVAVSPLLDAAALTAGAEVLLDESSTIVGEVEHSVSGQLLRVK +ESLPDGSLVLAGAADEERVVRRAPALAGEVLRHGDAVTVDPRLEWALARVELSEVDDVLL +EEVPDVTFDDIGGLGPQIERIREAVEVPFLHPDLYREHGLRAPKGIMLYGPPGTGKTMLA +KAVANALSARSAEGGRSFFLNIKGPELLNKYVGETERQIRIIFQRAREHAAAGSPVVVFF +DEMESLFRTRGSGVSSDVETTIVPQLLAEIDGVESLDNVIVIGASNREDMIDPAVLRAGR +LDVKIRVDRPDARGAVDIMARHLDEEVPLHVDEVRDAGSAEQAREELIGAAVTALYERSP +RTALAELTDITGATSTLHLADLVSGAVVADVVDRAKRAAVRDLLAADLDPAARGLRTRHL +LDAVDAVLADQADLLGTVAPGEWARTSGWRGPRLAELRMLPGAGGRP +>MHAAABBN_00894 +MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT +TARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPRDPEEGVETGAVVRG +GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG +GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV +TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA +LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL +FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR +VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGGDTALAE +LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA +VMEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA +>LFPAFLNI_01125 +MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT +AARNNRRMVELLEATRAEIATLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG +GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG +GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV +TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA +LSVRSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL +FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR +VDRPDAAGAAEIMAKHLTADVPLHADDVVAAGSADAARATLIARTVAALYDRGADTALAE +LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA +VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001186.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001186.fa new file mode 100644 index 0000000000000000000000000000000000000000..41c917cd5e254100070bd0e484a01ceab0c6b79d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001186.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_01715 +MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV +VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL +SMSLLRAVGDHGRLHSYERREEFADVARANVEAFFGAEHPAWSIHLGDAQEQMTRVHEPG +SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET +LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLATGEEALRLKKRSKVSEFKAEDVEAWQPA +DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAERGVDAYGGSIQEQDQD +>MOLHKGIG_01174 +MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV +VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL +SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG +SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET +LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFRAEDVEAWQPA +DEARWTPEALGERPITDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD +>NAFOICDF_01613 +MSDATAPETPAAPTTPDTAAPAGRPAGVTARRGPLRAGQRVQIKDAKGRLNTITLLPGGE +FHSYQGVLRHDDLIGGPEGIVVQNSSGHAYQVLRPLLNDFVLSMPRGATVVYPKDAGQIV +QQADIFPGAVVVEAGVGSGALSMSLLRAVGDAGRLHSYERRAEFAEIARGNVESFFGGVH +PAWSIHLGDAQEEMPKVHEPHSVDRVVLDMLAPWECLDAVATVLAPGGVWLNYVATATQL +SRVAEAIRASGKFTQIEATETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLAAGEDALV +MKKRLKVSEFTTEDVEAWTPSDGARWTPQALGERTVTDKKARKAAKEARLTARRARAALE +GRDPRTVGQDKD +>MHAAABBN_00893 +MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV +VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL +SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG +SVDRVVLDMLAPWECLDTVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET +LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA +DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD +>LFPAFLNI_01124 +MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV +VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL +SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG +SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET +LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA +DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001187.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001187.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f05aaa09f5de17dae1acc7ef991526abcc24696 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001187.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01716 +MSGAAARRIGSLRLGSVAGAPVLLSWTWLLIAVAIVLALGPQIRRALPELGAGAYGVALG +YAVLLALSVLVHEVAHALAGRAAGQRAEEIALTLWGGHTQFRGAHAGPLGTVLTAMAGPA +ANLALAGLAHLAARAVDGPSVAALLLDVSVWANLLLAAFNALPGAPLDGGRMVESAVWAA +TGSRDRGVEASGWAGRVIAAGIVAAALLAPLLQGRTPDVLFTALLIWAALTLWRGAGDAV +ARGRWGRRLAGLRLADLELAAVAVPEHLSVAEALAHADGGRRAAVAVDGAGLPRGVLDRT +AVGRLDAAARAGTPVAAAAVALAPQAVLEREALPEAGPELAAVLADPETPVWVLTDVRGL +VRSVVTRERILAAVHATRRP +>MOLHKGIG_01173 +MSGPASVRLGTIAGAPVRLSWSWLLIAAAITLAFGPQIQRALPSLGGGAYGVALGYAVLL +ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL +AGLAHLAARAVAGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA +RGVEAAGWAGRVVAVGVLAAVLGPPILAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW +SRRLETLRLEQVEAPAVALPEHLSVAEALAQADDGRRAVVAVDGAGRPRGVLDLAAAAGL +TPERRTTTALAAVAVALAPGAVLVRDDVPAAGPDLAARLADPQTPVWVLTDAHGLVRSVV +PRETILAAVDATRRP +>NAFOICDF_01614 +MSGPRALTLGRIAGAPVRLSPAWVAVAGAVVLLFGPQVARALPGLGGAAWLVALGYAALL +ALSVLVHEAAHAVAGRAFGQRPQEIVLTLWGGHTQFAAPQATPVGTVVTALAGPAANVVL +AGLAWALGAAADARGVPGLLVDATVWANLLLAGFNALPGAPLDGGRMVESAVWAATGSRD +RGVAAAGWTGRLIAAALVIGWVAVPLVRGERPGLVVSLLLVWVAVTLWRGASESVERGRW +GRRLAGVRLADLAIPALAVPVDADASAVLAGVPAGLAVVAVDEAGRPVGVLDRAALDGAA +ASARVPVAAACRAVAPHAVLAADSLPPSGGALVASLATAAESAADPRPGVPGLDSTPVWV +LTDGHGAVRSVLPRERILTALATASRPDPEEPRP +>MHAAABBN_00892 +MSGPASVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPLIGGGAYGVALGYAVLL +ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL +AGLAHLAARAVAGPSVLALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA +RGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW +SRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHTAAAGL +TPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRLADPQTPVWVLTDAHGLVRSVV +PRETILAAVDATRRP +>LFPAFLNI_01123 +MSGPASVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPSLDGGAYGVALGYAVLL +ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL +AGLAHLAARAVPGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA +RGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW +SRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHTAAAGL +TPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRLADPQTPVWVLTDAHGLVRSVV +PRETILAAVDATRRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001188.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001188.fa new file mode 100644 index 0000000000000000000000000000000000000000..d12077ce3d8ffde57932f5024a49962b638825df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001188.fa @@ -0,0 +1,28 @@ +>ACLBLIBL_01717 +MDGTLADTEPLWNASQRRLLAEHGGVWSEALADSLVGRPLDEGARRLQAAGLDLPVDEII +ERTMGAVTRGVADRVPWRPGARELLAALAEAGVPGALVTMSHAPLARALAERAPAAALDV +VVSGDLVARGKPDPEAYLLALDLLAARHPGLDAAGCVAVEDSPVGVAAAVAAGLPTVGVP +SVLPLPAGAATVEWDTLAGRAPADLAAVRDVAAGRAEDAPAPAGPGGRA +>MOLHKGIG_01172 +MSRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVVEHGGTWSEDLAASLVG +RPLDEGARRLQEAGLDLPVQRIIDLTMHEVVQGVVSGVPWRPGARELLVALAEAGVPGAL +VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYRLGLQLLAERTPGLTAADCV +AVEDSPVGVGAAMAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRQIAAARGP +GGDGAE +>NAFOICDF_01615 +MPRTPAAPAPVLPAALLWDMDGTLVDTEPLWNAVQRRLVEEHGGTWSDGLAASLVGRPLD +EGARSLRAAGLRMEVPEIIEATMAEVARGVEAATPWRPGALELLTAQAEAGVPGALVTMS +HAPLARVLAERAPAGALRVVVTGDRVSRGKPDPEAYLLALEELSAHVPGLRAEDCVAVED +SPVGVAAAVAAGLPTVGVPSVLPLPEGAATVQWGTLAGRGLADLAAVRPGAAG +>MHAAABBN_00891 +MPRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVAEHGGTWSDDLAASLVG +RPLDEGARRLQEAGLDLPVQRIIDLTMDEVVQGVVRGVPWRPGARELLVALAEAGVPGAL +VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYRLGLQLLAERTPGLTAADCV +AVEDSPVGVGAAMAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRRIAAARGP +GADGAG +>LFPAFLNI_01122 +MPRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVVEHGGTWSEDLAASLVG +HPLDEGARRLQEAGLDLPVQRIIDLTMDEVVQGVVGGVPWRPGARELLVALAEAGVPGAL +VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYQLGLQLLAERTPGLTAADCV +AVEDSPVGVGAAVAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRRIAAARRP +GADEPG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001191.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001191.fa new file mode 100644 index 0000000000000000000000000000000000000000..5796eef25af9471bb57bbb1493132a52378e9aad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001191.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01720 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSASDPGAAFTAITQIGTELAVLIYF +WRDITRIIGRWFQALAGRLPHSDPDVRMGWLIILGSLPIAVLGLLLQDWIDTEFRSLWIT +ATMLIVFGVLLALADRLGRQAKPLERLTVRDGVLYGFAQALALIPGVSRSGGTITAGLAM +GYTRSAAARYAFLLAVPAVFASGFYKLFQSLAEPGTQGPYGMGETFLATVIAFVVGYAVI +AWLMKFITTNSYMPFVWYRIALGLGLFALLGTGVISA +>MOLHKGIG_01169 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF +WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT +ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM +GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI +AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA +>NAFOICDF_01618 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSAADPGAAFTAITQLGTETAVLIYF +WKDISRIISRWFQALAGKVPHSDPDVRMGWLIIIGSIPIGVLGLLLQDWIDTEFRSLWIT +ATMLIVFGVLLALADRKGRQTKPLEKLTLKDGIVYGFAQALALIPGVSRSGGTITAGLAM +GYTREAAARYAFLLAVPAVFASGLYKVAKVVTEPGQAGPYGMGETILATAIAFVVGYAVI +AWLMKFITTNSYMPFVWYRIALGLVLFVLLGTGLIAA +>MHAAABBN_00888 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF +WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT +ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM +GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI +AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA +>LFPAFLNI_01119 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF +WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT +ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM +GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI +AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001193.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001193.fa new file mode 100644 index 0000000000000000000000000000000000000000..9705c3721d7baa2883219ba568cc71b91b104c62 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001193.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01722 +MREQLMSSTLDSIARGQKWEYLVITVSPDESLGDARRRLVEHAEYGRWELQRSVHFRGGA +RRYWLRRRVVRVASTLASA +>MOLHKGIG_01167 +MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA +RRYWMRRRVMRVASTLQTL +>NAFOICDF_01620 +MDGMREQLMSSTLDSIARGEKWEYLVITVAPHESLADARRRLVDHAEYGQWELQRSVHYR +GGTRRHWMRRRVIRVRSTLQS +>MHAAABBN_00886 +MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA +RRYWMRRRVMRVASTLQTL +>LFPAFLNI_01117 +MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA +RRYWMRRRVMRVASTLQTV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001194.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001194.fa new file mode 100644 index 0000000000000000000000000000000000000000..0e64a0002a34fbaab8e41c5fbd2bad5eca232f6a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001194.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01723 +MIQNAHDTPVSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAALCARLMEEAGMRPRL +FESSPGRVSVVGHLPGWDEDAPGLVVHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLSVLLHLTRTGRRPRRPLTVAFFADEEAGGVYGARWLVEHHPELFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGIAWLNLRAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDEQDPTPQLDALGQARSWVAGTLRTSSNPTGMT +SGYKHNVIPSTATGTVDARLLPGEEEAALATLQELAGPGVSIEPEHRDVALETPFSGDLV +ELMVASLQAEDPGAEVLPFMLGGGTDNKSLARLGITGYGFAPMRLPADLAFTSLFHGIDE +RVPVDALEFGCRVLERMLEPR +>MOLHKGIG_01166 +MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDEADPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPEVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE +RVPVDALEFGCRVLERMLEPR +>NAFOICDF_01621 +MDASTPSTAPSTADADVVEICRDLIRIDTTNHGGGRSVGEPEAAELCAAWMRKAGMEPEL +IESAPGRVSVVGRLEGWDPEAPGLVLHGHTDVVPAEPDEWTVDPFGAEFRDGMIWGRGAV +DMKGMDAMILSVLVHLARTGRRPRRPVVVAFFSDEEAGGVFGAQWLVAHRPELFAGCTEA +ISEVGGFSTDVAGTRAYLVQTGEKGLAWLNLRAQGAPGHGSAPHTDNAVTRLAGAMERIG +RHPWPLTYTKTTRQLLEEVAEITGTPFDERDPTPQLQALGHARDWVAGTLRTSSNPTGLT +AGYKHNVIPSTATGTVDVRLIPGEEEQTLAELADLAGDGIEISPEHQDTGLEVPFSGDLV +ERMASALDAEDPGAHVLPFMLGAGTDNKSLHRLGIAGYGFSPLQLPSGLEFTRLFHGIDE +RVPVESLRFGCRVLEHVLEPRA +>MHAAABBN_00885 +MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDSEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE +RVPVDALEFGCRVLERMLEPR +>LFPAFLNI_01116 +MVENIENPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMTEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHGIDE +RVPVDALEFGCRVLERMLEPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001195.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001195.fa new file mode 100644 index 0000000000000000000000000000000000000000..ead06afaf319a0784b0ded1104cc70dc65b6246e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001195.fa @@ -0,0 +1,101 @@ +>ACLBLIBL_01726 +MSRRFLSALLVHVPDIPEFASLPAAEQDELRAAGAAVQARLERSGTIDRPAVAAALWPAL +RRVHAVPRSPEREAAYAAFRAEAGPGLDDFALWSALRTADDVPGPDLADPAWAPGGEHAE +RVRTERADEVDLHRWVQWVAAEQLAAVQQRARAAGMRMGVMVDLAVGATRETADAWMLGD +VLVPGMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRDAGGIRMDHVL +GLFRLWWIPVGAGATQGAYVEYDHEAMLAVLTLEAERAGAVVVGEDLGTFEPWVQRRLAE +AGVLGTSILWFEQRDGEPLPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTV +DVAQERRRSADEVEAFLGAAVRRGLLDARDARVRPDDAAQREAQTVALHRLLAQAPSALH +SVSLVDAVGERRIQNQPGTTQDQYPNWTLPLGDREGRMLRVEDLASSASAARLFDAVEEE +LRASVPVGIGVSLHTSPLAQPGRGDAGGLNVYVRHAALALARRGVRMILLTRAEEPVGPE +SARVTRLEAGGEAPAVTVVELAVGPAAPLPKAELAALTDEFTAAARAWLASDAVPGGPVL +APQGLDGRGPGAPAAPPVAFVHGHYWLSAPTAAALAAATGAPHLHTMHTTAAVKMLEDPE +LREPGARIEAEGAVVREADLLVVNSPAEVVDLREALGVPRARTRVLPPGADLATFTPEGP +ALWPGDPDDDGALRVLFAGRIQRHKGPHLLVEALAVLRERAGGPGADPGVRLHVNGAPSG +EEGLDLPGLALERGVADLVTFSEPVRAEELAAQLRAADVVAMPSASETYGLVALEAQACG +TPVLAHRVGGLVHAVIDGASGRLVTEGSPEAWADALAAVLADRPAWDALAAGAVRHAAGH +SWEAYADGLLEAAAGLARRQDGA +>MOLHKGIG_01164 +MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV +EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR +LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA +AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR +RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV +HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR +VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV +PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF +RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV +LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA +QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA +LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA +SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR +VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA +DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE +VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL +RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE +GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY +AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV +TAVPRRSPGLDA +>NAFOICDF_01623 +MPENARALLRRLARAHGVQTEYVGQDGSDQSVADETLVRVLSALGVEVDADGVAGLTEAL +DAVDAAPWRDVLPPTVVARQGHRSTVPVHVARGAAVQVRLVQEDGRVVDLPTREAVGATL +VVDGQERVRHDLDLPEDLPLGWHRLEAVSETGSVARATLVSAPAALTTAAPFLARRGWGV +AAQGYSVTSSGSWGVGDAHDAGSLAELAAPHGADFLLLHPLHAVEPAGAPADSPYSPVSR +RFLSAFLIRVTDIPEFAALPAEEQKRLAAAGRAVQEAVLTGGTIDRAAVAEVLWPALEAV +WRAPRTSERDADYAAFRDRQGTGLDDFAAWSVLRRDALRAGVAGPDPTDPAAGPGSDGVR +RVRAERADELDFHRWVQWIADEQLAAAQERAREAGMRMGVMLDLAVGATRGSADAWMLGD +VLVPSMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTLMAHAGGLRMDHVL +GLFRLWWIPEGLGAPQGAYVHYDHEAMLAVLTLEAERAGVVVIGEDLGTFEPWVQRRLAE +AGVLGTSILWFEQEDGVPTPPEQYRRLCMAAVNTHDLPPTAGYLEGVHIDLRERLGLYTA +DVAAERRRSAAEVEAFLGAARKRGLLEATGPDGVETVEDRVVALHRLLAQAPSALHCVGL +VDAVGERRIQNQPGTLQEQYPNWTVPLGDADGRVLTVEDLAGTASVSRLFDAVAAELDAS +VPVGIAVAFHTSPLAQPGQGDAGGLNVYVRHSARALARLGVRMLLLTRAESPVGPSGVRV +TTLPQGEGAPDVTVVELAAGPQEPVAKEELPAHREAFTAAAREWLASADVPGGPLLGAAG +AAAARVRFVHAHYWLSGDTAAAVADDLGAPRVQTMHTTGAVKSAGDPGHPEPAERLAAEA +DLVRRADLLVVNSPAESRDLQELLDVDRDRVRVLPPGVDLESFTPEGPSRWPGGDAVGAD +ALRVLFAGRVQEHKGPHVLVAALAELRARAADGDPRVVLHVNGEQSGPADLDLPALAARL +GVADLVTFSPPVPPVELAAQMRAADVVALPSASETYGLVAVEAQAAGTPVLAHRVGGLVH +AVQDGVSGRLVIPNTASAWADALAAVREDRQAWDAMAPAAVRHARAHAWSGWAEGLLDAV +AGLPRP +>MHAAABBN_00883 +MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV +EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR +LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA +AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR +RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV +HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR +VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV +PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF +RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV +LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA +QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA +LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA +SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR +VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA +DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE +VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL +RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE +GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY +AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV +TAVPRRSPGLDA +>LFPAFLNI_01114 +MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAL +EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR +LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA +AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR +RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV +HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR +VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV +PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF +RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV +LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA +QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA +LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA +SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR +VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA +DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE +VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL +RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE +GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY +AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV +AAVPRRSPGLDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001197.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001197.fa new file mode 100644 index 0000000000000000000000000000000000000000..efcd48caa45b27645b71bb7b24ee5c772976ff60 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001197.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01728 +MTDRYGAFAASALGRRLTGALGLPQPVELRRHAPGEPVLHGSVLVLGAGPAAADARTLLA +SWGLEVADAPREGARLAGVVACFDDAAAPGDLGETVLQIGGALRSLGASSRVVTVSVDPE +AAAEPAVRAARQGVQGLTRSLAQEMRRGGTANGIVLGEGVPLTAPGAAGALAFLLSGRSA +YVSGQFLPVTTRDGATPADAARPLADKVAVVTGAARGIGAAIVRTLARDGATVVGVDVPV +AGESLAAVVNEVGGTALALDITAPEAGARILEHCRARHGRMDVVVHNAGITRDRMLANMD +AARWDSVIAVNTASQLAMNEAFLADDAREVTGEGLRIIGLASISGIAGNRGQTNYAASKA +GVIGLTAASAPALAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNSLQQGGLPQDVA +EAVAWFASDAAGGTNGATLRVCGQSKLGA +>MOLHKGIG_01162 +MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA +SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE +AATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA +YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA +AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDAVVHNAGITRDRMLANMD +AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA +GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA +ETVAWLASDAAGGTNGATLRVCGQSKLGA +>NAFOICDF_01625 +MPANDPYGDLVRTRLGRRLTGALGLPQPAELRRHTAGDPAVRGTVLVLGATSAADAARAL +VTAEGARAVAHPAEGERLAAVIACFDGVAAPGDLSDTALALGGALRSLEPSAHVVTVVED +PEEAEVPAVRAARAGVMGLTRSLAHEMRRGGVANGLLLRGGARLGDAGPAGALRFLLSGR +AAFVSGQFLPAAAGAGSAPASADARPLEGRVAVVTGAARGIGAAILRTLARDGATVVGVD +LPAAGEDLVRIVNELGGTALPLDITAPDAGARIVEHARARHGRLDVVVHNAGITKDKLLA +NMDAARWDAVLAVNTASQLAINEVLLSAEAADVVSPDIRIVGLASISGIAGNRGQTNYAA +SKAGVIGLTAATAPDLAARGGGITAVAPGFIETEMTAKIPLVTRELGRRVNSLQQGGRPE +DVAEAVAFLSSPAASGINGTTLRVCGQSMLGA +>MHAAABBN_00881 +MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA +SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE +AATDPALRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA +YVSGQFVPVSTADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA +AGETLAKVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD +AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGHGLRIVGLASISGIAGNRGQTNYAASKA +GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA +ETVAWLASDAAGGTNGATLRVCGQSKLGA +>LFPAFLNI_01112 +MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA +SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE +SATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA +YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA +AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD +AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA +GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA +ETVAWLASDAAGGTNGATLRVCGQSKLGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001198.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001198.fa new file mode 100644 index 0000000000000000000000000000000000000000..bee6b2c6603605d05b743a89f3087a85377ec0ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001198.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01729 +MTQPETTARPAVAGGALRPAVVVGGNRIPFARANTAYAEVGNQEMLTAALEGLVARFGLQ +GERVGQVSAGAVLKHPRNFNLTREAVLGSALASDTPAADLQVACATGMEAIGTLADKIRL +GRIDSAIGGGVDSISDAPVSLSDGARRALLRLNAAKTMKDRLAALKDLRPGHLAPEPAGA +GEPRTGMSMGDHQALTTHRWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFRGLDRD +NNLRPDSTPEKLAGLKPAFGRHLGEEATMTAGNSTPLTDGASAVLLSSEDWAAERGLPVL +AEFVDVENAAVDFVDGDEGLLMSPAYAVPRLLARHGLTLQDLDFVEIHEAFAGTVLSTLA +AWEDEEYCRERLGLPGALGSVDRAKLNVHGSSLAAGHPFAATGGRIVALLSKMLHEKGEG +SLGLVSVCAAGGQGIVALLRGR +>MOLHKGIG_01161 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTMKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQTQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR +>NAFOICDF_01626 +MSTESPRVPAETARPAIAGGELRPAVVVGSNRIPFARAFTAYAEVGEQEMLTAAIDGLVA +RLGLQGERLGQVSAGAVMKHPKDFNLTREAVMGSALSSETPAADIQVACATGMEAIGTLA +DKIRLGRIDSAIGGGVDSISASPMTVSESARRVLLQLNSAKTVKDRLKALSSLRPGQLVP +EPAAAGEPRTGMSMGEHQALTTHQWGITRQAQDELAAASHRNLGASYASGYQDDLVTPFR +GLAKDNNLRPDSTVEKLAGLKPAFGRHLGDEATMTAGNSTPLTDGASAVLLSSEDWAVQR +NLPVLAEIVDMENAAVDFVDGEDGLLMSPVYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LATLAAWEDEEFGRTRLGLPGAYGSVDRAKLNVNGSSLAAGHPFAATGGRIVGLLSKMLH +EKGEGSLGLVSVCAAGGQGIVALLRGR +>MHAAABBN_00880 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEAVGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLTTAKTMKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPVFGRQLGDEATMTAGNSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR +>LFPAFLNI_01111 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLIA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTTKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001199.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001199.fa new file mode 100644 index 0000000000000000000000000000000000000000..76d3709e6c562060a4e88510ffaf2dfcf1a82f66 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001199.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_01730 +MTVHEKLAPQSPTHTTEVPSDVAEIAPEHPEPGSLDSAALQDALLGAWAEDRRTARALVR +DPRLHRDPLLGMDEHRERVLGQLGVLVENGAVHRMFPKEFGGDDNHGGNIAAFADLVLGD +PSLQIKAGVQWGLFAAAILHLGTEEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIGTT +ATYDEAAGEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIRDED +GAFLPGVGGEDDGLKGGLNGIDNGRLHFDQVRVPRTNLLNRYGDVAEDGTYSSPIESPGR +RFFTMLGTLVQGRVSLSLAATTASFLGLHGAIAYGEQRRQFNASDPEREEVLLDYQNHQR +RLVDRLARAYADAFASNELLERFDGVFSGRADSDADRQELETLAAAIKPLATWNALDTLQ +ETREACGGAGFMARNRIPQMRADLDVYVTFEGDNNVLLQLVGKRLLTDYSHEFGRLNVGA +VSRYVVAQASDAIHRAGLHKAVQSVSDGGSERRSANWFKDPEVQRDLLTDRVRAKTADIA +GTLAGVRGKTQAEQAAAFNTRQHELIEVARNQGELLQWEAFTRAVQATRDESTRTVLTWL +RDLFALRVLEEDLGWLVAHGRLSSQRARSLRGYVNRLAERLRPFALELVEAFGLEPEHLR +MDIATQAEAERQAEAHAWFEARRAAGEEPEDEKAVRAREKAARGRRG +>MOLHKGIG_01159 +MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK +DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD +PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT +ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE +GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR +RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR +RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ +EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQFVGKRLLTDYSKEFGRLNVGA +VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA +GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL +RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR +MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG +>NAFOICDF_01628 +MTDIRTDAASAAEALPATDAVPHDVAEIAPEDPTPGALDAAALQDLLLGSWAEAHRTARG +LVKDERLHRDPALGMDEHRARVLDQLGILVEEKAVHRAFPADLGGQDDHGGSIAAFANLV +LADPSLQIKAGVQWGLFSSAILHLGTREHHEKWLPGAMDLSMPGAFAMTEIGHGSDVASI +ATTATYDEATQEFVIHTPFKAAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIR +DESGAFLPGVGGEDDGLKGGLNGIDNGRLHFDHVRVPRTHLLNRYGDVAEDGTYSSDIAS +PGRRFFTMIGTLVQGRVSLSLAASIASFMGLHGALAYAEQRRQFGGPEGSETLLLDYQNH +QRRLIDRLARTYADLFAANELLEKFDHVFSGAGDTDKDREELETLAAAIKPLTTWNALDT +LQEAREATGGMGFMAGRNRLPHLRADLDIFVTFEGDNNILLQLVGKRLLTDYSAEFGKLN +VGAVSRWAASEASDALHRVGLHKAAQSVHDRGDQRRAANWFKDPQVQRDLLTDRVRTRVA +DIASTLGSARGKSKAEQAAAFNSRQHELIEVARHHGELLQWEAFTRQVESLPAGQTRTVL +TWLRDLFALRLIEDDLGWLVAHGRVSSARARVLRGYVNRLAERLRPFALELVEAFGLEPE +HLRMEIATDAESVRQQEAADWFAARRAAGEEPVHEKTLHAGKR +>MHAAABBN_00878 +MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK +DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD +PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT +ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE +GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR +RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR +RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ +EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA +VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA +GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL +RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR +MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG +>LFPAFLNI_01109 +MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK +DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD +PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT +ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE +GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR +RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR +RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ +EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA +VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA +GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL +RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR +MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001200.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001200.fa new file mode 100644 index 0000000000000000000000000000000000000000..5ee4ca7657aa0a74f69d6f11ef0a94bf65065476 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001200.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01731 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGEPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANMAGHLGKLMHGVPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAEKTAYLGADAVIAVSDGMRRDILACYPEVDPEKVHTVHNGID +TEAWTPQTETDALEKYGIDPTRPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTPELAHEVNGLIAELRRTREGVVVIEGMIPRREVTQILSAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPIEQVADGTGAPADEDAFAADFAAALTRVLE +DPERATAMGEAGRARAIEHFSWEAIAERTIEVYEAVLR +>MOLHKGIG_01158 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR +>NAFOICDF_01629 +MRIDIVTKEFPPTIYGGAGVHVAELTRVLSSRADVHVHAFGGAREPDYHGATVTSYAQPA +GFESANGAVQTLVTDLDIVGDLDGADVIHSHTWYANMAGHLGGLMHGVPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAESTAYHGAAAVIAVSEGMRRDILRCYPDVDPAKVHTVHNGID +TQLWTPQTGTDALTKYGIDPDRPSVAFVGRITRQKGVPHLLRAALQLPEDVQLVLCVGAA +DTPELAREVEGLIGRLRAEREGVVVVEGMIPRGEVTQILSAATVFACPSIYEPLGIVNLE +AMACGTAVVASAVGGIPEVVDDGVTGLLVPVEQADDGTGTPVDEEKFAADLAKALSTVLA +DPERATAMGEAGRARAIEHFSWETIADRTMEVYAAVAR +>MHAAABBN_00877 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELIAELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR +>LFPAFLNI_01108 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001201.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001201.fa new file mode 100644 index 0000000000000000000000000000000000000000..d401b7a3f14b534dc2cbd22bb003b5cb71846f39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001201.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01732 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPQTTPGLPDDPTLFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRDWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVANEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTDSGLTVLAKDQSVPKPH +>MOLHKGIG_01157 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH +>NAFOICDF_01630 +MVEKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGEYRLIDFALSNLVNSRFREIVVLTQ +YKSHSLDRHISETWRMSTMLNNYVATVPAQQRRGKDWFTGSANAIYQSMNLISDARPDIV +VVIGADHVYHMDFQQMVDHHVASGAKATVAAVRQPLELADQFGVIETDATDPGRITAFVE +KPATTPGLADDPAQFLASMGNYVFDTDALVEALNADDANPESNNDMGGDIVPYFVGRGEA +GVYDFTTNEVPGGTPGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRAWPLYTRQSVSP +PAKLVRSASRRPGTAGDSILAQGVVISGGTVAQSVLSTDVRVGNEAWVEQSVLLDSVTVG +EGAHVRNAIIDKNVVIPAGARIGFDRAEDEANGYTVTDSGLTVLSKNQRVPDPR +>MHAAABBN_00876 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH +>LFPAFLNI_01107 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001202.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001202.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c0b38d22f7ee5dda433656667723badd27110d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001202.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_01733 +MPRPHAAVDLDATNVTRAEAAERSRLLTVSAYEVHVDVSGARDEAAETYPVEATLRFVCA +EPGAAAHVDWIHAGVDAVVLNGRELEPADVVGDARILLPELAAENELVLRGRSRYSRSGE +GLHRFTDPADGQVYLYTQYEPADARRVFPDFEQPDLKAAFTFALTGPADWVLASNRPEAS +RTEVRPGVVRVDFEPTLPQSTYITTLLAGPYASWEDRWDGHAGTDAPAVPLRLFTRQTMA +EAFDPEAVFDVTRRGLDLFHELFGVPYEWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFT +SRATAAQYEGRANVILHEMAHMWFGDLVTMRWWDDLWLKESFADFMGTLGVDEATDFETA +WVTFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRD +AFLDAARRYFRAHAWGNAELTDFMAALEAASGRDMGAWADAWLHTSGVPRLRVEAGDDGA +SMLHQEGADPVTGRPVLRPHALKVGVFTPDEAGVLRRTAQVAADVPGGADGAAVVLEGLT +VPAGVRLVLPNDEDLTYAALALDEASLQAALTHPIADPLAEATVWAALWSMTRDGELSAA +RFLEAVERLSAGIETVGVHTQVLAQAAAAVSQFAAAADRPSLRARLAETLAEQVRTLEAG +SDRQRTAARTWALVARADADLARPLAAALLGGTGAGAADGEAGEDAPGLAVDAEIRWLVL +QALAATGQADEARLDAELAAGRTAQTVTWHRLATAARPEPAVKAAAWEAVMAGRTADGVE +LSNDLLSATAAGFAAGDVELLAEHEAGFWPRLEQVWASRSNGLASRAIGGLFPGHQDAVA +GDAGAQESHPTLASAQRWLDEHPDAPGALRRLVVEHTDHLRRSLRVQAAQPTA +>MOLHKGIG_01156 +MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP +GAQTHLDWIHGGVESVALNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL +HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT +PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA +FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR +ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV +TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF +LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL +RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG +GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL +DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR +QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ +DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA +GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT +LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG +>NAFOICDF_01631 +MTDSPTLTRDEARARARLITVHDYDVHVDVSGAADASAAAYPVTATIRFDCAEPGAETWL +DWISASVESVELNGEALDPAVVASRSRVRLPDLAAQNTVTLRGTSLYSRSGEGLHRFVDP +ADGRTYLYTQYEPADARRVFPDFEQPDLKASFTFRLTGPADWVLASNGAEVGREDAGEGA +VTVAFAPTRRLSTYITALVAGPYAVVEDRWDGHAATGAEPLPLRVMCRRALAEHLDADEL +FRITKAGLDFFHDLFGIPYEWGAYDQAFVPEYNLGAMENPGLVTFTEHYIHDTAPTRGQL +EGRATTVLHEMAHMWFGDLVTMRWWDDLWLKESFADYMGTLAADEAAGFDESWTTFASRR +KAWAYVQDAYPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAFVGRDAFMEAARV +YFHRHAWGNAELDDFLAVLGAASGRDMSAWADAWLRTAGVPALAVEVDGDGAPVLVQSGV +DPRTGEPIRRPHVLRVGVFTPDADGALTRTAQVDADIAAGAERTTLPGLAVPDGPRLILP +NDEDLTYAAVALDEASLDAVLTRPVADPLAQATVWAALWSMVREGTLPAARFVGAVQELS +ASVAGVAVYTQVVSQAAAAVELYATAAQRGALRAGLGEHLLSALRSLEAGGDRQRAAVRT +LAVLARGDADLARRLETAVLEDAETGAPGLAVDAEIRWLVLQALAATGSADRARLDAALA +EERTAKTVVAHRLAVQAIPDPAVKRAAWDAVLAGEDAEGQALSNDLLSATASGFAAGGHD +LVDPFEPGFWGELEGLWSSRSNGLASRAISGLFPLHQDALPGDAAAQEAHPVLARAQAWL +DEHTAAPGALRRLVVEQTDALRRSLRVQAAQPTP +>MHAAABBN_00875 +MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP +GAQTHLDWIHGGVESVTLNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL +HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT +PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA +FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR +ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV +TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF +LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL +RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG +GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL +DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR +QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ +DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA +GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT +LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG +>LFPAFLNI_01106 +MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP +GAQTHLDWIHGGVESVTLNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL +HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT +PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA +FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR +ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV +TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF +LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL +RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG +GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL +DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR +QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ +DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA +GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT +LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001204.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001204.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c96909b467ae913eb68bdcfffb7e0c549efcea8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001204.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01738 +MKSEIHPDYRYVIFNDLASGEKILTRTTANSEKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGSK +>MOLHKGIG_01153 +MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGKK +>NAFOICDF_01633 +MKSEIHPDYRYVIFNDLASGEKILTRTTATSEKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGKK +>MHAAABBN_00872 +MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGKK +>LFPAFLNI_01103 +MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGKK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001206.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001206.fa new file mode 100644 index 0000000000000000000000000000000000000000..46e244c9dbe01cac23551db6bd262da2ff418339 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001206.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01742 +MTLPAPSDDWFLPDEDAVLQMRRVRVRRGQTDILGPLDWTVRAGERWIVMGPNGAGKSTL +LQIAATRLHPTGGEVAILEEVLGAVDVFELRPRIGLSSAQLAAQVPHEEKVQDAVVTAAY +GVTGTWRESYEDEDRMRALGLVSSWGLSRLAHRRFGTLSEGERKRVLIARSLMTDPELLL +LDEPAAGLDLAGREALVAQLSELARDEDAPALVLVTHHLEEVPPGFTHALLLRDGHAVAA +GPIEQTLTEGHLSAAFDTPLRVTRTGGRYTAVAQ +>MOLHKGIG_01150 +MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL +LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY +GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL +LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEEVPPGFTHALLLRDGGVVAA +GPIESTLTEEHLSAAFGTDLKVTRTGGRYTAVAR +>NAFOICDF_01636 +MNTAPQDPSPRPVVEHDVFTPDEDAVLQLRDVAVRRGAKQILAGIDWTVRAGERWVVMGP +NGAGKSTLLQIAASRMFPTSGDVAILDEVLGAVDVFELRPRIGLSSALLANQVRDDETVQ +DAVITASYGMTGRWREEYEVEDRARALGLVSEWGLSRLAHRRFGTLSEGERKRVLIARAL +MTDPELLLLDEPAAGLDVAGREALVGQLSELAADEDAPATVLVTHHLEEVPPGFTHALLL +ADGAVVQAGPLEETLTAEHLSTAFGTPLRVTRADGRYTAVAA +>MHAAABBN_00869 +MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL +LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY +GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL +LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA +GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR +>LFPAFLNI_01100 +MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL +LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY +GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL +LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA +GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001207.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001207.fa new file mode 100644 index 0000000000000000000000000000000000000000..303f9e5cb9f5aaa314c8081a7d58b7565187fff2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001207.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01743 +MSTLRRLVVTADPALLADRTPPAGVPDDAERLLEDGLLGWRFAADEWAAAPEPGPGWAVH +TLPAAVAEAPVPLVVTDVDSTLIRQEVIELLAAHAGREAEVAAVTERAMRGELDFAASLH +ARVEALAGLPVGVVDDVVRAIRPTAGALALIEAVTAAGGRVCAVSGGFSQVLAPLAQAWG +VHAYCANELEVHDGHLTGRVAGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGANDIDL +LDAAGAGVALCAKPVLREHADVVVDVPSFTPLRWLLGL +>MOLHKGIG_01149 +MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL +TVPATVAAAPAPLVVTDVDSTLIRQEVIELLAAHAGREAEVAEVTERAMRGELDFAASLH +ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG +VHAYCANELEVQDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL +LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL +>NAFOICDF_01637 +MTQARHLLYRAVPAGTDSPVAPAWAPLPADAEHLAADGLAGLRWEGSVPSAEEATALPED +WALASLPQSVAAAPTPLVVTDVDSTLIQQEVIELLAAHTGREAEVAAVTERAMRGELDFA +QSLHARVEALAGLPASVVDDVVARVRPTDGAVELIAAVNAAGGRVCAVSGGFTQVLAPLA +EAWGVHAYCANELEVRDGHLSGKVLGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGAN +DIDLLEVAGCGVALCAKPILREHADVVIDVPSFTPLRWLLGL +>MHAAABBN_00868 +MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL +TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH +ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG +VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL +LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL +>LFPAFLNI_01099 +MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL +TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH +ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG +VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL +LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001208.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001208.fa new file mode 100644 index 0000000000000000000000000000000000000000..85af4b38ddca86a895ba817c09614e365fc5d4d7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001208.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01744 +MTEKDLTGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQKIEEAGGRA +VAVGGDVTSAEDRAALLDAAVESFGSLDVLVLNASGGMESQFGEDYAMKLNRDAQAALAD +AALERMSAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFEAKGVGF +AVVSGDMIEGTITATLLDRAEPGAIDARREAAGRLYSVEEFAAEVAALVGRDDLEVGHTE +LVGGARDFLARGEG +>MOLHKGIG_01148 +MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA +VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD +AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFTEKGVGF +VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREGLEVGHTE +LVGGAEDFLGQD +>NAFOICDF_01638 +MTTQDLAGKGVVVTGSSRGIGAETAQLLAARGAGVVVNYRQKAPRANKVVQAIEAARGRA +VAVGGDVTVAEDRAALLDAAIDNFGSLDVLVLNASGGMESQFGEDYAMTLNRDAQAALAD +AALERMSAGGQIVFVTSHQAHFIDEVATMDAYEPVARSKRAGEDALRERIPAFEAKGVGF +VVVSGDMIEGTITATLLNRAEPGAIEARREAAGKLYSVEEFAAEVAALVGRTDLEVGHTE +LVGGAQDFLGQD +>MHAAABBN_00867 +MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA +VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD +AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF +VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE +LVGGAEDFLQQN +>LFPAFLNI_01098 +MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA +VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD +AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF +VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE +LVGGAEDFLQQN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001209.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001209.fa new file mode 100644 index 0000000000000000000000000000000000000000..f2c48f5431ec57e468602bbf9323c02cb8a9d6c7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001209.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01746 +MTSSAAGSRAGRPARAGRSTGPQVQGVTTASAARSEDREARMKVYLVQMLIRTVCFGAAL +FTTGWWQLLFILGAVALPYVAVVQVNNAGPRQAGSLRAVPAEGPELTARPADAPGPASPV +VLTGDVVDDPREVGPRALPPGSPSEGARRLPGRGAA +>MOLHKGIG_01146 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMRVYLVQMLVRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPEPVV +LTGDLVDDPRDRAPRALGRGSSSAGSPGLPGRGGA +>NAFOICDF_01640 +MAAIVREPDAVQGVTTAAAPRSADRDARTRVYVVQMAVRTACFIAALFTHGWWQILFILG +AVVLPYVAVVRVNNTGPREAGRRRDVARTAPAVPALPAEPSPVPTGPVVLVGEVVEDDDP +AARRALPAGSPGETGRGRP +>MHAAABBN_00865 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPKPVV +LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA +>LFPAFLNI_01096 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLHAVPAQGPALAPRPDDTAAPKPVV +LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001211.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001211.fa new file mode 100644 index 0000000000000000000000000000000000000000..706b6cd724ae880b82259e3051fd97c44c978623 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001211.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01748 +MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKILAGGGQPTAGSVTR +TGRIGYLPQDPKVEDMDQSGRDRILSARDLDHTIRRMREAEAGMAAVDDVERQRAMDRYS +RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM +LLDEPTNHLDHDSIVWLRDYLKTYPGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM +TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG +VEGERAADRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGEEAPDTGEVQEGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILGALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNEDYKDLITLA +>MOLHKGIG_01143 +MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR +TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS +RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIL +LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM +TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG +VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLGIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA +>NAFOICDF_01643 +MLTVTDLELRVGARLLMDEVSFRVAKGDKVGLVGRNGAGKTTLTRVLAGITQPTAGSVTV +SGRLGYLPQDPKVEDMDQSGRDRILAARDLDQTIRRMRAAEADMASEDDAARQKAMDRYS +RLQAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADTM +LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDAMRQTIDVYNM +NWKNYQAQRQQDEARRRREFANAEKKASALLAQAEKMRAKATKATAAQNMIKRAERMMRG +VEGERAQDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGTESPDTGEVIAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QCRTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILNALRQYEGAVVLVTHDEGAVEALAPERVVLLPDGDEDLWSDDYLDLISLA +>MHAAABBN_00862 +MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR +TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS +RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM +LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM +TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG +VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA +>LFPAFLNI_01093 +MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR +TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS +RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM +LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM +TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG +VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILNALQQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001213.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001213.fa new file mode 100644 index 0000000000000000000000000000000000000000..b36c7373359ff528e5da0a791c9a0af421f5e58b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001213.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01751 +MTETANQVPTEDVREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>MOLHKGIG_01141 +MTETANQVPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>NAFOICDF_01645 +MTDTAAQTPVEDIREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGKDQMRALGFNI +>MHAAABBN_00860 +MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>LFPAFLNI_01091 +MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001214.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001214.fa new file mode 100644 index 0000000000000000000000000000000000000000..ecc0c632475a75331a5fb6a0ebaf5328ffddafe4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001214.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01752 +MATLQITDLHVQIETENGPKEILKGLSLTIETGQTHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAAEQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAAQLE +AEGYARFEKAAAGV +>MOLHKGIG_01140 +MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA +>NAFOICDF_01646 +MATLQITDLHVQIETENGPKEILKGLSLTINTGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTAIDGEAPSLR +TWSKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAAEANEMGTLLITHYTRILNYIKPQHVHVLVDGRVAESGGPELAARLE +SEGYARFEKAAAEA +>MHAAABBN_00859 +MATLQITDLHVQIETENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA +>LFPAFLNI_01090 +MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001216.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001216.fa new file mode 100644 index 0000000000000000000000000000000000000000..674c63ec51a41e9afcdde31e0de9dc21c39e181e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001216.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01754 +MTDQIVQRDPVENADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD +ISGKKDEPEWMRNLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP +EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE +IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT +LIIADEDSYVHYIEGCTAPIYNSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR +AVVESGGTMEWVDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA +PNTSSSIVSKSVARNGGRAAYRGLVQVTEGAKNSANSVVCDALLVDTVSRSDTYPYIDIR +EDDVTLGHEATVSKVSEEQLFYLMSRGLSEDEAMAMIVRGFIEPIARELPMEYALELNKL +IELQMEGSVG +>MOLHKGIG_01138 +MTDQIVQRDSTETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD +ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP +EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE +IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT +LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR +AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA +PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR +EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL +IELQMEGSVG +>NAFOICDF_01648 +MTDQIVQQDSRGADPGVISEILEKNPELNAIGAYQYGWADSDAAGSSARRGLNEDVVKDI +SAKKSEPEWMTKLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWDDLPE +DIRNTYERLGIPEAERDRLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPEI +FEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERTL +IIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKRA +VVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEGATGETLSVAFAGKDQHQDTGSKMVHMAP +NTNSSIVSKSVARNGGRAAYRGLVQVNEGARGAANSVVCDALLVDTVSRSDTYPYIDIRE +DDVTLGHEATVSRVSEEQLFYLMSRGLAEDEAMAMIVRGFIEPIARELPMEYALELNKLI +ELQMEGSVG +>MHAAABBN_00857 +MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD +ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP +EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE +IFEEYFGSVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT +LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR +AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA +PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR +EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL +IELQMEGSVG +>LFPAFLNI_01088 +MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD +ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP +EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE +IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT +LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR +AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA +PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR +EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL +IELQMEGSVG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001218.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001218.fa new file mode 100644 index 0000000000000000000000000000000000000000..614cdf2b59b37afb787a92040b6fe55901d68834 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001218.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01756 +MVPRPVLTPDPAPRDEPVLRLRDVHRSLGRGRARTPVLRGVDLTARAGAVTVLLGPNGAG +KSTTLGLCHGMDRPDAGAVRVFGADPWRAPADLRARIGVMWQEGGLPPSVPARRFVGHVA +SLYRDPMPVEPLLERLLIADVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD +PETRPVVHEVVREQTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGSLADLTRVAE +GDVVDVDFGDAAPEAVRAWADALPEPLRAAGLAEPARLRVAGVHGPAELAALAASWHRHA +LMPTRFERAGLRLEQILRETAA +>MOLHKGIG_01136 +MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM +DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP +LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV +REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA +SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL +RLEQILRETAA +>NAFOICDF_01650 +MPETSPHPDAPALRLHEVRRTLGRGAARTEVLRGVDLEARRGAVTVLLGPNGAGKSTTLA +LCHGSDRPDSGTVRVFGRDPWRADADLRARLGVMWQEGGLPPSVTARRFVRHVASLHGDP +LDPDALLGRLRIDRVADRPIRRLSGGQRQRVALAAAVVGRPDLLFLDEPTAGLDPETRPV +VHDVVREHTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGTLAELTRVQDGDVVDV +RFDEARAADVRAWVAAAPASFRAVASAGAPAARVAGVRSPADLEALAASWTRAGLFPTRL +ERAVLRLEELLQSPDADTPSPERSR +>MHAAABBN_00855 +MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM +DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP +LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV +REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA +SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL +RLEQILRETAA +>LFPAFLNI_01086 +MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM +DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP +LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV +REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGPLSELTRVAEGDVVDVDFGDA +SPDAVRAWADTLPAPLRAAGLGESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL +RLEQILRETAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001219.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001219.fa new file mode 100644 index 0000000000000000000000000000000000000000..aac0a55e532790a5ca3ffcaf3f534bc2251d687e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001219.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01757 +MSAPIAPGSAEPRTAGQVPEPGTAPHAGAAPLATRVLRQAAYETGTALRNGEQLLVTVVL +PLLALVGVHVTGLLDEPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT +TPLGTLGLVAGKALSVVALLLVQVAVIGGVGLALGWRPEAAGILPAVVALALGAAAFTAL +GLLLAGTARPEATLAAANLLWVLFGAVGGTVFPSRVPGVDLLPSGALGSALRAALVDGAG +APIPLLVLALWCAVAVAAALRWFRWRP +>MOLHKGIG_01135 +MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH +VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV +AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR +PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT +LWGAVAVAAALRWFRWRP +>NAFOICDF_01651 +MSAPAAPIPASHAGAAPLGARILAQARYETVTALRNGEQLLVTLVLPLLALVGVHVTGLL +DAPGRNGLDLAVPGVLALAVISAAFTATAISTGFERRYDVLAALATTPLGTGGLVAGKAA +AVAAVLLLQTIVIGGVGLALGWSPDPAGIPPAVVALLLGAAAFTALGLLLAGTARPEATL +AVANLVWVLLGALGGTVFPSRWAWMDLLPSGALGTALRSALQDGAWAPSALAVLAAWTVM +AVAAALRWFRWRP +>MHAAABBN_00854 +MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH +VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV +AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR +PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT +LWGAVAVAAALRWFRWRP +>LFPAFLNI_01085 +MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH +VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV +AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR +PEATLAVANLLWVLFGAVGGTVFPARVPGVGLLPSGALGTALRAALLDGAWSPVPLLVLT +LWGAVAVAAALRWFRWRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001223.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001223.fa new file mode 100644 index 0000000000000000000000000000000000000000..045341f3cdfe01532ccac22199b98e590767d735 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001223.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01761 +MSTQQNPNTAALAEAGVSIWLDDLSRKRLDEGTLEELMATRSVTGVTTNPSIFAVALADA +GSYEGQLRELAAAGADVDEAVTALTTQDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAEGTARQAQELAAAVDRPNLMVKIPATVEGLAAITDVLAEGISVNVTLIFSLPRYRQVL +NAWLAGLEKARENGHDLSRIHSVASFFVSRVDTEVDARLRALGTPEAEALTGQAALANAR +LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTGLVAPRTVTTLPE +QTLEAVADHGEVAGDTVTGGYAEADALLDAVGAAGVSYQDVVDVLETEGLQKFESAWEEL +LGSVRDGLAAHR +>MOLHKGIG_01131 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR +LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE +KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL +LGSVRSGLDAHR +>NAFOICDF_01655 +MTTETTPATAALAAAGVSLWLDDLSRTRLNEGSLERLIATRNVTGVTTNPSIFAAALKDA +GAYEAQLAELAAAGADVDAAVTALTTTDVRRACDLLAPVHQETGGRDGYVSIEVDPRLAR +DTAGTVAQARELVALVDRPNLMVKIPATVEGLPAITEVLGAGISVNVTLIFSLPRYREVL +NAWLSGLELARANGHDVSRIHSVASFFVSRVDTDVDAQLRALAEQGRPEAGELTGRAGLA +NARLAYRAFEQMKDTERWSLLEAAGAPVQRPLWASTGVKDPALADTLYVTALVAPDTVNT +MPEKTLEAYADHGELTAEPVVGGYAQADADLDAIGELGISYTELVDRLETEGLQKFEAAW +DELLASVRAGLAAHR +>MHAAABBN_00850 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR +LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE +KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL +LGSVRSGLDAHR +>LFPAFLNI_01081 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRELAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR +LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE +KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL +LGSVRSGLDAHR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001224.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001224.fa new file mode 100644 index 0000000000000000000000000000000000000000..fcc4003dca9195c07bd6b8a7f84ae171d3210521 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001224.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01762 +MSTLGLSATGSALEAIDRHLPTLLEDRVASRLGAQDAGLWGEAAREESARRLGWIDLFED +SRALVRHIDALSRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA +LERDLERTVLVVSSKSGSTVETDSQRRVMEAAFREAGIDPRSRLVAVTDPGSPLHAECES +AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLTADDADNPGLQ +LGAALGGTAPLRDKLVFTDHGSGIDGLPAWAEQLIAESTGKDGTGLLPVVVADGDPETGW +DAPDMLQVQLVGEDAPAAPAHGVQVSGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA +KTAARSLLDAPARERTADRTVDGVELSGPEAVVSAADLAGVLRATADLVPENGYLAVHAY +LSRHDDAELEEVRADLARLAGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQVTGDADLDV +EVPGRPFSLGRLIAAQAAGDARVLVEHGRPVVTLHLPHRAAGIDAIRTAARAR +>MOLHKGIG_01130 +MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED +SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA +LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES +AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ +LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW +DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA +KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY +LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL +EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR +>NAFOICDF_01656 +MSTFGLTATGAALDAVDRHVPALVAERFASRLAAEDADLWGPDARDEAAKRLGWISLFEE +SRTVAAEAAALAEELRGQGLTRVVLAGMGGSSLAPEVIAATAGAELEVLDSTDPQQVAAV +LDHDLERTVLVVSSKSGSTVETDSQRRIVEAALAAEDIDPASRIVVVTDPGSPLEEASVE +AGYRAVFTADPTVGGRYSALTAFGLVPAALAGVDVESLLDEAEDVLDLVTADDADNPALQ +LGAAIGGTEPLRDKLVIQDLGSGIDGFGDWVEQLIAESTGKDGTGLLPVVVRPGDPETAW +EAPDLLKVTLVSESEESPAGGDGVRLHGSLGALLLTWEAATAVAGRLLGINPFDQPDVEA +AKAAARELLDSPAEEAEPGTVIHGVEVSGPESVTSADDLRGVLAAVRELVPEDGYLAVHA +YLDRHADVDLAGIRADLASALGRPVTFGWGPRFLHSTGQYHKGGPRNGVYLQVTGDAALD +VEVPGRPFTLGRLIAAQAAGDADVLRRLGRPVVTLRLRDRSAGIAALRTAAREA +>MHAAABBN_00849 +MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED +SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA +LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES +AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ +LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW +DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA +KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY +LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL +EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR +>LFPAFLNI_01080 +MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED +SRALVPHIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA +LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES +AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ +LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW +DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA +KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY +LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL +EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001227.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001227.fa new file mode 100644 index 0000000000000000000000000000000000000000..259d36cbd785e04f0104b743e620a1ae55875fe6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001227.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01765 +MDMLTLILQILVVVLSVVIVLLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRLTV +GTVAAWALLIVTLGVLPRLAMES +>MOLHKGIG_01127 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTMES +>NAFOICDF_01659 +MDILTLLLQIAVVALSVVIIMLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRVTV +SATVLWGLAIVALALIARFSVES +>MHAAABBN_00846 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTMES +>LFPAFLNI_01077 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTLES diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001228.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001228.fa new file mode 100644 index 0000000000000000000000000000000000000000..b238692a427c6f25a8a5a5363b6def8c8e27df0b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001228.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01766 +MAETAARVPLIAGNWKMNLDHREAVTLVQRLAWLLTDADHDHEDVEVAVFPPFTDLRAVQ +VLVTGDRLDVAYGAQDLSPEDSGAYTGDVSGAFLAALGCRYAIVGHSERRTIHGEDDALV +ARKAAAALRHGLSPVVCVGEGLDVRQAGRHVAHTVAQLEGSLVGLSAEDVARTVVAYEPV +WAIGTGEVAGAGDAQEMCAALRARVGELHGDDVAAGLRILYGGSVKSTSAPELLAQPDVD +GALVGGASLDAEEFARIVRFDQA +>MOLHKGIG_01126 +MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLSDADHDQEAVEVAVFPPFTGLRSVQ +TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV +ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV +WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD +GALVGGASLDADEFAKIVRFDQA +>NAFOICDF_01660 +MSVVQPVRVPLIAGNWKMNLDHQEAVTLVQRLGWLLGDADHEQGNVEAAVFPPFTDLRSV +QTLVAADRIGVAYGAQDVSAEDSGAFTGEVSGAFLAKLGCAYAIVGHSERRTLHHEDDAL +VARKAAAALRHGLVPVVCVGEGLDVRQAGRHVEHTVAQLRGSLDGLSSEDVARVVVAYEP +VWAIGTGEVASAADAQEMCAALRADLAERHGAEVAERVRVLYGGSVKSSSAPELLAQPDV +DGALVGGASLDADEFARIVRSDAAH +>MHAAABBN_00845 +MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRSVQ +TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV +ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV +WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD +GALVGGASLDADEFAKIVRFDQA +>LFPAFLNI_01076 +MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRAVQ +TLVTGDRLDLAYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV +ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV +WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD +GALVGGASLDADEFAKIVRFDQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001229.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001229.fa new file mode 100644 index 0000000000000000000000000000000000000000..afd0c0688e5abec91d68a78607ceded2192e5e95 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001229.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_01767 +MPAQTLNDLLEAGVAGRTVLIRSDLNVPLDGETVTDDGRIRASLPAIRQLADAGARVIVM +AHLGRPKGEPDPKYSLRPVAARMGELLGADVALAEDVTGPSARAAAEALADGDVLLLENV +RFDARETSKDDAERAELAAEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL +VAGELEVLTRLTQSPERPYAVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLDTVRAYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLPVDALTSGA +HGASAMGLDIGPETARAFAEQIRGAETVFWNGPMGVFEFEAFAEGTRAVAQALTEATAAG +GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALSGEGEA +>MOLHKGIG_01125 +MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM +AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV +RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL +VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA +HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG +GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA +>NAFOICDF_01661 +MTAQTLTDLLEAGVAGRTVLIRSDLNVPLDGQTVTDGGRIRASAPAIKDLADAGARVVVM +AHLGRPQGEPDPQYSLAPVARRLGEVLGADVQLASDVTGEDARAKAAALQDGQVLLVENV +RFDARETSKDAAERGELAREMADLAGEDGAYVGDAFGAVHRAHASVADIAGLLPAYQGPL +VAAELQVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLMEKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLETVRGYLERSGKDGAAEIVLPTDIVMASAFAKDAEHEVLPVDALTTG +AHGADALGLDIGPGSAAAFGERIRGARTVFWNGPMGVFEFPAFAEGTRAVAQALTEATQA +GGLSVVGGGDSAAAVRSLGFTDEQFGHISTGGGASLEYLEGKELPGVSALSGTDT +>MHAAABBN_00844 +MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM +AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV +RFDARETSKDDAERAALADEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL +VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA +HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG +GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA +>LFPAFLNI_01075 +MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM +AHLGRPKGEPDPAYSLRPVAARMAELLGADVALAADVTGDDARAKAAALQDGQVLLLENV +RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL +VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA +HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG +GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001231.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001231.fa new file mode 100644 index 0000000000000000000000000000000000000000..3cdaa843ea941b06a58b4c2949882fef4733c6ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001231.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01770 +MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAARDADDFAAVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEHFGSFDKFRAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQARFEAARQGASGLILPA +>MOLHKGIG_01123 +MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQARFEAARAGASGLILPA +>NAFOICDF_01663 +MTEFVLPELDYDYAALEPHISAKIMELHHSKHHATYVKGANTALEKLAAAREAEDFASVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEFFGSFDKFQAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQQRFEAARNGASGLILPA +>MHAAABBN_00842 +MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQARFEAARAGASGLILPA +>LFPAFLNI_01073 +MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQARFEAARAGASGLILPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001232.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001232.fa new file mode 100644 index 0000000000000000000000000000000000000000..16d0b1ed7ef2796aa1ab7de596ec466577ed9ae1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001232.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01771 +MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVSGRVVVEAELDHGASARRLRA +SITELYGLATEIVVVSGGNLRRGQRYVIRVVRGGEDLARRTGLIDQRGRPVRGLASALVT +GTTADTAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLDVAAKAREVRQ +ADRVVVRDGEAIATLLTAVGAEQTAALWRERRERKEVRATANRLANFDDANLRRSAQAAV +AAGAKVERALEILGDEVPEHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +AMADKRAAERGVPGTDTPAED +>MOLHKGIG_01122 +MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEVELDHGASARRLRA +AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS +GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ +SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV +TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +AMADKRAAERGIPGTDAASEG +>NAFOICDF_01664 +MALTMTLKEELARVPVGAVPERRAETATMLRFAGGLHLVSGRVVIEAELDHGASARRLRA +AITELYGHATEIVVISGGNLRRGQRYVIRVVRGGEDLARQTGLLDLRGRPVRGLPPALVQ +GSAADTAAVWRGALLAHGSLTEPGRSSCLEVTTPGPEAALALVGAARRLGVAAKAREVRQ +ADRVVVRDGEAIAALLTAVGADQTAALWQERRERKEVRATANRLANFDDANLRRSAQAAV +AAGARVERALEILGDDVPDHLGYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +SMADKRAAAEGIPGTAVDGA +>MHAAABBN_00841 +MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEAELDHGASVRRLRA +AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS +GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ +SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV +TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +AMADKRAAERGIPGTDAASEG +>LFPAFLNI_01072 +MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEVELDHGASARRLRA +AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS +GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ +SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV +TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +AMADKRAAERGIPGTDAASEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001233.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001233.fa new file mode 100644 index 0000000000000000000000000000000000000000..98b1ca99981851439d1606a05831859c7796989c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001233.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01772 +MTSPLTGQLPLPPGVGTAVRGPAGGMARPAIRVTALGGGHGLSASLTALRHVAGHLTAIV +TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVDAEEAT +LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGG +LRTRRVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALAAIELADWVVLGPGSLYTSVLP +HLLMPEVCQALDATAARRLMVLNLRTGDQETTGLTHADHLRVLHSHAPDLRLDVVIADVD +AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTD +>MOLHKGIG_01121 +MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV +TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFHSTEVPADQAT +LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR +LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIEMADWVVLGPGSLYTSVLP +HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD +AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVSIGEAMTH +>NAFOICDF_01665 +MTGPVTGPSTSSLPLPPAAARGAWATTSGTVRPQVRVTALGGGHGLSASLAALRLVAGHL +TAVVTVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVPE +AEATLDGHALGNLLIVALWELIGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDLLAED +DAGRLVRRHVEGQVALAQAAHDGRVVDVRLSPADAPATPEALAAIELADWVVIGPGSLYT +SVLPHLLMPEVRGALEVTTARRIFVLNIDTGTQETTGMTHADHLKVLREHAPGLQLDVVI +ADADAVADRAAVVQEARRLGARVAFSRVAHAANRLAHDPLRLAVAIDEAMSS +>MHAAABBN_00840 +MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAVV +TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT +LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR +LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP +HLLMPEVRSALAATAARRLMVLNLRTGDQETTGLAHADHLKVLRSYAPDLRLDVVIADVD +AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH +>LFPAFLNI_01071 +MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV +TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT +LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR +LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP +HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD +AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001235.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001235.fa new file mode 100644 index 0000000000000000000000000000000000000000..b1dfe38199a1b981d9b681ab82e85b04d6e5701f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001235.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_01774 +MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLGSYFQDPARLTTKTRTM +VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM +RGDRRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS +APCVGRISPAEHRELAQDFCDFMAGDAQRFIRELERAMQGAVEELRYEDAARLRDDIAAL +RRVFERNAVVLPESTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVSEPEM +VTHLLQQVYGDLAGEDRIPHEILVPAEPDDAAQLVEWLSGLRGARVNVRVPRRGTKADLM +ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEIAEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASMKDVLSRRFARLAEERAEGAPLSGQLEGE +EEGRDRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPV +VLPRTSEALYLLQRIRDESHRFAIAGHRGRRAKAMTASALDGISGLGPAKRTALLNHFGS +VAQIRAAGVERLTEVAGIGPTLAQTVHAALAPAEPTDTVEP +>MOLHKGIG_01119 +MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR +TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ +VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK +CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP +EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD +LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV +VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +ADDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF +PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF +GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES +>NAFOICDF_01667 +MADPRTYRPAPGEISTSPGVYRFRDPDGRVIYVGKAKNLRARLSSYFQDPARLATKTRTM +VFTASAVEWTVVASELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNERFPRVQVM +RGDKRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRAQAQDRPCLLGYIGKCS +APCVGRISPDEHRALAQDFCDFMAGDADRFVRELEKAMAGAVEELRFEDAARLRDDIAAL +RRVFERNAVVLAESTEADVFALHSDELETAVQVFHVRQGRIRGQRGWIMERVEDVGEDEA +VAELLTQVYGDVPDTERIPHEVLVPVLPAGAEQVTEWLSGLRGARVQVRVPQRGPKADLM +GTVRENAEMALKLHKTRRSGDLTTRSAALRELQDALEIDEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARMAEDRREGGVLTGQIDAE +EAEGERRRFAYPPSLVVVDGGPPQVAAAAEVLAELGLDDLPVVGLAKRLEEVWLPGDEFP +VVLPRTSEGLFLLQRIRDESHRFAIAGHRSRRTKAMTASALDDVPGLGPTRRRALLTHFG +SVERMRQAGPAGLTEVAGIGPALAEAVHAALTASDGGDTVAP +>MHAAABBN_00838 +MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRAM +VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM +RGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS +APCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIAAL +RRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEM +VAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLM +ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEVTEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVEGD +DQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLAELGLDDLPVVGLAKRLEEVWLPGDEFPV +VLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGS +VAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES +>LFPAFLNI_01069 +MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR +TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ +VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK +CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP +EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD +LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV +VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +GDDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF +PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF +GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001237.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001237.fa new file mode 100644 index 0000000000000000000000000000000000000000..b9d87f35fa9daff2ad181518b0f70a08554c2174 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001237.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_01778 +MSQIAPESPHPDTDAVAGDVTGRQGGGFTWDPAQYESFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLKRAREQAARTGAPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEECSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA +>MOLHKGIG_01115 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGAPANLRFEAVDASQW +RPSGATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGAAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MAGQKPA +>NAFOICDF_01671 +MSTVPAVTGRETAGFTWDPAQYEGFAEHRARPFHDLVARVEAEAPRVVVDLGCGPGTLTR +TLAERWPAAEVIGLDDSPAMLERAREGAADADLPNLRFDRVDASQWRPGPEVDVIVSNAM +LQWIPTHRRLIRRWLGDLHPGAWFGAQLPRPYQQASHATIVALADEPVFSEALHGVETTR +TVAPPEEYTRLFLEAGWTPSVWETEYQQVLTGPDPVLRWTSGAALRPSLQALAAWDAEEG +AAEGAGLLELFVARYRQAMREAYPPVPGVSDADGGPLTVFPVRRMFLVGRKPGE +>MHAAABBN_00834 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA +>LFPAFLNI_01065 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001238.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001238.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff1930468ba6ac139ac385265749472fd35cab87 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001238.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_01779 +MTSPATNPPSLTDRIDALPPTPDADDVFGAFAAWTEVRGISLYPAQEEAALELVQGRHVI +LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR +FLLMSATLGDTTRLEADLIERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA +REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV +KSGKRKSPPAGFVSWGPATFERLVAAEPEPLVSRMQITHSMLLNILDRPGDPVVAVRRLL +RGTHETPARQAILMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALELLDPAEPDHALDVVSVIEATLDPPRQVLSAQVKKAKGEAVAAMKAEGMDYND +RMRALDEVTHPQPLADLLEQQFEVYRASAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY +GIARSEGVLLRYLTDAVKALRQTVPEASRTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIEELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEELARLSGDLSA +DDWADALDAYFGDHEDIDDGPAARGTELFRVAESPDVAPPVELAGSRWWAVRQVLKDPDG +VHDHGVNAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>MOLHKGIG_01114 +MTSAATNPPSLTDRIDALPPAPDADDVFGAFAAWTEDRGISLYPAQEEAALELVQGRHVI +LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR +FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEEFVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA +REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV +KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND +RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY +GIARSEGVLLRYLTDAVKALRHTVPEAARTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA +DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG +DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>NAFOICDF_01672 +MTPSATNPPSLTDRLDALPASPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGRHVI +LATPTGSGKSLVALGAHADALAHGKVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +SVNADAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQLPLLELPQAR +FLLMSATLGDTSMLERDLAERTGREVAVVAHAERPIPLSFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAVGLASISVTTKEEKEAIAERIAGFRFSAGFGKTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQEGRLKVISGTDTLGVGINVPIRTVLLTALSKFDGEKTRILQS +REFHQIAGRAGRAGFDTQGYVVVQAPEHVIENKAAERKAAAKFAGIKDEAERAKRMKQSV +KGSKRKTPPQGFVSWGPATFDKLVASEPEPLVSRMRITHSMLLNILDRPGDPVLAVRRLL +RATHETPARQAQLMRRALGIFRELLATGVVEVLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALDLLDPAAPDHHLDVVSVIEATLDAPRQVLSAQVKKAKGEAVAAMKAEGMDYSD +RMRALDEVTHPQPLAELLEQAFERYRQDAPWLAEFELSPKSVVRDMFERAMGFGDYVRFY +GLARSEGVLLRYLTDAVKALRQTVPQEDRTEDLQVLLDWLDEMVKQTDSSLLEEWEDLMS +GDIAELRRDLESLEPTPPPRLTDNAAVFRVMVRNAMFHRVRLFGDEQDARLAELSGDLSA +NDWADALDAYFDEHEDIDDGPDARGQEFFRVATAPGARCPVELEGSRWWAVRQVLKDHDG +DHDHGINAVVDLEASDEAGHPAIRVVSVGAPVPGWDL +>MHAAABBN_00833 +MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI +LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR +FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA +REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV +KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND +RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY +GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA +DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG +DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>LFPAFLNI_01064 +MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI +LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR +FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA +REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV +KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND +RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY +GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA +DDWADALDAYFDDHEDIDDGPAARGPELFRVTAAPDVAAPLELAGPRWWAVRQVLKDPDG +DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001239.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001239.fa new file mode 100644 index 0000000000000000000000000000000000000000..5f528aec01894778cc9ede5d5059e0f954bae788 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001239.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01780 +MSAPAPRVPGDPRGFAPLEPARHRVGERTELYDGTVAVDHWFTVPVDHALTLAEAEAQDA +AGTGVGPHGRGTLTVFAREIRAAGDADGARPWALYLQGGPGGAGPRPARGGGWIGALASE +HRVLLLDQRGTGRSTAASVAALTAPGAFASDEALAEHLVHLRAPSIVRDAEMVRLALGAA +PWTTLGQSFGGFCTLTYLSFHPEGLRRCLVTGGLAPLTGHADRVYQATYARMRDRAHEFF +ARHTGDRAAWAEAVALIRAAEQAGEPVRLPDGGLLTVARAQALGMLLGGNTRVDRLHWIL +AEAVDRSGPAPRLSETFLAAVAEQNDRHVNPLYTVLHESIYAQPAELAGGRAATDWSAAR +VLAEHPDFDPDAADAPLPTGEHVMPASLELDPHLRPLRGAARLLAERTDWGPLYDVEALA +RNIVPVAAAVYTDDVYVDRDLSLETAGRVRGLRVWETDAFHHDGLADDGPAIVRRLLEMT +GEGAAPAAAEGAERSDSAPAASETTTAPGPVD +>MOLHKGIG_01113 +MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP +HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD +QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ +SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR +DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT +GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD +FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA +AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT +TTAPDPVD +>NAFOICDF_01673 +MTRTGTGDAAFVPGDPRGFAPVGPAAHREGERTVLFDGTVAVDHWFTVPVDHALTLAEAL +AQDAAGTGLGPGGRGTLEVFAREVRHPEDPEGERPWLLYLQGGPGSGGPRPARLGGWQCE +LAQHHRLLLLDQRGTARSTPVTAATLAGLPDDAARAAYLTHLRAPQIVQDAEMIRVALGA +PPWTTLGQSFGGFCTLSYLSWRAEGLERCLVTGGLAPLTGHADRVYRATTARMHARWQEF +LERHPQDAGHWAEAVALIRAAQDDGDPYVLPDGTALTVGRAQQLGMLLGGNTRVDGLHWV +LAEAVDRSGGEPRLSPGFLAAVAAQTTRAVNPLYAVLHEAIYAQPAALTDGRGATAWSAQ +RVLAEHPDSSPAADPAPVPTGEHVLPWSFETEPELRALAGVAALLAAKDDWGALYDLDAL +AANEVPVAAAVYTDDVYVDRDLSLETAARVRGLQVWETDAFHHDGLADDGPGIVRRLRGM +LGA +>MHAAABBN_00832 +MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP +HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD +QRATGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ +SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR +DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT +GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD +FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA +AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT +TTASDPVN +>LFPAFLNI_01063 +MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP +HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD +QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ +SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR +DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT +GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD +FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA +AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT +TTAPDPVD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001242.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001242.fa new file mode 100644 index 0000000000000000000000000000000000000000..6f698fce335c4835a3736a55f580a39be606f569 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001242.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_01785 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW +LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGEEMDRDV +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII +RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRI +ADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSLDREEGQERAGGGPAVDAASL +PAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ +>MOLHKGIG_01108 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW +LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII +RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI +ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRAPATGEGAEAPAVDPASL +PAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ +>NAFOICDF_01677 +MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAW +VIEQLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTPEEYIAQMVTLRRGQEMDRDA +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGQYELSQADGVVEQII +RPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKI +ADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSLDHEPPAGEVPSGSPAVDPAA +LPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ +>MHAAABBN_00827 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW +LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII +RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI +ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL +PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ +>LFPAFLNI_01057 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW +LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII +RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI +ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL +PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001244.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001244.fa new file mode 100644 index 0000000000000000000000000000000000000000..717771e97114e062b4ce55a53d2fd1eb3dc8e542 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001244.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01789 +MSAPPARCTVLPRLAAGEDGWIVHELEVRRSRFLTVLGRVADEAQARAMIAALRRRHHDA +RHVCSAFVLGPERSVARSSDDGEPAGTAGTPMLEALTARETAPGRTDLTDVCAVVVRWFG +GVKLGAGGLVRAYSESVSAALDTTPLVTRSRRAILAVDAPHAQAGRWENELRAAGVAVLD +AGYGAAGVRLRVGVPDSDAQRADFAARLADITAGAGRAEPIGTEWIDHD +>MOLHKGIG_01105 +MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRLEDEAQAREMVAVLRRR +HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV +RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV +SVLEASYGAAGVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE +>NAFOICDF_01680 +MDSPAPPAGGPVACTVLAAGALAEDGWVVHEEEVRRSRFLAVLARTPDEEAARAVVATLR +RRHHDARHVCSAWILGPGRRRMRSNDDGEPAGTAGVPMLEALSLRDTGGGATDLTDVTAV +VVRWFGGVKLGAGGLVRAYSDAVSRALDAAPLVRRTRRARYELAAPHGEAGRWAHELELT +GASLEGVRWDGPQAVIDLAVPDVPDGHSALASAVARITSGSAVAAPAGHVWVDGALA +>MHAAABBN_00824 +MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR +HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV +RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV +SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE +>LFPAFLNI_01054 +MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR +HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV +RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV +SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001245.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001245.fa new file mode 100644 index 0000000000000000000000000000000000000000..819378fae14b1492688c7fbd5b218985c303d904 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001245.fa @@ -0,0 +1,37 @@ +>ACLBLIBL_01790 +MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRDDALAGR +PDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRPVLEAEV +GPTRQVARDRTFTVTVSTRR +>MOLHKGIG_01104 +MSEPLPRGVTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHDAADLLLLDTLAGWI +ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGEA +GELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGVVLLAGGRDKHMSPRM +NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVPGVGSLHLVAHAGAFG +GAAADPGSRLLLASLADDPRPPGRLVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVAS +TLATARANRVADRVRAVRDDALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARV +LEPGGRLWCVWNSHLRYRPVLEDLVGPTRQTARDRTFTVTVSERR +>NAFOICDF_01681 +MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD +AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN +LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV +LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG +RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR +AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD +DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP +VLETAVGPTRQVARNRTFTVTVSTRR +>MHAAABBN_00823 +MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDTADLLLLDTLAGWI +ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET +GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM +NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG +GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS +TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV +LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR +>LFPAFLNI_01053 +MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDAADLLLLDTLAGWI +ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET +GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM +NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG +GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS +TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV +LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001246.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001246.fa new file mode 100644 index 0000000000000000000000000000000000000000..db214b414f7c3db41fd86edd6c06cfa8a8f49d92 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001246.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01791 +MTTTSNAPQVAINDIGTAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVESNEWMEGFESERAAWEQQY +ADAQSRWEQHKEQVRRSFEEEANAGADTGAGMGGSSYSSEAPASDGGTLASDEALAALRE +KLTGN +>MOLHKGIG_01103 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN +>NAFOICDF_01682 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKVKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRQGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQDVTVEVLDVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDQLFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDDEGNYKYPEGFDVETNEWMEGFESERASWEQQY +ADAQTRWEAHKEQVRRSLEEEAQAPAGNASTASSYSSEAPASDGGTLASDEALAALREKL +TGN +>MHAAABBN_00822 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN +>LFPAFLNI_01052 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001247.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001247.fa new file mode 100644 index 0000000000000000000000000000000000000000..99e5ab8f0614a7239c9c91f9488485991eb8e311 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001247.fa @@ -0,0 +1,85 @@ +>ACLBLIBL_01794 +MAADPTPEDPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR +PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTITLEGYEA +DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG +VSPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLTQYGDLDGVLAHADEIKGKKGEALR +AHLDDVRRNRRLNALVRDLDLPIGLEAMALEMPEREPVEELFDALQFNRIRERVFEVFSE +RIGETAPAAQVEEAPEFTEAATAQDVADFLAAEAGNLLGVHVDVEGPALLPKRKVPVPGT +FGTAVGVALVGEHAGLHVSLDADAPDPALLAALREALGEGGLSKAVHDLKRVLKAIAEPA +EATALEAGTPLDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLAAPREPAEADAQGA +FDLDGGAAAAERAARAADAVRAAWVVRRLSVLFTPQVLERGAQRLLQELEIPLARLLARI +ELTGIAVDAQALETLRADFSEAAAAAQESAWASVAEETGGMKVNLGSPKQLQEVLFEHLD +MPRTRKTKTGWSTDVDSLQDLLEQTRHPFLENLMRHRDATKLRQTVEGLLETVAPDGRIH +TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADRVAGEDAVLLSADYSQIEMR +IMAHLSEDAGLIQAFREGEDLHSFVGSQVFGVAPDEVSSEQRAKVKAMSYGLAYGLSSFG +LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGYTSTIEGRRRYLPDLSSDN +RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLAEHGMASRLLLQVHDELILEVPAAE +LEQATALLQERMGRAAELAVPLDVHVGQGRSWHDAAH +>MOLHKGIG_01101 +MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR +PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA +DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG +VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR +EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGE +RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT +FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT +EGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS +FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM +ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN +MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH +TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR +IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG +LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN +RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE +LEKATALLKERMGRAAELSVPLDVHVGQGRSWHDAAH +>NAFOICDF_01684 +MGENSTEARPRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTSMLLTMIRQQAP +THVAVAFDLSGPTFRSAEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTKEDFEAD +DIVATLSAQAEAQGWDVCVVSGDRDAFQLISERTQVLYPKKGVSDIPPMTAADVEAKYGV +RPEQYPELAALVGESADNLPGVPGVGPGFAAKWLQKYGDLDGVLAHADEITGKKGEALRA +HLDDVRRNRRLNALVRDLDLDVSLDAMELTMPEREVVEELFDALQFQRIRERVFEVFAER +LGSAAPAAPVAEAPAAVLAATADDVHAFVSAHAGTLLGLHVEIDGPDLLPKRKVPVPGTF +GTPVGLALAAEDAALYVDLTDADADPGLVAALGDLLAEDGAAKAVHDLKRTLKAIAVPTG +PTALPADTSLHGVVDDVALSAYLIQPDRRDTDLATLSQAHLQEPLEAPESAAAGAQGAFD +LDGAQEEAERTARAARAARSAWVVRRLSQAFTPQVLERGAQRLLQEMEIPLARLLARMEL +AGIAVDGDALSALLADFTDRAEAAKESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMP +KTRKTKTGWSTDVDSLQDLLEQTQHPFLENLMAHRDATKLRQTVEGLRETVAPDGRIHTT +YSQTVAATGRLSSLHPNLQNIPVRTEAGRRIREAFVAAPVDGEPAELLSADYSQIEMRIM +AHLSEDAGLIEAFNSGEDLHSFVGSQVFGVDPDDVTSEQRSKVKAMSYGLAYGLSSFGLS +KQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGFTSTIEGRRRYLPDLTSDNRQ +LRDMAERAALNAPIQGSAADIIKRAMLDVQAGLVEQGLRSRLLLQVHDELILEVPASELD +AATALLQERMGRAADLSVPLDVHVGHGGTWHAAAH +>MHAAABBN_00820 +MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR +PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA +DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG +VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR +EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE +RVGEDAPPPEAEAAPEFTEATTAEDVRSFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT +FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT +EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT +FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM +ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN +MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH +TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR +IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG +LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN +RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE +LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH +>LFPAFLNI_01050 +MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR +PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA +DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG +VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR +EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE +RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGTLLGVHVDVEGPALLPRRKVPVPGT +FGTPVGVALVGEHAGLHVSLDGDAPDPALVGAVREALGEGGLAKAVHDLKRTLKALAAPT +EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT +FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM +ELTGIAVDVDALTGLREDFTVAADAAKESAWASVAEETGGMQVNLGSPKQLQDVLFERLN +MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH +TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIRGVFVADEVAGEQAVLLSADYSQIEMR +IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG +LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN +RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE +LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001248.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001248.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff4ff868b419d1c2d7f36c225bbbd8c126344cb3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001248.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01795 +MTDHAERADAAPAPTSDLVYRPGVTPELTDAQREAACAAAGLTPELVAALGGATVSPLAQ +KMGIRFLELTPERAVATMPVAGNEQPAGLLHGGAHLVLAESLGSMAAKLHAGPERGVVGI +EIGATHHRAARSGLVTGTATAIHLGGTLTTHEVVMTDEQGRRLSTARITNMVLRGRG +>MOLHKGIG_01100 +MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAVISPLAQKMGL +RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA +THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP +>NAFOICDF_01685 +MTDTTTAPERAQALLAGLTFHAGIRPELTDEERAALATAAGMTPAVQEALGGPAVSHLAL +KMGIRFLELSAERSVATMPVAGNEQPVGLLHGGAHLVLAESLGSLSAKVHAGPHRGAVGT +EIGATHHRSVRSGLVTGTATAIHLGRTLTTHEIVMTDEEGRRLSTVRMTNMLLDPR +>MHAAABBN_00819 +MSEHTATTPAASDRVYRPGVTPELSPAELAAACAEAGLTPELVAALGGAAISPLAQKMGL +RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA +THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP +>LFPAFLNI_01049 +MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAAISPLAQKMGL +RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDHNVVGVEISA +THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLDAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001250.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001250.fa new file mode 100644 index 0000000000000000000000000000000000000000..76874463f45aafaa7435a0f67c21996ebc182811 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001250.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01797 +MPVDYDWSHLGIDVAVALLAVAALVSAYRIVKGPLDADRAVSGDLLTFSILGMLVLFGVR +MDNPFTFDLVLVAAIVAFLSGMSLARALTRGKR +>MOLHKGIG_01098 +MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV +RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR +>NAFOICDF_01687 +MSGLLQDYDWSLAGIDLAIALLLVAALVSAVRILRGPLDADRAVSGDLLTFSVLGMVVMF +GVRAQNPFTFDLVLVAAIVAFLSGMSLARALTRGKR +>MHAAABBN_00817 +MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV +RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR +>LFPAFLNI_01047 +MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV +RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001251.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001251.fa new file mode 100644 index 0000000000000000000000000000000000000000..89b73b73de62735f163264b1f4a5a5b4eed317f8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001251.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01798 +MHADPSSDRPVPADGTVVLAPGRASALSWPWRWLVFWCWYAWALVTSSEAVLKDLVTPGD +QARSGIARIRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGARGEEPGDPGATRLLYVHG +LYADDADALRGEIHDMERRLLHAMRKQGVA +>MOLHKGIG_01097 +MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI +ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA +DALRAEIHDMEARMLHAMRKTGVA +>NAFOICDF_01688 +MTVHHPDGGVDLTPGTASAASWPLRWLLFWCWYAWALVTSSGAVLHDLLTPGDQARSGIA +RVRSNCRTDAEVTLFSALITLTPGTLTLGTRREGAQGQEPGDPEARRLLYVHGLYADDAD +ALRAEIHDMEARMLHAMRRTGVAR +>MHAAABBN_00816 +MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI +ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA +DALRAEIHDMEARMLHAMRKTGVA +>LFPAFLNI_01046 +MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI +ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA +DALRAEIHDMEARMLHAMRKTGVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001254.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001254.fa new file mode 100644 index 0000000000000000000000000000000000000000..1335bc269ab5cb5f14fcd1cf1c71205b89ef38a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001254.fa @@ -0,0 +1,77 @@ +>ACLBLIBL_01801 +MDEARHGLVRLGALVDRASGSVAPRVHLLIPACVLGAFALAGVFTVDDLPAVVGTPSRWH +DWALVVLVGAGVVATIRAKTRISAMVVVGVVGFGVTLWFFTLGAVDVALTQLLVEVLTVC +VMVLLLRRLPGRFRDEEAPRRVQAVVAATIAGVAATVGVLAFTGRSEMSEIAHFYLTQTY +AQAGGVNVVNVILVDFRALDTLGEMTVLGATGLTVAALLLNRRPAPPQRSAVDLRSPLAH +VRENLVHIRVFGRVFGVLIIALSVLLLLRGHYEPGGGFIAALVAGAGYALLYLAADHDTD +RRLQWPYLTLIGGGIALGALTGVAGYLTGKGFLGAAGVKILGYGLSTTLAFDLGVYLAVL +GLIVAAFSLLGPERSETEAGAEPDPTSPIADPAAEQTTGQTTEPTTAPGTAPTPAAAREE +TSR +>MOLHKGIG_01094 +MLLTSLLLTLLSVVAAVPASRALGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA +VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL +LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR +TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH +AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS +QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM +PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY +SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEASATFWGVPVLAAAAGVALGLLPGVLD +TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF +SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ +PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE +VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY +LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR +SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA +DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV +YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR +>NAFOICDF_01691 +MLLTSLLLTLLAVVLAAPLGRTLGRDAGWVLALPLLTSAGALVSARAGGGGETVVERRPW +IPSLGAHLDLRLDGLAFVFALLVLVVGAGILAYSSRYLPRDRDEARAGSFYTLMTAFAAS +MLLLVLADNLVVLFVAWEFTSFASFLLIARSGDHARRPAIRTLLVTVGGGLCLLAAVALT +AARTGTASLSGALASDAWADPGFAAPVAALLAVAAFTKSAQFPFQSWLPDSMVAISPVSA +YLHAAAMVKAGIYLLLVFSPVLAGTPVWSALLIGSGLTTALLGAVSAIRRHDLKGLLAYS +TMSQLGLLVTAIGVGTPTALAAAVVHTVAHALFKSTLFMLIGVVDHEAGTRDLRDLAARH +VRMPVTGAAIAVAAASMAGLPPLLGFVSKEGLLDAALGAQGPAWLPGLVTAGIALTSVFT +VAYSGRLVLGALGVWGTAPAGAADMWSAGRGEDVHEAPAAFWAVPVLGVVVTLVLGLVPG +VLDEAVAAAATAAAGAPVHAHLALWHGVTPALLVSAGVIAAGLALVAARRPVERVASHAG +LPFSGLGVVDGILRGAVSLGAAVSRVSGGIAPRAHLLMPALVLGAFAVAGVVASPDLPAV +VGQPSRWHDWALVALVGVGVAATLRARTRIAAMVVVGTVGFGVTLWFFTLGAVDVALTQL +MVEVLTVCVMVLLLRRLPARFSAESTPHRAGAVAAAVIAGVASTLSVLAFTGRREISDIA +QYYLDRTYPDAGGHNVVNVILVDFRALDTLGEMTVLGVTGLTVAALLMNRRPAPPQPSAV +DVRSPLAAVHENLVYARTFGRALGPIILVLSVLLLLRGHYEPGGGFIAALVGGAGYALLH +LSADTDDEPRLRWPYLALIGGGVTLGTVAGLAGYLTGKGFLGSASVKVLGYSLGTTLAFD +MGVYLAVLGLIVAAFRLLGPDNATADDAAPAPTTGGESAREEAAR +>MHAAABBN_00813 +MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA +VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL +LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR +TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH +AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS +QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM +PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY +SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD +TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF +SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ +PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE +VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY +LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR +SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA +DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV +YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR +>LFPAFLNI_01043 +MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA +VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL +LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR +TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH +AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS +QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM +PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY +SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD +TPVSYAAEAASGAEVHAHLALLHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF +SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ +PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE +VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY +LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR +SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA +DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV +YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001258.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001258.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a44b59499b75963e042c9ba2a657db07305da3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001258.fa @@ -0,0 +1,135 @@ +>ACLBLIBL_01807 +MQHPSKTPHADPFRAFAAQPEAAGLYDPEQEKDACGLAAVATLRGPATHKIVQDALTALR +ALEHRGAVGADEGTGDGAGIITQVPDALLRATVSFELPAAGEYAVGTAFLPQDEAARTAA +QEAIAEAAVVEGLDLLGWRPVPTDESVLGPGSRAVVPVFEQLFLAVSAGEDVEAPGQSLD +ARAWRLRRRAQRSGVYFPSLSSRTLVYKGMLSTAQVEPFYPDLSDERYVTRLAVVHSRFS +TNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGELRHPLLGEVPEEMFPIVSASGS +DSASFDEVAELIHLAGRPLSHAIMMMVPEAWENHTTMDEDRRAFYQYHSMLMEPWDGPAA +IAFTDGVQLGSVLDRNGLRPARYWETRDGLVVLASEVGVLDIDPATVVRKGRVKPGRMFL +LDTEQGRIIEDEEVKAEIAASAPWKDWVADSLRRIEDLPEREPVRYHGDSVRLRQRLFGY +TDEEVRTIIEPMARHGAEPLGAMGTDTPIAALSPRPRLLFDYFTQNFAQVTNPPLDSIRE +EQVTSMRTCIGPQASLLAAGKVTTDAVEIPFPVLDNEQLARIAAVRAEDGTRRALKVKGL +YLVAGGAEEMRSRLKEICEQVSAAVQRGVQYVVLSDRDANAQWAPIPSLLLTSAVHHHLL +ASASRTRTSLLVEAGDVREVHHVAVLIGYGASAVNPYLSMETAEELVRTGTLTGVTEQEA +TRNLIHGLGKGVQKIMSKMGISTVASYCGAQTFEALGLSRSFVDRYFTGTRSPMDGVGLD +VIAAESAARHATAFPVDGSSASTVGPRGTSGLPVGGEYKWRREGPPHLFNPETVFRLQHA +TRERRYDIFKDYTRRVDEQSADLMTLRGLLGLATKGRERVPVSEVESVESIVKRFSTGAM +SYGSISQEAHETLAVAMNRLGARSNSGEGGEDPERLLDPERNSRVKQIASGRFGVTSLYL +STATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIEDLAQ +LIHDLKRANPQARVHVKLVSETGVGTVAAGVTKAKADVVLISGHDGGTGASPLNSLKHAG +TPWELGLSEAQQTLRLNGLRDRVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVVSGC +IMMRVCHLDTCPVGVATQNPELRARFTGRPEFVVTFFEYIAQEVRELLAELGLRSLDEAI +GRQDLLHKDAAIGHFKTEGLDLSGVLSDAGVPEEAPRRRLTEQDHRLQDQADQRWLDQVA +DAVVTETPVTVTDRLVNTDRSVGTLLGHRVTAARLDDELPRDTIRIELTGEAGQSLGAFL +PAGVSITLSGDANDYVGKGLSGGTVALRPAPEAPFAAEENMIAGNVVGYGATSGRLFLNG +RVGERFLVRNSGAVAVVEGIGDHGLEYMTGGTALVLGNTGRNLAAGMSGGVGFFLDLDPA +QLNPLAVKDDELLLGRPEGADRALIRELLEEHRAATGSDLAARLLAELDGPAESAEALWE +RFTTVLPRRYAAVQEIRTDSRDAGTDPDGDAAWARILEVTRG +>MOLHKGIG_01089 +MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ +HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV +DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT +EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL +GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF +PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM +EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR +VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL +QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN +PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR +LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT +SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV +SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS +PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL +QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST +GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS +LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED +LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK +HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV +SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD +EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID +HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA +GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT +SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA +WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG +DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG +>NAFOICDF_01696 +MTVAPLSAPTPRSGRSDDPFVRYAAFPEPQGLYDPARETENCGLAVIATLRGTPGHDIVE +HALTALRALEHRGAVGADEGTGDGAGLLTQLPDELFRAVLDVELPPVGEYAAGIAFLPPL +EGERAEAKAAVEELAQAEGLDVLAWRVVPTDPSALGTGSRAAMPSFEQVFLALAEGEDGT +EPGQSLDVRAWRLRRRTQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDPRFTTRL +GIVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEELF +PLISPIGSDSASFDEVAELLMLSGRPLTQAVMMMIPEAWENHATMDPARRAFYQYHSMLM +EPWDGPAAVAFSDGTQVGAVLDRNGLRPARYWETRDGLVVLASEVGVVSIDPADVVRKGR +VAPGRMFLVDTEQGRIVEDEEIKAEVAAAAPWEEWVSQNLLDLDALPEREHLRPSSESIQ +QRQRIFGYTAEELRVLVGPMARDGAEPLGAMGTDTPIAVLSKRPRLLFDYFVQSFAQVTN +PPLDAIREEQVTSMRTGIGPQGNVLSAERVHTRQVDVPFPVIDNDQLARIQHLRDGDGGR +LALKVTGTYRVAGGAEELRTRLKEICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT +SAVHHHLLASANRTRTSLVVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEI +EGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFAGTTS +PLDGVGLEVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL +QHSTRERRYDVFKDYTRRVDGQAEELMTLRGLMRLRSEDRTPVPISEVEPVESIVRRFST +GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS +LYLTTATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED +LAQLIHDLKRSNPAARVHVKLVSESGVGTVAAGVAKAKADVVLISGHDGGTGASPLNSLK +HAGTPWELGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVVAALLGAEEFGFATAPLVV +SGCIMMRVCHLDTCPVGVATQNPELRSRFTGKPEFVVNFFEFVAQEVRELLAELGFRTLD +EAIGHRELLDVDAALHHWKTEGLDLSGILADPSVGRRAGAADAPMRRMVDQDHDLAAHID +NRLIARLGDTLATGAPVVMDESVVNTDRSIGTMLGHHVTSTRLADELPADTITVRLTGEA +GQSLGAFLPAGVTLRLDGDANDYVGKGLSGGRVVVRPDATAPFAAEDNTVAGNVIGYGAT +SGELFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALVLGETGRNLAAGMSGGRA +WILDLDRADLNPLAVREGDLLLSTPSAADRERIAALLRTHRAETGSAVAERLLADLDAGG +DAAQGVWDRFTTILPRRYDLVLRTRAEAVAEGLDPDGEAVWDRLLEVTRG +>MHAAABBN_00808 +MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ +HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV +DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT +EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL +GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF +PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM +EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR +VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL +QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN +PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR +LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT +SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV +SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS +PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL +QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST +GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS +LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED +LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK +HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV +SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD +EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID +HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA +GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT +SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA +WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG +DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG +>LFPAFLNI_01038 +MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ +HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV +DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT +EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL +GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF +PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM +EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR +VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL +QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN +PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR +LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT +SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV +SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS +PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL +QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST +GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS +LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED +LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK +HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV +SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD +EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID +HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA +GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT +SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA +WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG +DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001260.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001260.fa new file mode 100644 index 0000000000000000000000000000000000000000..af3e81e07bf41ae2667cccdab4b6fceb13e69e0e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001260.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01810 +MTVHSKTAAALDAARRAGRTGLVAYLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP +VMDGPVIQAATQASLRAGFRVADVFEIIRRVTQRVDAAVLVMTYWNLVDRMGVDEFARRL +AEAGGAGLVTPDLVPEEAGAWLEASDRHGLDRVFLTAPSSTDERVRLAVESSRGFVYAVS +VMGVTGARDAVSTAAETVVRRAEEAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR +ALGEGGPQAVGALARELAAGAVREG +>MOLHKGIG_01087 +MTVNSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAADNGADVIELGLPYTDP +VMDGPVIQAATQAALQAGFHVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL +AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS +VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR +ALTDGGPQAVGALARELAAGAVREG +>NAFOICDF_01698 +MSTPDQQHEATAEKPSTAGDAIERARAAGRTALIGYLPAGYPSIDESVEAAVQLGENGVD +VIEIGLPYSDPVMDGPVIQAATSHALANGFHTRDVFEVVRRITERTEAAVVVMTYWNLVD +RMGVDEFARRLAEAGGAGLVTPDLVPEEAGEWFEASEEHGLDRIFLTAPSSSDERVRLAV +ESSRGFVYGVSVMGVTGARGKVSDAAERVVARAKAAGARNVCVGLGISSADHVREIGSYA +DGAIVGTALVKALRDGGPEAVGALARELAAGTAKES +>MHAAABBN_00806 +MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP +VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL +AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS +VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR +ALTDGGPQAVGTLTRELAAGTVREG +>LFPAFLNI_01036 +MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP +VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL +AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS +VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR +ALTDGGPQAVGTLTRELAAGTVREG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001261.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001261.fa new file mode 100644 index 0000000000000000000000000000000000000000..df6dd8d995e748c046b1877ee067490ad32b289e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001261.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01811 +MSADRPSTEPTVEFEGPYQGQSGPYFGDYGGQWMPESLMAALQEVQRTYEEARQDPAFEG +ELRTLFRDYVNRPSLLSDVPRFAADSPGVRIMLKREDLNHTGSHKINNVIGQALLARRMG +KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG +ARTLKDAINEALRDWVASVDTTHYLLGTVTGPHPFPAMVRYFHSVIGEEARQQVLAQTGR +LPHAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGLETGRHAASITLGRTGVLHGA +RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRAVYEPVTDTECMDAFLRLTRT +EGITPAIESAHALAGALRLARRWADEGLVGPDTPEGEERIIVVNLSGRGDKDVATAAAWF +GLGQADAEKDPLEELTPGEEQ +>MOLHKGIG_01086 +MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEEARQDPAFEA +ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG +KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG +ARTLKDAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR +LPDAVAACVGGGSNAMGLFHGFLDDPGVELYGFEAGGEGLETGRHAASITLGRTGVLHGA +RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT +EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF +GLGTATEEKDPLEEMTPGEEQ +>NAFOICDF_01699 +MTSTESVDVAGPFQDQPGPYFGRYGGQWMPESLMAALKEVADTYEAARQDPEFLAELEDL +YANYVNRPSLLTEAPRFAAEVPGVRIFLKREDLNHTGSHKINNVIGQALLARRMGKTRLI +AETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVTIGARTLK +DAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQTGRLPDAV +AACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGVETGRHAASITLGRTGVLHGARTYLM +QDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRATYEPVTDTECMDALLRLTRTEGITP +AIESAHALAGALRLARRWRDEGLVGEGTPEGEERIIIVNLSGRGDKDVATAAAWFGLGEA +DEQKDPLEEMTPGEEQ +>MHAAABBN_00805 +MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA +ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG +KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG +ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR +LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA +RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT +EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGEERIIIVNLSGRGDKDVATAAAWF +GLGTAAEEKDPLEEMTPGEEQ +>LFPAFLNI_01035 +MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA +ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG +KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVAIG +ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR +LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA +RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT +EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF +GLGTAAEEKDPLEEMTPGEEQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001262.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001262.fa new file mode 100644 index 0000000000000000000000000000000000000000..6e5d36d10a2e52b84f2a7502c93c0f949b921773 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001262.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01812 +MSVLQEIIDGVREDLAPRRRDVPEARLAELVAAAPAPRDAHAALLGGRTDPAGIRVISEV +KRSSPSKGALAEIPEPAALARAYERGGASAVSVLTEARRFGGSLADLDAVRGAVDLPVLR +KDFTVTEYQIHEARAPGADLVLLIVAALDDAELTGFLQLTESLGMHALVEAHTPEEIERG +VTAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESDEQIKAYAAAGADA +VLVGEALVRHGAPEEALRAFRAASLTVR +>MOLHKGIG_01085 +MSVLQEIIDGVREDLEPRRRALPEARLSELVAATPAPRDAHAALHGGRTDPAGIRVISEV +KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR +KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG +VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV +VLVGEALVRHGAPEEALRAFRAASLTVR +>NAFOICDF_01700 +MPETVLDSIVAGVLEDLAPRREAVPEARLQELIAQAPAPRDAYAALRDGRSDPAGIHVIA +EVKRRSPSKGALAEITEPAALAASYADGGAGAISVLTEQRRFGGSLADLDAVRAAVARPV +LRKDFTVTEYQILEARAHGADLVLLIVASLDDARLRGFRELAESLGMHALVEAHTSEEIA +RGVDSGARILGVNVRNLKTLDVDPDRYAALAGDLPEDVVRVAESGVESEAQVRQYAAAGA +DAILVGEALVRHGAPADALRAFRAASLTVR +>MHAAABBN_00804 +MSVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVISEV +KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR +KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG +VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV +VLVGEALVRHGAPEEALRAFRAASLTVR +>LFPAFLNI_01034 +MSVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVISEV +KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR +KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG +VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV +VLVGEALVRHGAPEEALRAFRAASLTVR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001263.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001263.fa new file mode 100644 index 0000000000000000000000000000000000000000..f6cb782616f9c693f25d739ce6462d7239a9c667 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001263.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01813 +MSHTANTEHTTRRAARNGAVEDVVVTEDGRVLNDPTHLELPDHGNTPGGWAMVALVLVGF +VAGCIGLLADWMIVVWIGVALIVVGVLVGIVAGRGGSARSGHRAH +>MOLHKGIG_01084 +MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL +VGFVAGCVGLLADWSVVVWIGVALMAVGVVVGIVAGKAGAGRGQHGH +>NAFOICDF_01701 +MSHTEATVNHTAQAGAHAAGHTTGHTASREVVVTEDGRVLNDPTHAKVPGHGNSPAAWAM +AGLVVLGFLAGCIGLLNDALVIVWIGVAVIVVGVLVGIVGGKAAGRSDH +>MHAAABBN_00803 +MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL +VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH +>LFPAFLNI_01033 +MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL +VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001264.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001264.fa new file mode 100644 index 0000000000000000000000000000000000000000..24a73d852519dcd06d44cd1bef060fb793f7dd8f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001264.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01814 +MRRRTVVLAALAAGSLVLLAAGQTWVVGSGLTGGLSEEATTSGGAAAPGATAMALVVLAG +ALALTTARRVGVVVVGALLVLAGIVIVTGAAGAALDPAGTAASAVAEATGTTAAAGSYAV +TAWPWVAVTGGVLAALCGAVAALAGRGWVSVRRYEKAEATDAAEPAAPGRAAAPGRTEAE +RRRTEQMDAWDELSRGNDPT +>MOLHKGIG_01083 +MRRRTVVLAALAAGALVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT +>NAFOICDF_01702 +MRRRWIVLAALLAGVLVLAATGQTWVTASGLEGSPVPQATAGGGRVAPVATALALVVMAG +ALALTTARRVGVVLVGVLMTLAGVVIASTAVTAALDPVAAAAGAVSELTGTTAPAAAYAV +SAWPWVSAAGGVMAAVLGVATLVVGPRWAASRRFESPATADEPAAAAPPSRHVDRMDAWD +ELSRGEDPT +>MHAAABBN_00802 +MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT +>LFPAFLNI_01032 +MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001265.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001265.fa new file mode 100644 index 0000000000000000000000000000000000000000..18210cca63280a8e55e0eec09a6d08a26de94821 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001265.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01815 +MSAATTPSREEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESAAPGAV +WSRYSFVGAGSAVTLTSRDGQAHWQGVPPEGLPTEGRALDVLAACLRLLRTDARTHLDGA +LPHLVSGMAGFLGWNTVRAWERLPNPPQDDLGLPDLAMNLVTDLAVHDALDGTVTLIANA +VNGNGLATGAEGAYEDALARLDAMVDQLAAPAAEPVSTVPRRWLDADADEVAAQAEDRWG +AAGFREAVGKAQEAIRDGEVFQAVVSRRLSVTTGATGADVYRVLRMVNPSPYMYLFSFET +PDGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATLEDDRLLGKDLMEDEKERAEHL +MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMREDVDALDVLRAAFPA +GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG +AGVVADSDPDAETAETVTKATAPLRSVLTAGEMGRA +>MOLHKGIG_01082 +MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA +WSRYSFIGAGSSVTLTSRNGEAHWQGTPPEGLPTQGRALDVLAACLRLLRTDVRAEVGGV +LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA +VNGNGLATGADRAYDDALARLDAMVERLAAPAADPVSDVPRRWLEADADEVAAQAEDRWG +AEGFREAVAKAQRAIRDGDVFQAVVSRRLSVTTDATGLDVYRVLRTVNPSPYMYLFSFET +PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATEKDDRLLGKDLLEDEKERAEHL +MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA +GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG +AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA +>NAFOICDF_01703 +MSGVVPSREEFLAVAPTSRVIPVVRRVLADGLTPLAIHRRLADSRPGTFLLESATPGAAW +SRYSFIGAGSAATLTARGEDAVWLGEPPEGLPTEGRALDVLAESLRLLSTDARTRVDAAL +PHLVSGMAGFLGWPAVRAWERLPHPPEDHLGLPLLAMNLISDLAVHDAQDGTVTLIALAI +NGDGLATGAERAYDDAVARLEDMVARLRAGAEDPVDEVPRRWLDATAEEVAAEAEDRWGA +AGFRDAVGRAQQAITDGEVFQIVVSRRFSVDTAASGVDVYRVLRMVNPSPYMYLFSFQTP +DGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATPEDDRLLGKELAEDEKERAEHLM +LVDLSRNDLSRVCEAGTVEVTQFMELEAFSHILHLVSHVEGRLRDDVTSLDALRSAFPAG +TLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSVTLAGRQAHVQAGA +GIVADSDADAETAETVTKATAPLRAVLTAAELRGA +>MHAAABBN_00801 +MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA +WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV +LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA +VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG +AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET +PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL +MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA +GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG +AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA +>LFPAFLNI_01031 +MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA +WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV +LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA +VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG +AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET +PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL +MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA +GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG +AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001274.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001274.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcc3829f2a3948be20ec69530d00f7e02acdb5f2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001274.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_01826 +MSGEGQGRQGRGRGGSGGGSRGGAGGGSRGGSRNGSGGGPRGGSHGGPRGGSGGARRESG +GEERRDAQGRTRSRGRSGAGRRYSAQAPAQRSRTADPARRVAFEVIRAVHAEDAYANLVL +PGRIRQARLDRRDAGFATELAYGTLRGIGLYDAVLARCVDRPLEKIDPPVLDALRLGAHQ +LLAMRVPAHAALDATVALVRAEIGAGPSGFVNAVLRRVAERPLEDWLADVAPAEGGDAAL +AVRASHPVWIVRALRQALAAHRGTRHVADRDAELGALLEADNASPVVNLVALPVPGGREG +LSAALEDGAEPGPLAPDSALHAGGDAGRLTGVREGVLRVQDAGSQLTARALAAAPAAAAE +GRPERWLDLCAGPGGKAALLAALAAERGATLVANEVAEHRAELVRQALGAVPAAAWTVRA +GDGRAIADAPEAAGGFDRVLVDAPCTGLGALRRRPESRWRRTPADLAELTGLQSELLDAA +AAVLAPGGVLAYVTCSPHVAETTVQVQDLLRRRPELELLDAGAVLSEVALGDLRLDEGEP +GGDEAAGAAAPDDVAARTAQLWPHRHGTDAMFLALLRAPSDTPESPERTRG +>MOLHKGIG_01060 +MSREGQAGQGRGERGARGERGRAPRPDPQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR +TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA +ILTRCVDRPLEQIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA +VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHIADRDAE +LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR +EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPADAWTVRTGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR +RPESRWRRTPADLAELTGLQAELLDAAVSVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH +PELELLDARTALDTVALDDLRLDEAEPAGAPKPGDVVARTAQLWPHRHGTDAMFLALLRA +PGA +>NAFOICDF_01716 +MSAGQDGSTGRGAGQGGRGRGGAEGRQGPGGRQGAGGQDRRDAQGRQLNRGASGTGRHRT +TLAPKERARRADPARRVAFEVVRAVHAEDAYANLVLPARIRQGRLDRRDAGFATELTYGT +LREQGLYDAVLARCVDRALDALDAPVLDALRLGAHQLLGMRVPAHAALDATVALVRAEVG +AGPAGFVNAVLRRVSERPREDWLAEVAPADGGDTARAVRHSHPAWIVRALRQALAGHPGT +ADVEDRDAELEALLVADNAAPVVNLVGLPVPGGREALASALGDGAEPHPLTPDAALHAGG +DAGRLPGVREGVLRVQDAGSQLTARALAAVPAASGRDAGGRKAERWLDLCAGPGGKAALL +AALASERGATVLANEVAPHRADLVRSALAGVPASAWEVRTGDGRTIAEDAPAGGFDRILV +DAPCTGLGALRRRPESRWRRTPADLAELTGLQAELLDAAVGVLAPGGVLAYVTCSPHVAE +TLVQVQDLLRRHPVLEQLDAPAALQDVAVADLGLAAPEDADPVLARTAQLWPHRHGTDAM +FLALFRAPVA +>MHAAABBN_00779 +MSRERQPGQGRGERGARGERGRAPRPDAQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR +TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA +ILTRCVDRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA +VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHTADRDAE +LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR +EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPAGAWTVRTGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR +RPESRWRRTPADLAELTGLQAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH +PELELLDARTALDAVALDDLRLDEAEPAGAPEPGDVVARTAQLWPHRHGTDAMFLALLRA +PGA +>LFPAFLNI_01007 +MSRERQPGQGRGERGARGERGRAPRPDPQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR +TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA +ILTRCVDRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA +VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHIADRDAE +LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR +EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPADAWTVRAGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR +RPESRWRRTPADLAELTGLQAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH +PELELLDARTALDAVALDDLRLDEAEPAGAPKPGDVVARTAQLWPHRHGTDAMFLALLRA +PGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001278.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001278.fa new file mode 100644 index 0000000000000000000000000000000000000000..9d7e2ea1a3b08fa2d3df7c25c3ed890a1e81d22d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001278.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01834 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGEVSFDTYIPDPAHPSQAQAVERLRRFAAAL +GRGSGSGGGFLSGLFGGGRKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVE +YTNLVGALSFRKAVDVLKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVHLVATSNTL +PGSLGEGRFAAQDFQREIQVLAEQFEVIRVDGEDYRHRGLSAAPDPLPDDQVVSTAEANF +PDSGVLAVDDFDALTAMLSRVHPSRYRELVKDVDVIALHDVKTITEQATALRFVVFADRL +YDKDVPVVASGVPFDDLFTQEMMHGGYMKKYFRTVSRMTALVREGQLGIAEEK +>MOLHKGIG_01052 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPTQAQAVERLRRFAADL +GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT +NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG +SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD +AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD +KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK +>NAFOICDF_01724 +MPQTVHLADRSPQVSADQLLAGLHPSYRFGEVSFDSYIPDPAHPSQAQAVERLRRFAASL +GGPRGGSGGGGFLGGLFGGGRKRGPEPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF +VEYTNLVGALSFRQAVDVLKGYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN +TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPEPLADDAVESTAQA +NFPHADVVSVDDFAALTAMLSRVHPSRYRELVKDVDVAAFHDVQTITEQATALRFVVFAD +RLYDKDVPVVASGVPFDQLFTSEMMHGGYMKKYFRTVSRMTALVREGQTGETVEK +>MHAAABBN_00765 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL +GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT +NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG +SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAVVEATAQENFPD +AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD +KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK +>LFPAFLNI_00993 +MAQIVHLADRSPQVTPDQLLSGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL +GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT +NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG +SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD +AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD +KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001279.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001279.fa new file mode 100644 index 0000000000000000000000000000000000000000..5f88721e8c1297f16e0d22ba5272cbb05f37774d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001279.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01835 +MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE +LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN +GGRDKWIAEGRETTREVPTVARGEYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPEY +TGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGDD +VIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR +>MOLHKGIG_01051 +MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE +LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD +GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY +TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD +VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR +>NAFOICDF_01725 +MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE +LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN +GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE +YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD +SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR +>MHAAABBN_00764 +MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE +LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD +GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY +TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGDD +VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR +>LFPAFLNI_00992 +MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE +LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD +GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPEY +TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD +VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001281.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001281.fa new file mode 100644 index 0000000000000000000000000000000000000000..c5f4fbbec46c75d1a7067c7e5debf3da4e8777b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001281.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01837 +MAKTGRGRGRAHGAATPAVAALETAGVPYTLHTFEVDLDAGGERFGVQVARAMGVPPERM +FKTLMVAAPDGGLAACVVPVSGQLDLRAAAAVLGVKRLALADLALVERRTGYVRGGVSPL +GQRHRHPVLLDSSALDAPVMYVSGGQRGLDLELAPADLAAATDAVVAPIAAR +>MOLHKGIG_01049 +MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL +FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL +GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVRVTGAVVAEIAAG +>NAFOICDF_01727 +MGRRKAADAAHGAATPAIRALVDAGVPHRVLSFDVHLDAVGERFGVQAAKALGVPPERTF +KTLMVALPDGSLAACCVPVSGQLDLRAAATALGVKKVAMADLAVAERRTGYVRGGISPLG +QRQRHPVVVDSSALDGDVLYVSAGQRGRDLELAPADLVAVTDAVVAPIAAR +>MHAAABBN_00762 +MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL +FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL +GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD +>LFPAFLNI_00990 +MGQRKKDRSARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL +FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL +GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001282.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001282.fa new file mode 100644 index 0000000000000000000000000000000000000000..02f24c6be546d3690c77c7450bfec961f28f1bb8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001282.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01840 +MLDRHARGATTRVFTPVARALLRAGVSPDAVTVVGTLGVSLGALVLFPLGELFWGTLFIT +AFVFSDLVDGIMAREAGTTGRWGAFLDSTLDRVQDAAVFLGLSLWGFGVGGEPAVGTLAA +VCLALGMLVSYVRAKAEALGLTANVGIAERAERLVAALVLAGLTGLGLPPAFLAATLGLL +AAASLVTVGQRVAAVRSQTRRAA +>MOLHKGIG_01048 +MLDRHARDLTTRLFTPVAHTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWSAHVGIAERAERLVAALVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMAAVRRQARDDA +>NAFOICDF_01728 +MLDRRARGTTTALFTPLARRLLRAGVTPDAVTVAGTVGVSAAALLLYPAGHLFWGTIVIT +LFVFSDVLDGVMAREAGTTGPWGSFLDSTLDRVQDAAIFLALSWWGFGVGAHPAVGVLAG +VCLALGMLVSYARAKAESLGFTAAGGIAERAERLIVTLVFAGLTGLGLPSAVLTAVLGLL +ALASLITVAQRVAGVRRQSRTA +>MHAAABBN_00761 +MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMVAVRRQARDDA +>LFPAFLNI_00989 +MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMAVVRRQARDDV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001283.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001283.fa new file mode 100644 index 0000000000000000000000000000000000000000..fb3971598660295264e65a647eedfedb32fd6987 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001283.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01841 +MTRPEASDADARDLARASADASATDGFALPGAPDAFERFWNAHRMAYVTQGSDQVKDEHT +CPFCAAPQRSDEASLIVHRGRAAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTAEEAAEMA +ELTQTAMLALGHATRAAGYNLGMNQGSVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN +MSQTLGETREILAGVWDEAAADHARLQEANARAAAERAGRRDEDRP +>MOLHKGIG_01047 +MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT +CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA +ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN +MSQTLGETRQILADVWDRAAQDHAARQAANARAAGEHPRPGAGGPA +>NAFOICDF_01729 +MTTTPHDDAAEVSADGAPAGERPYGDPAADAAALDGFELPGTPDAFDRLWNPHRLAYIQK +GPEQVKDEDTCPFCAAPGRDDASALIVHRGATCFVILNLFPYNPGHLLICPYRHIPMYTD +ATAEETAELADLAQTAMIAFELATRPKGYNLGMNQGVAGGAGIAAHLHQHVVPRWTGDGN +FLPIIAQTKNMSQTLGQTREILADVWPQALAEHAERRARNAAAAAQAPRADA +>MHAAABBN_00760 +MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT +CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA +ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN +MSQTLGETRQILADVWDRAARDHAARQAANARAAGEHPRPGAGGPA +>LFPAFLNI_00988 +MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT +CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA +ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN +MSQTLGETRQILAGVWDRAARDHAARRAANARAAAEHPRPGAGDPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001286.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001286.fa new file mode 100644 index 0000000000000000000000000000000000000000..5474d31da5ef9277aca988b1fdc284400e64af47 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001286.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01845 +MGVLTQSVAVERAADGTPQGLRWNGRDYVLAEPPVRWFERRRWWAEEVRAEKGRGAGLVD +HEIWRLQVRLARAGSAPVQTVDVAHHLDSGRWRLVRVHEQARDLRRSA +>MOLHKGIG_01044 +MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPVRWFERRRWWAEEVRAEKGRGAGLVD +HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA +>NAFOICDF_01732 +MGTFTQSVAVERDRQGAPARLHWEGREYVLAERPLRWFERRRWWAEEARAEKGRGPGLVD +HEIWRLQVRLARAGNAPVRTVDLAHHLDSGRWRLVRVHAPAQERTLSRTA +>MHAAABBN_00757 +MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPMRWFERRRWWAEEVRAEKGRGAGLVD +HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA +>LFPAFLNI_00985 +MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPVRWFERRRWWAEEVRAKKGRGAGLVD +HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001287.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001287.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4f9aaf0c88692bb092d77692c16cd79cc869cb6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001287.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01846 +MCGRYVMARAAGDLVALGGGELPDERLELRRSWNVAPTSDVPILLEREADGAVRRELHVA +RWGLVPSWAKELAVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKAPAPGAKG +PDGKAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAEAAGRDPWVLSTTILTMAAP +DADDEDEVLGSLGDLHDRLPVPLDAETMDAWLTPGRLGSAEEADALVGQVCAGAYDVAAG +WVLRPVGTAVGNVRNDGPELIQAEEPAQGTLL +>MOLHKGIG_01039 +MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGTRGGDG +GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY +EWKTPEPGAKGPDGRIAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV +LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ +VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL +>NAFOICDF_01736 +MARAAGDLVALGGGLLPEEGLELRPNWNVAPTADVPILLEREDAGVVRRELHVARWGLVP +TWAKELSVGSRAFNARSETVTSKPTFRSAVRARRCAVPVEGYYEWKAPEPGSTGPDGKAA +VKQPFYVHPAGGGDGEGPVIWFAGLYEWWKDAGAEARGDDPWVLSTTILTMPSPADDEPG +VLGELADLHDRLPMPMGPAAMDSWLSPDKLGSADEAAALVDEMTAQAYDVARGWELRPVG +RAVGNVRNNGPELIAPPAEVQDALL +>MHAAABBN_00752 +MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGARGGDG +GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY +EWKAPEPGAKGPDGRAAKKQSYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV +LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ +VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL +>LFPAFLNI_00981 +MCGRYVMARATSDLVALGDAETNEELVLRQSWNVAPTAEVPILVAHADDVGAGVTRRIHV +ARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKTPEPGAK +GPDGRAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWVLSTTILTMAA +PDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQVCAGAYDVAA +GWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001289.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001289.fa new file mode 100644 index 0000000000000000000000000000000000000000..8fd587d792c12f930c91d15b9523252af2eff36f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001289.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01848 +MARIDHLVTSGTFSLDGETFDVDNNVWLVGGAEQCIVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGGATGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH +>MOLHKGIG_01036 +MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPALLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLLSLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH +>NAFOICDF_01738 +MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH +>MHAAABBN_00749 +MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLLPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH +>LFPAFLNI_00978 +MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDAVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001293.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001293.fa new file mode 100644 index 0000000000000000000000000000000000000000..8cbc5c8fdc6cf0d1a7f2bb335611ddd0152dadc0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001293.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01858 +MTEVTDTVKTNHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE +RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVLTNIAFMESVHAKSYSSIFSTL +ASTKEIDEAFRWSRENENLQRKASLIVERYDGEDPYKRKIASTLLESFLFYSGFYWPMYL +SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEEKREELKAFTFELLFELYEN +EVEYTHDLYDAVGLSEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE +NHDFFSGSGSSYVIGKAENTEDADWDF +>MOLHKGIG_01027 +MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE +RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL +ASTPEIDEAFRWSRENRNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL +SGHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN +EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE +NHDFFSGSGSSYVIGKAENTEDEDWDF +>NAFOICDF_01745 +MTEPHHGPSVHDHLVEAINWNRIQDEKDNEVWQRLVNNFWLPEKVPLSNDVQSWNQLTDD +ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVYTNIAFMESVHAKSYSSIFST +LASTKEIDEAFRWSRENPNLQRKAQLILERYDGEDPYKKKIASTLLESFLFYSGFYWPMY +LSSHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEERREELKAFTFELMFELYE +NEVEYTHSLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTDVNPAILSALSPNSD +ENHDFFSGSGSSYVIGKAEATEDEDWDF +>MHAAABBN_00742 +MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE +RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL +ASTPEIDEAFRWSRENRNLQAKAGLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL +SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN +EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE +NHDFFSGSGSSYVIGKAENTEDEDWDF +>LFPAFLNI_00971 +MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE +RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL +ASTPEIDEAFRWSRENPNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL +SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN +EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE +NHDFFSGSGSSYVIGKAENTEDEDWDF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001295.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001295.fa new file mode 100644 index 0000000000000000000000000000000000000000..fdd9cadce29e47e598168001a6c6a9406ca9fc74 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001295.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01860 +MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREPT +LGATAPYVLLTPTYGGGDGPGAVPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLAGY +IIARKCQVPLMYKFELMGTPEDVDSVRGGLEGLWT +>MOLHKGIG_01025 +MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT +LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY +IISRKCQVPLMYKFELMGTPDDVERVRGGLEGMWT +>NAFOICDF_01750 +MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP +TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA +GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA +>MHAAABBN_00740 +MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT +LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY +IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT +>LFPAFLNI_00969 +MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT +LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY +IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001297.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001297.fa new file mode 100644 index 0000000000000000000000000000000000000000..b4e3da2a0063c284703f0815fef78d750d0e12b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001297.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01865 +MTARDAAGGPAVTRNDAESRYELHDGGTLLAVLDYRDNGTAVALTRAFTIPVHRGHGHAA +TLTAGAVEDIEARGGAAGGRQIVPLCWYVAQWLEEHPEKAHLVAPR +>MOLHKGIG_01023 +MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG +AVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR +>NAFOICDF_01758 +MDASDSPTTFTRNDAASRYELHDASGELLAALDYRDNGTAVSLTRAFTVPVHRRQGHAAT +LTAGAVADIEARGGAAGGTTVVPMCWYVARWFEEHPEKAGLLDAR +>MHAAABBN_00738 +MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG +AVEDIETNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR +>LFPAFLNI_00967 +MTTGGCPGMSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRG +HAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001298.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001298.fa new file mode 100644 index 0000000000000000000000000000000000000000..41f96fd2c4409b17f981f8e5b82c994668ae38f7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001298.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_01866 +MPVTGDELRAGLLSEREKNVLAAADAEDAGRIYLLQMHRVYQGALTISATEAESGTDEEA +KALAASVVADHQEDMQRMVEVLADMGAIGADASHTALPSGYTGPIKIEGTGADGGPVPSD +FVPEPVQRVQSFRATQRPVLPTSSSPGDAEDRRGRDSATASPSPTPADTARPSPSPSSAA +SPSPSATTGSPSGTNR +>MOLHKGIG_01021 +MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL +ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE +PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM +GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRSFRATQKPVLPSSSS +PSSSSASGSASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSPSASR +>NAFOICDF_01762 +MNRATDATAPVCPVRWSAAAGGLLGLSLVLAGCGTSAQPVPAGSGSNTYLEGVLATPSAT +KADPLAADQRFVASLLQNQYQVVQEADHVLSRPDMDGEVRDMAQQHKDVANQRIGDLSSR +LQAWGLEVPAAPEPLVDDTKPSGRPTGDPSEIQASKGQQAAADIRAGLLTASDQSALVTA +DDDAAGRIYLLQVHRLLQGGVSLAGTESDEGTDEETKKIASDLIDADRPRMQRILEKLGE +NGVVAAVPSPTAPNSGYQGPISLPSQAGGDGANVDYTPSALYEMWSTLPPPATSSSADGS +STGPSPSAQPTPTPADTASPRPTPGASAQPGAASSTASTTGAASTRNG +>MHAAABBN_00735 +MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDEVLGKDGVDQEIRATAERMKSEHEERARRL +ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE +PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM +GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS +PSSSSASGPASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSSSASR +>LFPAFLNI_00965 +MSRADIAPARVHPRRWSVAVGGALLSITLATGGCSVVEEPGQTGDTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL +ESMLEGWGVPSDDVRGAGAEATPSAQPESTEDAEPAEIVGDELRAGLLSDREKNVLAAAE +PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLAEM +GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS +PSSSSASGSASASGRDAEDQRGRDTASASPSPSPADTAQATPRPSSGASPSPSASR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001299.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001299.fa new file mode 100644 index 0000000000000000000000000000000000000000..90cd62e3209ffc06039f09c53e7dc231b3d420b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001299.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_01867 +MTGPAAPWESIDAAPVHVEVHQDGERIVGASVEHTQMNEAGELDPDPQTVGWYGAPQWGT +DPGERSPYAGILAGHVVYYGVKDVFWNLDAVRAGDVVVLTYDDGSQAVFEADADAVSVEK +EALTQDPANRWAWEPGGDDARLTLITCDLVPGTGMAGNAFNNWVVQATRVA +>MOLHKGIG_01020 +MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR +FTPSPATTATPTPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS +EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV +GWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE +ADSDAVSVEKEALTQDPANRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV +A +>NAFOICDF_01763 +MSTTVKRAVWALLLLICLGVGAFALRGMFAFGDVPISAAPTVSARASTASSTPSAATGSP +SSTSASASAGPSVPAATSASSAAASTTTPASPTSSTTTPASPTSSTTPASTEAAAPAVGA +ASSTATASSSATPTGTDSRMTKPAASWERITAAPVHIDVYADGEQVVGAPVELVQTRDDG +ELNPDPQMAGWYGPPQWTTTPGERSAHPGVIAGHVIHSGLKDVFWNLQTLKAGSIVVITY +DDGTQAEFRTDFDVRSMDKDDLTQSPDYAWAWELPEAGNKVTLITCDLVDGSGMTGWSTN +NWVTQATRIG +>MHAAABBN_00734 +MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR +FTPSPAPTATPIPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS +EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV +GWYGPPQWGTTPGERSRYAGVLAGHVVYYGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE +ADADAVSVEKEALTQDPAHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV +A +>LFPAFLNI_00964 +MNTTVRRALWVVLLLLCLSLVFLALRGVLAVGAVPISAAPTLSATASVSPSSAATTREAA +VPVETQELAGTPTPSEEPTPTEEPAPSEEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQD +GEQIVGAGIDLTQLDEGGDLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRD +VFWNLGDVRAGAVVVVTYDDGTQAAFEADADAVSVEKEALTQDPSHRWAWEPGGDDAKVT +LITCDLVPGTGMAGNAFNNWVVQATRVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001300.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001300.fa new file mode 100644 index 0000000000000000000000000000000000000000..6f4c06f9e0157ea558e76b2722a8956c17777f4d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001300.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_01868 +MEERLLRAFVTVAEAGTVSAAAQRLDLVQSALSRQLQRLQRELRLPLFARVGSRLELTTA +GEAFLPVARRVLAAHRQAEQAARTLASGSLAEVAIAAPGTTLIDVVLPFVATLDEDDPRP +RVAETQLDDSLQDAVARHDLVVMPMAPGPTVQALHLIDLPVWAYVAPGHPWADRADVALE +ELVDVRVVAPSRSFMARRVLDGAVAVAGLTAPELSEANSGRVAQALVATGAGVAVVTEDP +AFGLVPLRVLLDGRALSVGLHAAWRADHFAAATLARIAASLQDFVRTRYPQPGPADDIPV +TTRASPLSAAPSQ +>MOLHKGIG_01019 +MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRLELTTA +GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP +RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD +DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALTEANSGRVAQALVAAGAGVAVVTEDP +AFGLTPVRVIAQGRTLTVRLHAAWRGDHFAAETLEAIARRLQAFVRDRYAEPGDDAPGRG +RSA +>NAFOICDF_01760 +MDSIAAGGRALDLDHLLDPALLRTFVAVVDEGTVTAAARELGLGQSALTRHLQRLQRDLG +LALFAPEGARLRITPAGQAWLPVARSLLAAHAHARQAARILAAGRLTELSLGAPGTTLID +VVIPFLTVLGEGDPAVRVTETQLDDSLQDSVARLDLVVLPSTPPDDVAALPLQSMPVWAC +VAPGHPWADRDELDAAELAGARLVLPSRSFKARRVFDAALEVAGAAPRQVVEANSGRVAQ +ALAANGTAVAVVTEDPAFGLRPLPIRAGGRRLEVHLHAVWRRDHFAAEEIAGVAAQLRVF +VRRRYDVAEAQDDADGSLSRAVSVD +>MHAAABBN_00733 +MDEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRFELTTA +GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP +RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD +DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP +AFGLTPVRVIAQGRTLAVRLHAAWREDHFAAETLQALARRLQAFVRDRYAEPGDDAPR +>LFPAFLNI_00963 +MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVGGRLELTTA +GEAFLPVAREVLVAHRRAEQAARTLASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP +RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD +DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP +AFGLTPVRVIAQGRALAVRLHAAWREDHFATATLEKIARRLQAFVRDRYAEPGDDAPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001301.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001301.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ee56d3baa52064ffe477ab500c236c8c6d9a3e3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001301.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01869 +MSSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGNR +LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISGQ +TRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGPF +APEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEGF +LPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVTG +RAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHADD +RIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPLT +IGEDLLKEGLSEVTKALQSA +>MOLHKGIG_01018 +MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR +LIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE +TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF +APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF +LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG +RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNADD +RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT +IGEDLLKEGLSEVTKALQSA +>NAFOICDF_01761 +MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN +RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG +ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP +FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG +FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT +GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD +ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL +TIGEELLREGLAEVTTALQSA +>MHAAABBN_00732 +MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR +LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE +TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF +APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF +LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG +RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNADD +RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPLT +IGEDLLKEGLSEVTNALQSA +>LFPAFLNI_00962 +MTATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR +LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPGE +TRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF +APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF +LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG +RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNADD +RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT +IGEDLLKEGLSEVTKALQSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001302.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001302.fa new file mode 100644 index 0000000000000000000000000000000000000000..52b97d9cc9b7c9b9daa23df9f0b302c85b8b51ba --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001302.fa @@ -0,0 +1,16 @@ +>ACLBLIBL_01870 +MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK +YGVGLVPEDEFGGTGVRRIFTAEKSRRLEAMENEGGPAYEDDI +>MOLHKGIG_01017 +MYPTPMTFDVARAGRALAQVSARTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK +YGVGLVPEDEFGGAGVRRIFSAEKSRRIKAMENEGGPAYEDDI +>NAFOICDF_00705 +MESQHISNGDMTRAARILVKVSAQYIAREANVTKEELRDFEKGRHDLSEKKQERVRAALE +ELGAEFLPDGPNGGYGIRLKFGRSRIYSLERCEGEGGPRLTTESDRRTQAHVPFSEPDSN +LPFHLEDRTTASLRILVPLRLGRLWPSHLASVPGMEARAR +>MHAAABBN_00731 +MYPTPITFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK +YGVGLVPEDEFGGTGVRRIFTAEKSRRIEAMENEGGPAYEDDI +>LFPAFLNI_00961 +MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK +YGVGLVPEDEFGGAGVRRIFTAEKSRRLEVLENEGGPAYEDDI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001303.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001303.fa new file mode 100644 index 0000000000000000000000000000000000000000..b88e91ae340232495e4a2fb2066b6fd050ce067d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001303.fa @@ -0,0 +1,49 @@ +>ACLBLIBL_01874 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG +ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP +VAEKTDREMDRLIGNIDELTAEIDAAAPWEHPRAAELDTISFRHWLEQESDDPEAIDNVS +IYIASGMLTKPSHTFSMLQALLMAASAGSFRNLVDEDFILDQRVEGGMQSVSLAMAAELG +DDVVLGQPVRTLRWTEPDPSTADEKNGVAADVRNGVAHDGDAGDVVALTDDYEVHARYAV +LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL +VQEIYDNTNRGENLAGGAPGEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL +GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY +QHVDGAIRMGEAAALAIAEREATDAGQPTG +>MOLHKGIG_01014 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG +ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP +VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS +IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG +DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV +LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL +VQEIYDNTNRGENLAGGAPGKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL +GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY +QHVDGAIRMGEAAALAIAEREATDAGQPTG +>NAFOICDF_01230 +METPSDVIVVGAGLAGLVAARTLAEAGLSVRVLEREAEVGGRQRTRTVDGFVLDRGFQLV +NPAYPELPRHADVDALGLRPFGAGVRVRTRRGLALLADPRREPRLAARTLRDGVRHGLLD +ARELAALSRWAAPALAAPRVAKHRMDAPLIEAWDRAGVRGPLRDAVLEPFLRGVLADPDL +TTSSRFTELLVRMFVLGTPGVPARGVAALPEQLAARVRAAGTRVTTGASVTAVRPAADGV +VVDVAGGAPLHARAAVLAVGPEAFTGLLPEAATDRLPVPSRGLTTWWFRAPSAPARERFL +AVDGTGSGPLVHTAVMTAAAPGLSPDGTPLVEATALLDPSAPAVTDAQARAHAARIWGVD +ASDWDLLARDDVPHALPVQAAPLRLRAEARVAERVYAAGDHRDTASIQGALVSGRRVAER +LLHELPR +>MHAAABBN_00728 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG +ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP +VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS +IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG +DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV +LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL +VQEIYDNTNRGENPAGGAPGEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL +GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY +QHVDGAIRMGEAAALAIAEREATDAGQPTG +>LFPAFLNI_00957 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG +ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP +VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS +IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG +DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV +LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL +VQEIYDNTNRGENLAGGAPGKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL +GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY +QHVDGAIRMGEAAALAIAEREATDAGQPTG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001304.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001304.fa new file mode 100644 index 0000000000000000000000000000000000000000..57ea6e8cf0195bdafa1b1fec3a8702a52eaf7bc9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001304.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_01882 +MRLILLRHGETDWNAGDRYQGRTDVELNAVGERQARRAAVGPVGDLLEEAAELVAVASPL +ARARRTAEILLEARVGAADLALDEQLMELHGGDWEGLGLTAIAQRWPEEHRSWRAVPALD +AGPVGGETLRAAGERALGALRGRVPQHWAVYAAAL +>MOLHKGIG_01008 +MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL +ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE +GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI +>NAFOICDF_01809 +MRLVLLRHGETDWNALDRYQGRTDVPLNALGERQAAAAAAGPVGELLRSAEDLVAVSSPL +IRARRTAEIVLEDAVGAVELAVDSRLVELGGGEWEGLDFTEIGARWPHEHHAWRTVPDLD +GGPVGGEVLRAGGERVLAAAAAHVPEDWSTPRPARVPDARTLLIVAHGAVIRAAAGLALA +LEGADFAHLARVSNARAVILDGTFAGEGPGAWSLLGYDV +>MHAAABBN_00722 +MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL +ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE +GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI +>LFPAFLNI_00951 +MRLILLRHGETDWNALDRYQGHTDIELNAEGERQARRAAGGPVGDLLEDAEELVAVCSPL +ARARRTAEIVLQARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAVPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLAVAHGALIRAATGLLLRHE +GEAFAAMERIGNARAAVLQGAFAPATEGWGDWTLEGYGI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001305.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001305.fa new file mode 100644 index 0000000000000000000000000000000000000000..2823a1a519e54bcb979f107ea28b675cea1d35b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001305.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01883 +MTVPQTTLDALTVAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE +EALLKEEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLA +EEHTRPDAAGEGAADDAAPHAS +>MOLHKGIG_01007 +MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE +EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP +EESTRPDAATQDDGASASHAS +>NAFOICDF_01810 +MTVPQTTLDALQVAAAAAAEKVATHIVAVDVAERLGLTDAFLIASGASERQVNAIVDGIE +EDLLVKEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDSPAIDLGLP +EEATRPDDALDAAAQD +>MHAAABBN_00721 +MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE +EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP +EESTRPDAATQDDGASASHAS +>LFPAFLNI_00950 +MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE +EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP +EESTRPDAAAQDDDASASHAS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001306.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001306.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a301329b9f9df77d4b1ab36636222c1fb584b83 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001306.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01884 +MAVSSRTTASEPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVIFVPTGQP +WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGMTYTVDTLRDLRRLHPDAELF +FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLTDMGLKDDVSLMEIPAMAISSTDC +RERVARGRPVWYLVPDGVVQYIAKHHLYVSDEETP +>MOLHKGIG_01006 +MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP +WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF +FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC +RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS +>NAFOICDF_01812 +MTSATRDPAPPPTSRRHRLGVMGGTFDPIHHGHLVAASEVAAEFGLDEVVFVPTGQPWQK +SDTRVSPAEHRYLMTVIATASNPRFTVSRVDIERPGNTYTVDTLRDIRAKRPDSELFFIT +GADALNQILTWKDVEELWDLAHFVGVTRPGYQLEDYGLSEDISLMEIPAMAISSTDCRRR +VERGRPVWYLVPDGVVQYINKHHLYTPEGDRP +>MHAAABBN_00720 +MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP +WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF +FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC +RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS +>LFPAFLNI_00949 +MTVASRTPVTAPTAGRARRPRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP +WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF +FITGADAMGQILTWKDVDELWGLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC +RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001307.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001307.fa new file mode 100644 index 0000000000000000000000000000000000000000..85cacf41f9db0ef02cb9e9b3be64e1dc4d839a33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001307.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01885 +MLNTSLVLAAAEGPHVVNELPIPTVWYGIIVFALLMAALLATMSMRSRALRLPEPTTAVQ +HHGTGHGSHTPGH +>MOLHKGIG_01005 +MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ +HHGTGRGSHTSGH +>NAFOICDF_01813 +MLNSALVLAAAEEGHHVVNELPIPPVWFGIIVFLLLMAGLLAILSMRSVGLRHAEPTTAV +QHHGTHGTGSHSAGH +>MHAAABBN_00719 +MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ +HHGTGRGSHTSGH +>LFPAFLNI_00948 +MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ +HHGTGRSSHTSGH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001311.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001311.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a28f5e2dd260275292d5caf71c862f600f05abf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001311.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_01889 +MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF +ALSAGSVAFGQRRGRKVVDIVPAAE +>MOLHKGIG_01001 +MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF +ALSAGSVAFGQRRGRKVVDIVPAAE +>NAFOICDF_01817 +MAHKKAGSSSKNGRDSNPQYLGVKRFGGQDVNAGEILIRQRGTKFHPGRNVGRGKDDTLF +ALSAGTVSFGQRRGRKVVDIVAAGE +>MHAAABBN_00715 +MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF +ALSAGSVAFGQRRGRKVVDIVPAAE +>LFPAFLNI_00944 +MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF +ALSAGSVAFGQRRGRKVVDIVPAAE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001314.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001314.fa new file mode 100644 index 0000000000000000000000000000000000000000..153f37a9b8e61a8fd8fdb682c89073e5b507e6cd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001314.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01892 +MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVIIVERSILA +ADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLFAGARFARW +YWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNIQTGTLPA +SPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD +>MOLHKGIG_00998 +MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT +ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW +YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA +PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID +>NAFOICDF_01838 +MDVTETAENPPAPRAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIIIIVERS +ILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLFAGARF +ARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRNLQTGA +LPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR +>MHAAABBN_00712 +MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT +ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW +YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA +PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID +>LFPAFLNI_00941 +MSMPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVIIVERAL +LTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFA +RWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTL +PAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001315.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001315.fa new file mode 100644 index 0000000000000000000000000000000000000000..834ab94c5ea8152972980c56fe7f314900461274 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001315.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_01893 +MAQHIEETLVLVKPDGVERNLVGEILARIERKGYVIADLKMLTPTRSMLERHYEEHQGKP +FFDPLVDFMASGPVVAVRVTGNSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGESVQKN +LVHGSDSSLSAERELGIWFG +>MOLHKGIG_00997 +MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP +FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN +LVHGSDSTLSAERELAIWFG +>NAFOICDF_01839 +MTHHPEETLVLVKPDGVERRLTGEIIARIERKGYEVVDLKMLVPTREMLAAHYEEHEGKP +FYEPLLEFMGSGPVVALRLAGDRVIEGFRSLAGATDPTVAAPGTIRGDYARDWGAGVQKN +LVHGSDSTLSAERELAIWFA +>MHAAABBN_00711 +MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP +FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN +LVHGSDSTLSAERELAIWFG +>LFPAFLNI_00940 +MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP +FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN +LVHGSDSTLSAERELAIWFG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001317.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001317.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f801c21d1c7ffb47c006eff8ee1713969f74feb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001317.fa @@ -0,0 +1,100 @@ +>ACLBLIBL_01895 +MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPALNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP +DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL +AVDLVGAHATELGYADADAARAAVTETIPGARLGGLAYEPLFTDVFDAHADETFTVNGRD +LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA +REDVGRGDLREIAGVQVFEANRTIVRALRGLGRVAREASYEHSYPHCWRCRTPLIYRAVT +SWYVKVTQVKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD +HPDYPLQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV +EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD +RPAFSNVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLVV +TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT +GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRQRFFDEDTAAMDVLYTALEAF +ARAAAPLMPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS +ALRKGAGRRVRLPLPRLSVVVPDAEGLEGTYARIVADELNLKDVSLTELSDEAIARYGIG +TELKLNFRELGKVYGKQVPLVKKAVDAGSYEETADGLAVTLADGATVTLDPALYELRTVS +TGAPEGTAVGVLPGAAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR +IDGPAAVVAALEAHRDLVAEETLTVELELVDSGEADPRKDPADDAMKTVAVTVAKADA +>MOLHKGIG_00994 +MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP +DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL +AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD +LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVMLSVDSGARFLPLFA +REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT +SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD +HPDFPRQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV +EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD +RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV +TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAA +GRMLREVKAGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF +TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS +ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG +TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS +TGAPEGTAVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR +IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVSVAKADA +>NAFOICDF_01842 +MYPLASTDPAGATPASPLLPEIEQRILRYWDEDGTFQASIDARPAVNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDRFNDACRSSVLKYTEEWRRYVTRQARWVDFDNDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWHDETPLSNHELRMDDDVYKMRQDPSVTVSFPILGLPDDAALVP +AGGADAALADELAGVHVLAWTTTPWTLPTNAALAVGPEIEYAVVPAGPEGATVAAAERFL +LAVDLVGAHAKELGYADADAARAAVERTVLGARLGGLRYEPLFTDVFEAHAGETFPVGAR +TLTLDGVHRILVDDYVSTDDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDEGARFLPLF +AREGQGRGDLKDIAGVQVFEANRTIIRALRALGRIAREASYEHSYPHCWRCRTPLIYRAI +TSWYVSVTKVKDRMLELNEDITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWES +DHPDYPLQEVYGSLAELEEAFGRLPRNADGEVDLHRPWIDDLTRPHPDPEAAAAGATMRR +VEDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALF +DRPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGSDAMRWFLMASPILRGGNLI +VTEEGIREATRQVILPLWNAWHFFTLYANTAHDGGARPEGYRASERHTAEDPLDQYVLAA +CGTMLRQVKAALDAYEVSDAADALRAFMDTLTNWYIRRSRERFFAEDTAAMDVLSTVLEA +FTRAAAPLLPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADALVARMDLVRSITSAG +SALRKGAKRRVRLPLAAMSVVVPDAAALEGTFTRIVADELNLKEVRLTELSEEAISRYGI +GTELKLNFRELGKHFGRQVPLIKKAVDAGAYAEGEQGLDVTLADGAVVTLAPELYELRTV +STGAPEGTAVGVLPGGGFLVLETAVSAELAAEGVARDVIRAVQAARKDAGLDVADRVRTR +IEGPAPVVAALESHRDLVAQETLTVELDLVDSGAADPRRDPADDAMKTVAVAVAKAQA +>MHAAABBN_00708 +MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPAFNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDKFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP +DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL +AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD +LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA +REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT +SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD +HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV +EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD +RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV +TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAT +GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF +TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS +ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG +TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS +TGAPEGTTVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR +IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA +>LFPAFLNI_00937 +MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP +DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL +AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD +LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA +REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT +SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD +HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV +EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD +RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV +TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT +GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF +TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS +ALRKGAGRRVRLPLPGLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG +TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS +TGAPEGTTVGVLPGTAGFLVLDTQVTAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR +IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001318.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001318.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b1cb9330410e9612583f93f853744f6cfbffbce --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001318.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_01898 +MTASDLYPTSLRLLGRPVLMVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGARAAGVPAPILTLNPTSEGA +RA +>MOLHKGIG_00991 +MTASDLYPTSLRLLGRPVLIVGGGRVAGRRVGALLDAGALVSVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAIALALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPISTLNPTSEGA +RA +>NAFOICDF_01845 +MTASDLYPTSLCLLGRPVLIVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVA +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNPTSEGA +RA +>MHAAABBN_00705 +MTASDLYPTSLRLLGRPVLMVGGGRVAGRRMGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNSTSEGA +RA +>LFPAFLNI_00934 +MTTSDLYPTSLRLLGRPVLVVGGGRVAGRRMGALLDAGALVTVVAPKPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSVVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPILTLNPTSEGA +RA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001319.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001319.fa new file mode 100644 index 0000000000000000000000000000000000000000..20222ff42de70419218e7f1bf28affec4eeb5099 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001319.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01899 +MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSARRTGLAGWDWSRVLLPVAAVV +LLVAIWQVAAWLAGARGEPITGPGDVLGAFGALWAQGLVQQAVATSVGRAVVGFALAVVA +GVGLGLLLAQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVILTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGAPMGVGLGTLLHQGRTESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG +LLEGSTR +>MOLHKGIG_00990 +MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV +LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV +GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGGPMGVGLGTLLHEGRAESDLAVVLCAVLAILAVGVLVELTAFGPAERRMLRRRG +LLEGSTR +>NAFOICDF_01846 +MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV +LLVAIWQVAAWLAAARGEPITGPGDVLRAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV +GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGGPMGVGLGTLLHQGRAESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG +LLEGSTR +>MHAAABBN_00704 +MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV +LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV +GVGLGLVLGQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG +LLEGSTR +>LFPAFLNI_00933 +MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV +LLVAIWQAFAWLAGARGEPITGPGDVLGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV +GVGLGLVLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG +LLEGSTR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001322.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001322.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab3e7140ba67ff9af183fc438527ed4622cc4988 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001322.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01902 +MTLTHAPDPGTVSPAGPDVLDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPPIYYAHEREVFRRDGMWRAVGEHSR +PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF +>MOLHKGIG_00987 +MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR +PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF +>NAFOICDF_01849 +MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR +PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF +>MHAAABBN_00701 +MTLTHAPDPGTVSPAGPDVQDALEAEAIHIVREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR +PAENEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF +>LFPAFLNI_00930 +MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR +PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001323.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001323.fa new file mode 100644 index 0000000000000000000000000000000000000000..466ae638421b23cff67acf83325db9913c025ca1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001323.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01903 +MSTVPPTRPTEELERLQALAESGAAELGWDAPAAAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWTGTAKTECGIH +V +>MOLHKGIG_00986 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>NAFOICDF_01850 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>MHAAABBN_00700 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSLDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>LFPAFLNI_00929 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHSMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001326.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001326.fa new file mode 100644 index 0000000000000000000000000000000000000000..342c454f45cf71e345167831ee5a82497b852b08 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001326.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01906 +MDVSHTTENQSPRAAVVTGATTGIGRATALELARRGWRVYAVGRRAERLDALAAQAREEA +VPGEVVPAPLDVTDEAAVAGLVARVDTDGGIDTLVNIAGGARGTDFVGAGNREDWEWMYR +ANVLGTLAMCQAFLPGLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTAALRLE +EAEHNVRVIEVLPGMVHTEEFSLMRLGGDAAAAEKVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVIRPVAQAAQHKVIRR +>MOLHKGIG_00983 +MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG +VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR +VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE +EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVMRPVAQAAQHKVIRR +>NAFOICDF_01853 +MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG +VSGDVVPAPLDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR +VNVLGTLTMCQAFLPMLRTHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE +EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVMRPVAQAAQHKVIRR +>MHAAABBN_00697 +MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG +VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGVGDRADWEWMYR +VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE +EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVMRPVAQAAQHKVIRR +>LFPAFLNI_00926 +MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG +VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR +VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE +EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVMRPVAQAAQHKVIRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001327.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001327.fa new file mode 100644 index 0000000000000000000000000000000000000000..ffbce65f9cdaf7ad27ac1c79b3aaf40befc213b1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001327.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_01907 +MAENTQGTDTPIDASTASTPAAGAVAVPDKPGLEGLEEKLTARWAQEGTYAFDPRTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMTGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPTKPYIEGYTPPAQPAKNQRDWDVVSRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWSMTYRTIDDVSRAVSQRAFLRNVAAGDAYLSEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYPFTAADGTQVFIETTRPELLASCSALVAHPEDERYQPLFGTMVRSPLFDVEVEV +KAHELAKPDKGSGIAMVCTFGDLTDVTWWRELQLPTRTLIGRDGRFAAETPEWISSEAGR +AFYAESIAGKTVFSAKEAVVTALTEAGLMDGEPKKVQHAVNFYEKGDKPLEIVTSRQWYI +RNGGRDADRREQLIARGRELDWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYRL +DAEGEPVYDEPIVPEDAALPVDPVAETAPGFTEDQRDQPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDEEFFANVFPFDLRPQGHDIIRTWLFSTVVRADALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILEEFGSDAVRYWASSARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATRDAVVRTPDDAARVTNALDASLLARLATTVEQATAAFDAYDYARALNVTE +SFFWQFTDDYVELIKDRAYGGHGEAEQASVVAALATTLDSLLRLLAPFQPFATEEVWSWW +RTGSVHRAPWPGLESEAAGLRAAAEGGDPQVLAVVAQVLGRVRKAKSEAKVKQRTQVRTA +TVRAAAAQLDALRGGLADLKGAGNVADVTLTEADGELEVTDIELAPAEEA +>MOLHKGIG_00982 +MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV +FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR +QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI +RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL +DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE +QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW +RAGSVHTAAWPGAADEVASLSFAASAGDAEVLPTVAQVLGGIRKAKSEAKVKQRTEVRSA +VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVDDD +>NAFOICDF_01854 +MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV +FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR +QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI +RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL +DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDDAFFSSVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAVSVEQATRAFEAYDYARALNVTE +QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW +RAGSVHTAAWPGAADEVASLSFAASSGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA +VVTGPAEWLEKLRGGLADLKAAGNIADLSLTQGEAGEAAPLTVSDVQLAPVEDD +>MHAAABBN_00696 +MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV +FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR +QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI +RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL +DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE +QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW +RAGSVHTAAWPGAADEVAALSFAASAGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA +VVTGPTEWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVEDD +>LFPAFLNI_00925 +MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV +FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR +QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI +RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL +DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAATVEQATRAFEAYDYARALNVTE +QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW +RAGSVHTAAWPGAADEVAALSFAASGGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA +VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPAEDD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001329.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001329.fa new file mode 100644 index 0000000000000000000000000000000000000000..477283eb0bf177442e83c9467d66ce32df95dacf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001329.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01910 +MSENTQPVVDFYFDPTCPFAWITSRWILEVEKVRDIQVKFHQMSLYMLNEGRDLPEDYRR +STDRGLIPGRGTQHVGAEHPERLAEWYTALGTRIHNEGQKDYEAALTGAAVDLGLDPAPI +LAATETDAEDERLREKQRAAEELVGNDVGTPVVSFNGTAFFGPVLTRIPRGEEAGRIFDG +AVALAEYPYFYEIKRARTTDPQFD +>MOLHKGIG_00980 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD +ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD +GAVALADFPYFYEIKRARTTDPQFD +>NAFOICDF_01857 +MSENTAPVVDFYFDPTCPFAWITSRWILEVEKVRDLSVTFHQMSLYMLNEGRELPEDYRR +HTDRGLMPGRATLHVGEHHPELLSDWYTAVGTRIHNEGNQDYEAVVTGAAAELGLDAAPI +LEATRTDAADDDLRAKQRAAEELVGNDVGTPVVSFDGTAFFGPVMTRIPRGEEAGEIFDA +AVRLAQFPYFYEIKRARTTDPQFD +>MHAAABBN_00694 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD +ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD +GAVALADFPYFYEIKRARTTDPQFD +>LFPAFLNI_00923 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD +ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD +GAVALADFPYFYEIKRARTTDPQFD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001331.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001331.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f3b515afc83130adf15bfca84777e8afcba9557 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001331.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01912 +MTQFPAGLPTGTPSMPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS +ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIQAQEINRMRVWMEQTLASLTN +RTPEEVSRDIDRDKFLSAEQALEYGLVDEVLASRKITRPAG +>MOLHKGIG_00978 +MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS +ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLQIHAQEINRMRVWMEETLASLTN +RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA +>NAFOICDF_01859 +MTQFPAGLPVGTPSQAAPSARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS +ADDIMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHANEINRMRVWMEQTLASLSN +RTPEDVSRDIDRDKFLSAEGAKEYGLVDEVLAPRKITRTGA +>MHAAABBN_00692 +MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS +ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN +RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA +>LFPAFLNI_00921 +MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS +ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN +RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001332.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001332.fa new file mode 100644 index 0000000000000000000000000000000000000000..123d6d97a945ca10fed50405105601e5dba75873 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001332.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01913 +MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV +LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAKEA +LEYGFIDHIADRAASVTGGGGVQG +>MOLHKGIG_00977 +MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV +LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA +LEYGFIDHIADRAASVTGGGGVRG +>NAFOICDF_01860 +MTDLTPRMTSVEPTQREDYLYNQLLKNRIIWLGSDVRDDNANAICSQLLLLSAEDPEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGAPGKRYATPHARI +LMHQPSGGIGGTESDIRIQAQLILHMKQIMAELTAAQTGQSVETILEDNARDKWFTAQEA +LEYGFIDRIAQSAASVTGGGGVEG +>MHAAABBN_00691 +MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV +LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA +LEYGFIDHIADRAASVTGGGGVRG +>LFPAFLNI_00920 +MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV +LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA +LEYGFIDHIADRAASVTGGGGVRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001333.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001333.fa new file mode 100644 index 0000000000000000000000000000000000000000..28d5a747d64f8771e82c22016865fb256eba0c5e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001333.fa @@ -0,0 +1,47 @@ +>ACLBLIBL_01914 +MVKSTAENLSPTRVKLNVEVPFEEVKPSLDKAYKDIANQVQIPGFRKGKIPARLIEQRFG +REAVVDQAVNEGLNTWFSAAISEAELTPISRPEVDVTATPDSENAEGPVVFTAEFDVRPT +IELPDYKGLKVTVEPAKATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTASVDG +EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFESTLNGGEHDGKTAVVKLELTAV +KERELPEADDEFAQLASEFDTIDELKEDLKKQAAEDAVNRQGVEARDKVLAELAKLVEVP +VPDGVITEQVEQHFSAGGHAAGDDHDTPEHRAELEANTREAFANEVILDEVAEAEEVTVD +QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEFAEVTDTDGK +AVDLKAFVTPGGQEALDAEAEGADPAEAEEKPAKKAAAKKPAAKKAPAKKKAEEKADDAE +ASEQA +>MOLHKGIG_00976 +MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG +REIVVDQAVNEGLNTWFSAAIAEAEVTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT +IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG +EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV +KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP +VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD +QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK +AVDLTAFVTPGGQEALDAEAEGAEAEGADEAEEKPAEKAPAKKKSTAKKAPAEQADDAEA +AEQA +>NAFOICDF_01861 +MVKSTAENLSPTRVKLTVEVPFEEVKPVLDKAYKDIAMQVQVPGFRQGKVPARLIEQRFG +REAVVDQAVNDGLNTWFGQALAEAEVTPISTPEVDVTATPAAAEGPVEFTAEFDVRPTIE +LPDYKGIEVTVEPAQATDEDEQAQLDALRSRFGTLKDVDRPAAKDDFVTMDLTATVGEEQ +VDQAQGLSYQVGAGTMLDGIDEALEGLSAGEDATFETTLNGGEHDGETATVKLVLQAVKE +RELPEADDDFAQLASEFDTIAELKEDLKKKAAEAAETRQGVEARDKVLAELGKLVEVPVP +ENVIAEQLEQHFSQGGHSAGDEHDTPEHREELEKNTREAFANEVILDEVAEAESVTVDQG +ELIEYIFATSAEYGMDPNQFAMMLDQAGQIPMIMGEVRRRKALAKVLEHAVVTDTDGNAV +DLTAFVTPAAAEEEKAEEKPAKKAPAKKAAAKKAAAKKPAAKKAEAEESEEA +>MHAAABBN_00690 +MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG +REVVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVVFTAEFDVRPT +IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG +EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV +KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP +VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD +QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK +AVDLTAFVTPGGQEALDAEAEGADEAAEQA +>LFPAFLNI_00919 +MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRKGKIPARLIEQRFG +REIVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT +IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG +EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV +KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP +VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD +QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK +AVDLTAFVTPGGQEALDAEAEGAEAEGADEAAEQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001335.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001335.fa new file mode 100644 index 0000000000000000000000000000000000000000..0d15863cc2d9519a233af353422ddd075712961e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001335.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_01918 +MPEGHSIHRLARQFTDVFGGWPIRASSPQGRFAEGAARMDGQVLEAARAHGKHFFADLAD +GHVLNVHLGMYGAWSFGGDERFDAASSIGAPRRIGEREVHADGAAAAEPDRDDDGWVLPP +PPVPTVRLRVRAEHGWADLIGASTCRLLTPAEAGDVVAKLGPDPLNDDDPAPFLDLAGRT +RRPIGAVLMDQAAVGGIGNIFRAEALFRAGLDPWRPSNAVPREVLRRLWSDNAELMREGV +RLGRIVTTRPEHRPGVPAEQAWPEHANYVYQRQGSPCLVCGQDAIVVEGMAARKLYRCTV +CQR +>MOLHKGIG_00972 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT +RRPIGVVLMDQAAVSGIGNIFRAEALFRVGIDPWRPARDVSASELESLWADNAALMREGV +RLGRIVTTRPEHRPGIPAEAAWPEHASYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS +>NAFOICDF_01866 +MPEGHSIHRLARQVQDVFGGQALAASSPQGRFADGAALLDGRVLERAWAHGKHFFADIEG +GLTLNVHLGMYGAMTFGGDEAFAAASSIGAPRRIGETEDHGALAAAEPPPARPTVRLRLR +SAHGWADLIGAGTCRVLTPQELAEVTSKLGPDPLNDDDPAAFVARAARTGRPVGVVLMDQ +SMVGGIGNIYRAEVLFRAGLDPWTPARDVGADVLAALYADAQALMRDGVRLGRIVTTAPE +HRPGVAAEDAWPEHANYVYRRQGMPCRVCGQDAIVREEMAARNLFRCTDCQR +>MHAAABBN_00685 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPASTVRLRLRAEHGWADLIGANRCRALTRAEAADVVAGLGPDPLNDDDPAPFYDLARRT +RRPIGVVLMDQGAVSGIGNIFRAEALFRAGIDPWRPAREVSAPDLAFLWADNAALMREGV +RLGRIVTTRPEHRPGIPAEAAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS +>LFPAFLNI_00915 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT +RRPIGVVLMDQAAVSGIGNIFRAEALFRAGIDPWRPAREVSASDLAFLWADNAALMREGV +RLGRIVTTRPEHRPGIPAESAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001336.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001336.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba91bf50fef10a3a0c18c137749ed6f65719b879 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001336.fa @@ -0,0 +1,80 @@ +>ACLBLIBL_01920 +MSSSARLNITREEAAQRAAALTVDAYEVSLDLTRGPERFRTASTVTFAASEDAVGTHTWI +DFVASQAPEVTLNGERVAVEDYDGARLPIGPLAAQNTLVVEGLGDYSNTGEGLHRFVDPV +DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVEN +EDQLSGVDAAVWEFVPTPRISSYITALVAGPYAAVHSELTSADGRTIPLGVYCRASLVEH +LDADNVFELTRQGFEFFEAQYGHPYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VPEAMVERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTRYTGSWT +TFSSMEKNWAYRQDQLSSTHPIKAQIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MAGVRAYIAKHAWSNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGV +ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA +EAAGRRRPALILPNDDDLAYAKLRLDHASWEAASTRLKDVDSSLARTLLWGAAWDAVRDG +EASAAWFADLILANIGHEQDSSVVQTLLRQLATSLGQYLPEEQSTAARAAVADRLWGLVA +GAEDGSDSQLQFVKAFALHARTAAQLDRLAGVVDGTHTVPGLDLTTDLRWELLTALVAAG +RAGEAEIAAAEREDATATGALAAIQARAAVPTAEAKQAAWDRVMAGELSNTEQRQALIGF +ARAHEAALLAPFADAYFEGVEAMWDSRSHEMAETAAVLGYPAAQVSDETAQRATALSEKT +AGTRAGLSRVLAEGRDETVRALAAREHAAAHVHEVSASA +>MOLHKGIG_00967 +MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI +DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV +DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN +EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH +LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTGAWT +TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MVGVRAYIAKHAWQNTELPDLMTELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT +ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLIRTERFELDVAGEVTEVV +EAAARRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG +EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA +EAEDGSDNQLQFVKAFALHARTTAQLDRLSALVDGTRTVPGLDLTTDLRWELLTALVAAG +RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAVWDRVMAGELSNTEQRQALIGF +ARVHDAALIAPFADAYFEGVEAMWDSRSHEMAETAATLGYPTAQVTPEIADRATALSERL +ADTRAGLSRVLAEGRDETIRALAAREHATAHVHQVHAGA +>NAFOICDF_01868 +MTTAAAMNITREEAAARAAALTVESYQVALDLTRGAERFGSTTTVTFSAADEAVGTQTWI +DFMATQAPEVTLNGQAVDVADFDGARLPIGPLAAENTLVVDGLADYTTTGEGLHRFVDPV +DDEVYLYSQFEVPDSRRMFAVFEQPDLKATFAFTVTAPAHWAVVSNQPEAAHRTLGVVET +PEAPEGVDAAVWEFTPTPRISSYITALVAGPYKSVHSELTSADGRTVPLGVYCRGSLFEH +LDADEVFDLTRRGFEFFEAQYGHPYPFDKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VTDAVRERRAITILHELAHMWFGDLVTMKWWNDLWLNESFAEFMSTLAAAENTRYEGAWT +TFSSMEKNWAYRQDQLSSTHPITAEIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MAGVRAYIEKNAWSNTELPDLMTELEAASGRDLSEWTRLWLETSGVNTLAVQVDADYAGT +ITSLRLHQSAPDGSPAAPGDDVLRPHRIAVGFYDLDEATGRLTRTERFELDAAGEVTEVA +EAAGRRRPALILPNDDDLAYAKIRLDDASWETAGARLADVDSSLARTLLWGAAWDTVRDG +EASAAWFVDLILTNIGREQDSTVIQTLLRQLATAISQYLPEERSAQVRADAANRLWMLVE +QAEPGSDAQLQFVKAFALHAREEGQLTALADVWDRSSELPGLDLTTDLRWELLTALVAAG +RAGETEIAAAETEDPTATGALAAALARAAVPTAEAKQTAWDQVVAGTLSNTTQRQVLLGF +QRAHDPALLAPFTDAFFGSIQDVWGSRSHEMAETVAVLGFPSSQVCQEVVDRATALSDEV +RGTNAGLARTLAESRDEMARALKARAAA +>MHAAABBN_00680 +MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI +DFVAGQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV +DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEDSRRTLGVVAN +EENLQGVDAAVWEFTPTPRISSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH +LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT +TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT +ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA +EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG +EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA +EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAG +RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF +ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTSQVSRETADRATALSERL +ADTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA +>LFPAFLNI_00913 +MTTVAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI +DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV +DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN +EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH +LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT +TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT +ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA +EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG +EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA +EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAS +RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF +ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTAQVTREIADRATALSERL +AGTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001337.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001337.fa new file mode 100644 index 0000000000000000000000000000000000000000..810d1cacae60914cd739c8705b7c645f1d0c6870 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001337.fa @@ -0,0 +1,37 @@ +>ACLBLIBL_01921 +MKHTFALRTEWTGNRGTGTSGVRDYDRSVVIQDAAVGEIHASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGLVVTGMACAAEGVLEVDGDGAGRFAAVTLRPEVALQDEAD +RERADALHAEAHRLCFIANSLSAPVSVEPAVAGSGAAASGGPALPDHSSRLGAPLAVLRP +RVAKRPSQVTGLAERPTEVEPVMKAGAPAPVDQMQARDAAAGRAASPATPAPAAETAAPG +QAASFYEAVGGRETFDRLTAEFYARVREDELLSPMYPQDDFEGAQRRLLMFLEQYWGGPR +TYSEERGHPRLRMRHAPYRIDPAARDAWLTHMRAAVDTLGLSPLHEAELWDYLERAAHSL +QNSA +>MOLHKGIG_00966 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGAPTLPDHSARLGAPLAVLRPRV +AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQAASFYD +AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG +HPRLRMRHAPYRIDPAARNAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA +>NAFOICDF_01869 +MKHTFSLRAEWTGDRGTGTTGVRDFDRSVVIQESEVGEIHASAARPFRGDAAKWNPETLL +LGALAECHVLSYLHAAATGGLVVTGMTCAAEGTLEVDSDGAGRFASITLRPEVALRDEAD +RARADELHAEAHRMCFIANSISAPITVEAGPGSSPTRGDGAALPDHSARLGAPLAVLRPR +VANRPTRVTGLADRPTEAEPVVRADAPSGAEQARARDEATARGERPPSATPIATPAPGAT +PAASPATAAPGQATSFYEAVGGHPTFEKLVHVFYQGVREDPLLAPMYPHQDWDGAEERLR +MFLEQYWGGPRTYSERRGHPRLRMRHMPFTVDPAARDAWLRHMRAAVDAVELSPLHEAEL +WDYLERAAHSLQNSA +>MHAAABBN_00679 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGTSTLPDHSARLGAPLAVLRPRV +AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPTGATPGTPAVPGQATSFYD +AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG +HPRLRMRHAPYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA +>LFPAFLNI_00912 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFIAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVTVEPVRPEALPTGTPTLPDHSARLGAPLAVLRPRV +AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQATSFYD +AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG +HPRLRMRHASYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001338.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001338.fa new file mode 100644 index 0000000000000000000000000000000000000000..5dd4c3768c7dce03ba856bab6fa92f1b21dcbfdb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001338.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_01923 +MPQRHPAPRPGRAPARPASAPKDPTDMLRGILELNRADADPLTGQPRFTGTTPRQAHGRV +FGGQVLAQALAAASRTISADRPVHSIHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLA +TQNEKAILALTCSFQEPAEAALDHQVAMPEGVPAPEDLPSTADVLGRINHPIAQEWAWAR +PFDIRHVTPAIYVDPAPEAENRNMVWMKTFTPLADDPALHVAALTYASDYTLLEPVLRQH +GVAWIQPGMSVASLDHAMWFHRPARADEWLLYVQHSPSAQGARGLGTGSVFTRDGTLVAT +VAQEGMIRMPEGAAARRARLQGAAQRFALRTVLRRSWRR +>MOLHKGIG_00964 +MLRGILELTPAAPDPVTGQVRFTGTTPRQTRGRVFGGQVLAQALAAASRTVPAARPAHSL +HGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAILALTCSFQEPAGSALDHQV +AMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSRPFDIRHVTPAIYVDPAAETENRNMVW +MKTFTPLADDPALHLAALTYASDYTLLEPILRQHGVAWIQPGMSAASLDHAMWFHRPARV +DQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVATVAQEGMVRLPEGAAARRARVRGAAQR +MAMRTVLRRSWRR +>NAFOICDF_01872 +MSPKPPARPATAPQDPTEALRGLLDLTDAGPDPVTGEPRFEGRTPAQVGPRVFGGQVLGQ +ALAAASRTVPTARSAHSLHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAIL +ALTCSFQEPTGSALDHQVAMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSRPFDIRHVT +PAIYVDPAAETENRNMVWMKTFTPLADDPALHLAALTYASDYTLLEPILRQHGVAWIQPG +MSVASLDHAMWFHRPARVDEWLLYVQDSPTAQGARGLGRGHVFTRDGELVATVAQEGMIR +LPEGHAATAAKAKNVVQRAAMKTVLRRTWRG +>MHAAABBN_00677 +MPQRHPRPRPGRAPARPASAPKDPTDVLRGILELTPAAPDPVTGQVRFTGTTPRQTHGRV +FGGQVLAQALAAASRTVPAARPAHSLHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLA +SQNEKAILALTCSFQEPAGSALDHQVAMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSR +PFDIRHVTPAIYVDPAAETENRNMVWMKTFTPLADDPALHLAALTYASDYTLLEPILRQH +GVAWIQPGMSAASLDHAMWFHRPARVDQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVAT +VAQEGMVRLPEGAAARRARVRGAAQRMAMRTVLRRSWRR +>LFPAFLNI_00910 +MLRGILELTPAAPDPVTGQVRFTGTTPRQTRGRVFGGQVLAQSLAAASRTVPGARPAHSL +HGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAILALTCSFQEPAGSALDHQV +AMPEGVPRPEDLPTTADVLGGINHPVAQEWAWARPFDIRHVTPALYVDPAPETENRNMVW +MKTFTPLADDPALHRAALTYASDYTLLEPILRQHGVAWIQPGMSVASLDHAMWFHRPARV +DQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVATVAQEGMIRLPEGAAARRARVRGAAQR +MALRTVLRRSWRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001344.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001344.fa new file mode 100644 index 0000000000000000000000000000000000000000..9af1377af74623b68e4d651f795e52e353cdd826 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001344.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01931 +MSETSTPAPENAPLVWIDCEMTGLHPHVDELVEVAVLITDAELNILDEGIDLVIRPSEAA +LAQMDPFVRDMHTTSGLLPELEHGLTLENATARVMEYLTARVPAGKALLAGNTVGQDKLF +LSAYMPAVVEHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY +RAAVMAPSPGPTSEEAQAIARVVAEAQA +>MOLHKGIG_00956 +MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSAAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAEVVSGAQA +>NAFOICDF_01883 +MSETSTPAPESAPLVWIDCEMTGLDPDVDVLVEVAVLITDSELNVLDEGLDLVIRPTPEA +LAQMDPFVRDMHTSSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNSVGQDKLF +LARYMPAVIDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY +REAVMVPAPGPTSEEARAIAEVVSGAQA +>MHAAABBN_00669 +MSETSTPAPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNTLDEGIDLVIRPSAAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAEVVSGAQA +>LFPAFLNI_00902 +MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSEAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAQVVSGAQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001347.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001347.fa new file mode 100644 index 0000000000000000000000000000000000000000..63336920a8538e785167174e513010ac78fe4bfb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001347.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_01995 +MASIRPITVYGEPVLHTRAAEVEVIDDEIRRLVEDMYVTQDAARGVGLAAPQVGVGLRVF +TWTYPHSGDAPSVGHVINPVLTVLDKASQEATDPDEHTEGCLSVPGHGYPLQRAPRVRLA +GQRVDGEMFEFVAEGWFARVMQHEYDHLNGTLYVNRLEGRWQRRWKRAQRAERMNVPGVT +WLPGTDEDPFGHDELDEAEAIEQHGPDADHGRADGA +>MOLHKGIG_00943 +MASIRPVTVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF +TWTFPDSGDAPNVGHVINPVLTHLDKAPREEPHPDEHTEGCLSVPGLGFPLQRPTRVRLS +GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT +WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA +>NAFOICDF_01892 +MPSIRPITVYGEPVLHTRAAEVEVIDDSIRELVEDMYVTQDVANGVGLAAPQVGVGLRVF +TWTFQDTGDAPNLGHVINPVLTMLSKPSTEEPDRHEDTEGCLSVPGHGFPLKRSAHVRMT +GQRMDGSTVDIEATGWFARILQHEYDHLNGTLYVNRLEGKWARRWKRAQRAERLNVPGVT +WLPGTDPDPFGHDVDVDEDAPAHEHHDHDHEGHDHAQEAR +>MHAAABBN_00662 +MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQDAAHGVGLAAPQVGVGLRIF +TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS +GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT +WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA +>LFPAFLNI_00893 +MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF +TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS +GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT +WLPGTDEDPFGHEEIEDHEH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001348.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001348.fa new file mode 100644 index 0000000000000000000000000000000000000000..38beff8559418ed7912c6cd68d6d7140d0dcdf95 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001348.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_01996 +MADTASTQTPEWNTQQELAERMVPLLGSLYRENNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQDAPLSVAATYPLVEAMAAMDLGAANVDLAELAARHKESGQEVQAFLDAELAEVKGKG +GEGLGEPQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLVKRASLLRR +DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTAHGIKDALVIDNTGRWRDD +EGLSQHLQAKGVKKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV +IQDDYGIDHGHVETVHAYTNDQNLTDNFHKGSRRGRSAGLNMVLTETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAILNLELNKATSVEELNARLKQESLTGVLRGQVGYVDSPEVV +STDFVGSDRAGVVDGLATLVNNEGKNAILYVWYDNEYGYSHQVVRVVSGPRPGRDQAPSA +RPWSASGPCCSIASASSSSSCPKGSSSVPGSQVTPGTFMRSARCARFQRRCHLPSRRLT +>MOLHKGIG_00942 +MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQEAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKHKASGQDVQAFLDAELAEVKGKA +GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR +DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD +EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPQDTIVSAASCTTNGITPVLKV +IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAILNLELTTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV +STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ +A +>NAFOICDF_01894 +MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQEAPLSVEATFPLVEAMAGMDLGAANIDLAELAAKQQASGQDVQAFLDAELADVTGKS +GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR +DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDV +EGLSQHLQAKGATKVLLTAPGKGDMKNIVFGVNSDDILDEDTIVSAASCTTNGITPVLKV +IQDEYGVQHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVITETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAIINIALEKPTSVEEINARLKQESLTGDLRGQIGYVDSPEVV +STDFVGSDRAGVVDGLATIVNNEGKNAILYVWYDNEYGYSHQVVRVVEKMAGQQVPSFPK +A +>MHAAABBN_00661 +MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQQAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKQKASGQDVQAFLDAELAEVKGKA +GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR +DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD +EGLSQHLQAKGAAKVLLTAPGKGEMKNIVYGVNSDDITPQDTIISAASCTTNGITPVLKV +IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAILNLELTKPTSVGELNARLKQESLTGPLRGQVGYVDSPEVV +STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ +A +>LFPAFLNI_00891 +MADTASTQTPEWNTQQNLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQEAPLSVESTYPLVEAMAAMDLGAATVDLAELAAKQKASGQDVQAFLDAELAEVKGKA +GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR +DSIHGPFDGTIVVDEDRDVIIANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD +EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV +IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAILNLELNTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV +STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ +A diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001350.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001350.fa new file mode 100644 index 0000000000000000000000000000000000000000..c5c0039d8c9f02b3d3c91d9a23d1f24862d6d8a1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001350.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_01999 +MLILLPPSEGKTAPRSGAPLRLEDLALAEHDAVTAARRDLLARLAEASAAPDALETLGVG +ASLAGEVAANTSLATAPAAPGHRVFTGVLFDALDHASLSPGAKRRARDAVLVFSALFGAT +SLADRIPAHRLSVGARLPGLPGLAAHWRPVLAPALDAVAQADGGPIVDCRSGGYAAMWKA +PAERTATVDVFQLRGGEPTVVSHFAKHTRGLVARALLEAGARATGALDRAAEVVAAAGAG +DVEGRRWDVELVAPSGAKPGSLRVVLPEA +>MOLHKGIG_00940 +MLILLPPSEGKTAPRSGAPLDLDALALADDAAVTGARADLLTRLAAVSAAPDALAALGVG +ASLTGEVEANTRLASAPAAPGHRVFTGVLFDALDHASLSAAAKRRARASVLVFSALFGAT +ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG +HGWEVELARPSGAKPGALRVILPEG +>NAFOICDF_01896 +MLILLPPSEGKTGPRSGRPLDLSSLTLADDDAVTAARAELLPRLAEASARPDALDILGVG +ASLADEVAANTRLATAPSAPARKVYTGVLFEALDLTSLSPAAKRRAASDVLVFSALFGAT +TPGDRIPAYRLPVGARLPGMPGLAAWWRPRLAPALDGYAEARGGVVVDCRSGGYAAQWKA +PAERSLAVDVFQLRAGRRTVVSHFAKHTRGLVARALLEAGSRAAGTPATAADVVARAGDG +GVPGQRWEVELVPPTGRKAGSLQVILPEE +>MHAAABBN_00659 +MLILLPPSEGKTAPRSGAPLDLDSLALADDAAVTGARADLLTRLAAVSAAPDALTTLGVG +ASLAGEVEANTRLAVAPAAPGHRVFTGVLFDALDHASLSAAAKRRARLSVLVFSALFGAT +ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAEQTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLDRVADVVARAGDG +PGWEVELARPSGGKPGALRVILPEG +>LFPAFLNI_00889 +MLILLPPSEGKTAPRSGAPLDLESLALADDAAVTGARADLLTRLAAVSAAPDALTALGVG +ASLAGEVEANTCLASAPAAPGHRVFTGVLFDALDHVSLSSAAKRRARASVLVFSALFGAT +ALADRIPAFRLSVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG +HGWEVELARPSGAKPGALRVILPEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001351.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001351.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd5fb4a29e4fe3a49f8bb5bc5739abf113cbf590 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001351.fa @@ -0,0 +1,32 @@ +>ACLBLIBL_02000 +MLEADADARAVEAEAPDAVGQDAAAPQAPTPTGRLHHVEVWVADLAAAEAGLGWLLGELG +YVLGEGWAEGRTYQGAGEYIVLESGPDVVGGAHERTRPGLNHLAFRAGTRARVDELTAAA +RERGFRLLFADRHPHAGGADHYAAYLEAPDGFEVELVAVED +>MOLHKGIG_00939 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHDDMRRLAAEARSVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGEQWDAGASEVPVAAPAKASTTSASAVAESGLEADADVRAVE +ADGPDAVASPEDATPAPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGEGWAEGRT +YQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRARVDELTAAARDRGFRLLFEDR +HPHAGGPDHYAAYLETADGFEVELVAVED +>NAFOICDF_01897 +MAERTLQVEADGGSRGNPGVAGYGALVRDPATGDVLMTDAAPLGKASNNVAEYSGLIAGL +EMAKTLDPDARVHVKMDSKLVVEQMSGRWKIKHEDMRRLAQQARAVLPPSRVTYEWIPRA +QNKDADQLSNEAMDAGARGGRWDAGASKVPVTAPSAPTSAGAPAAEPDKEPLEEPPVPEE +RTRPRPVGRLHHVEIWAADLDAAVESLGWLFEQVGYAPGDAWAEGRVYRGAGDYLVLESG +RDVAPGGHDRLRPGLNHLAFRAGTRADVDRIAAQAADHGFTLLFEDRHPFAGGRDHYAAY +LETADGFEVELVADPA +>MHAAABBN_00658 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHDDMRRLAAEARAVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGGQWDAGASEVPVAAPAEASTTSTSAVAESGLDADADVRAVE +ADGPDAVASPEDATPGPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGEGWAEGRT +YQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRSRVDELTAAARGRGFRLLFEDR +HPHAGGADHYAAYLETADGFEVELVAVED +>LFPAFLNI_00888 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHEDMRRLAAEARSVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGEQWDAGASEVPVAAPAAAGSTAAEASTTSASAVAESCLDAD +ADVRAVEADGPEAVASPGDATPAPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGE +GWAEGRTYQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRARVDELTAAARDRGF +RLLFEDRHPHAGGPDHYAAYLETADGFEVELVAVED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001352.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001352.fa new file mode 100644 index 0000000000000000000000000000000000000000..41c9dd4ba72474cccfaa30d1d647430d8b4ff261 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001352.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02001 +MSEVTAPPAVQARLLELQELDTALDQARTQIRRLKADPELARLRARAQELEDALPEVEDA +ARTADRAGAEASEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDGTLTALLDEHEGAA +LEAMEAADEAESRLAAARQALEQARAEVDARAAEVRREGQVVTQRGRDLTQRRTALAAVF +PAPLLALYEKARERNGGIGAARLVGRRSQASGTELSPADVARIEALPPAAVARCPESGAI +LVRG +>MOLHKGIG_00938 +MSEVTAPPAVQARLLELQELDTALDQARAAVHRLQADPEHARLRARAQEFEEALPGLQDA +ARTADRAGAEATEKAAATRARRDRTRERLETGQGGPKELQAMQHEDDTLTALLDDHEAAA +LEAMEATDAAESRLSKGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF +PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI +LIRD +>NAFOICDF_01898 +MNRVTAPAAEQARLLELQQLDLGIGRAKTRLAQLRADAALADLQKAVAAAEEAAAEQEAH +ERETDAAAAQASERATTTRARRDRTRAHLDAGDGGSKELTALQHELEGLESLLAEHEGAA +LAAMEAADEAEEALARARAAVDEARAAVAARADEVRAEGRRVTEEGRELAALRAGLAGRL +PADLLARYEEARAANAGIGATRLEGRRTGAGTELSPADLDAVLATPADEVAVDPETGILI +IRA +>MHAAABBN_00657 +MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARALELEEALPGLEDA +ARTADRAGAEATEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDDTLTALLDDHEAAA +LEAMETADAAESRLAKGHAALEQARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF +PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI +LIRD +>LFPAFLNI_00887 +MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARAQEFEEALPGLQDA +ARTADRAGAEATEKAAATRARRDRTRERLETGQGGSKELQAMQHEDDTLTALLDDHEAAA +LEAMEAADAAESRLAQGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF +PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI +LIRD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001354.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001354.fa new file mode 100644 index 0000000000000000000000000000000000000000..67baf8ae02af2f878382c9981499b4acb41f9508 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001354.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02003 +MTDSPRTEPLGASSAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE +SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE +AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSDGYCRVVIDPKLA +KVRRNYSAWLVDA +>MOLHKGIG_00936 +MTDFPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE +SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE +AEARFFADEIARAQENYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA +KVRRNYSAWLVDA +>NAFOICDF_01900 +MSETPETPSTPAAHAPRVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGHTPDPDYEA +VCTGQTGHAEAVRVRFDEAQVPAEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDEA +EADFFRSQLARAQELYEAPIVTTIEPAAAWHPAEWYHQDFYASRPGNGYCRVVIDPKLAA +VRRRHAAWLTDGA +>MHAAABBN_00655 +MTDSPRTEPLGASDAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE +SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTSHDPTSLNRQGADVGTQYRSAVFAHDE +AETRFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA +KVRRNYSAWLVDA +>LFPAFLNI_00885 +MTDSPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE +SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE +AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA +KVRRNYSAWLVDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001356.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001356.fa new file mode 100644 index 0000000000000000000000000000000000000000..659a8c88ee20daddecaf0d7668b61c345a4fb678 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001356.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02005 +MGLLARIKEDLDNVRSHDPAARGDLEVALVYSGLHAVWAHRIAHRMWRHERLRMPARILS +QATRAATGIEIHPGATIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH +PTLRDGVVVGAGAKILGPVEIGAGSAVGANAVVVKDTPADAIATGIPATYRLRRSPAEGK +PLVDPAEYVDPAMWI +>MOLHKGIG_00934 +MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS +QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH +PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPSEGK +PLVDPAEYVDPALWI +>NAFOICDF_01902 +MGIRSRIKEDIATVRSHDPAARGDLEVVLAYSGLHAVWSHRVAHRMWQVGRLKTPARLLS +QAARALTGIEIHPGATIGRRLFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLEKVKRH +PTLRDGVVVGAGAKILGPVEIGEGTSVGANAVVVKDTPPDSIATGIPASVRLRTSPAEKK +PLVDPAEYVDPAMWI +>MHAAABBN_00653 +MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS +QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH +PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK +PLVDPAEYVDPALWI +>LFPAFLNI_00883 +MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS +QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH +PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK +PLVDPAEYVDPALWI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001357.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001357.fa new file mode 100644 index 0000000000000000000000000000000000000000..37adbcf9aed5e2d0052791a5c24ea191fe614d7f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001357.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02007 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSHGRTDQFVAEHGDEGA +FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRR +REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA +WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS +SQREVRAAAREVLQAGVDEAAVPAVTDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE +YGWSLDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTARHPEPGTRAEGQPLNLLFAPEF +AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPAEGDPTQD +>MOLHKGIG_00933 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA +FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRR +REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKIAAQFEGEPCCA +WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS +SQRAVREVARETLAAGVDEEAQRAPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE +YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF +AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD +>NAFOICDF_01903 +MTETSTVRGTADIGVTGLAVMGANLARNFARHGYTVALHNRSRAKTDALVAEHGHEGSFV +ATETLEELVGSLASPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRRRE +AALAEKGLHFVGVGVSGGEEGALNGPAIMPGGPEESYAALGPLLEDIAASYDGEPCCAWI +GTDGAGHYVKMVHNGIEYADMEVIGEAFDLLRRVAGIEPAEQAQVFDAWNQTELASYLIE +ITAEVLQQVDAATGAPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSAQ +TEVRATAREVLAAGVESAPAVSPQDRDAFVEDVRQALFASKLVAYAQGLDMLSAAAIEYG +WALDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTSRHPEPGTRAEGQPLNLLFAPEFAQ +AMAEALPAWRRVVGAAVAAGVPVPVFSSALAYYDGLRADRLPAALIQGQRDFFGAHTYRR +TDRDGSFHTLWSGDRTEVDGDGAPVVMPQPAEGDPTDETAR +>MHAAABBN_00652 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA +FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRR +REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA +WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS +SQRAVRQVARETLAAGVDEEAQRAPQDTDTFVEDVRQALFASKLVAYAQGMDMLAAAAEE +YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF +AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDFFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD +>LFPAFLNI_00882 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA +FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLEEGDIVIDAGNSHYEDTRR +REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA +WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS +SQRAVREVARETLAAGIDEDAQRVPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE +YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF +AQAIAEALPAWRRVVGTAVASGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001358.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001358.fa new file mode 100644 index 0000000000000000000000000000000000000000..a459d7b8aba5e94aa46ce885b06baf7544d6e997 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001358.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02008 +MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR +EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARVVA +LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDEQYRRFMNQVP +LFEKMLADDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK +EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD +AVGD +>MOLHKGIG_00932 +MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR +EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA +LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP +LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK +EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD +AVGD +>NAFOICDF_01904 +MELLQPDAPRENLREFIDNLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYEERLSR +EEYEIEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARTVA +LSKPTERELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDHQYDLFMRQVP +VFEKMLVEDGVHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK +EAMFLHTDTDHAPWISIKSNDKKRARLNAMRYFLSRFEYEGKDHDVVGVPDPLIVQRGRD +AVGD +>MHAAABBN_00651 +MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR +EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA +LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP +LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK +EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD +AVGD +>LFPAFLNI_00881 +MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR +EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA +LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP +LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK +EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD +AVGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001361.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001361.fa new file mode 100644 index 0000000000000000000000000000000000000000..0c6b4bc12d52c4c925aa7abd1f0f0e036406b319 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001361.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02011 +MTDAAYLVAVAVVAGAVTFALRALPFALLRPLRESVLAARLAVWMPAGVLTILAVVMLLD +AAALAPGAPVDPRRVAHALIAAVVTVAVHLLGGRRTLLSIAAGTLAYVLLVNLA +>MOLHKGIG_00929 +MTGAAYLVAAAVVAGLVTFCLRAVPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD +AAALAPGEPVDGTRVAHALFAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA +>NAFOICDF_01910 +MIDGVVHPGYIVAAALVAGGVTFLLRALPFVLLRPLRESRLVARLAVWMPAGILTILAVV +MVLDSAALAPGDPVDWPRVGCTLAAGAVTVLVHLLGGRRTLLSIGAGTLAYVLLVNLAL +>MHAAABBN_00648 +MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD +AAALAPGEPVDGTRVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA +>LFPAFLNI_00877 +MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD +AAALAPGEPVDGARVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001362.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001362.fa new file mode 100644 index 0000000000000000000000000000000000000000..3849df533600c46c0f2c336808748cc04f1e136e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001362.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02012 +MNAPSLQPSPYPAPPPSRGAEVRAGVRLSLAAGLGLFPLGVAFGMLVVQAGLPAWVAPLF +SVVVFAGSVELLLVSLAVAATPLLTIAVTVFLVNFRHVFYAFSFPLRVVRHPLARLYSMG +ALIDEAYAIAAAHPRGWTAPRLIALQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFALVA +LFIVLALDAARTRAQAPLVLAAALAVGVGLLVAPGQLLVAAFAVYAAVLIALHVLARRGV +DLPLPAPTPATGPVPVVAGPAPGEEPR +>MOLHKGIG_00928 +MLTIMSSSTESLRAPVTPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP +LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRFARIYS +MGALIDEAYAIAAARPRGWTGPRLVAMQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFAL +VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR +GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR +>NAFOICDF_01911 +MTEITPPSPAASGVPDALPTRRAEVAEGVRLSGPAGLGLFPLGVAFGMLVVQAGLPGWAA +PLLSVVVFAGSVELLLVSLLAAGTSLAGIAVTVFLLNFRHVFYAFGFPLRVVRNPLARLY +SMGGLIDEAYAITAAHPRGWTAPRLLATQVSLHLYWVVGGLVGVVAAGLLPAPVEGLEFA +LTALFIVLALDAARTRRHVLLVLAAAAAVGVGLVVAPSALLVASFLGFVAALMAAHVAAE +RGARLPLPAVKELGATSPGAAEAAELTTVDAEAGR +>MHAAABBN_00647 +MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGVAFGMLVVQAGLPAWVAP +LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS +MGALIDEAYAIAAAQPRGWTAPRLLAMQIALHAYWVLGGLAGVAVAWLLPVPVEGLEFAL +VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR +GTALPLPEPVPVTGPVPVVAAAGERAVTDAEPGVEEDPR +>LFPAFLNI_00876 +MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP +LFSVVVFAGSVELLLVPLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS +MGALIDEAYAIAAARPRGWTGPRLVAMQVALQAYWVLGGLAGVAVAWLLPGPVEGLEFAL +VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR +GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001363.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001363.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5e2bc9cfb4c6dd3b0006e52b8987757d050f43b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001363.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02015 +MAEEPGAVPALRDDRGQDWPWPPTRGPEDAAAPRATWLVLLPGAFTPVCTGELGWLGELA +TDLAADDVAVRVIACDAAPVLRRVREELGLPEDLVLLSDFWPHGAACAALDAFDAASGRA +RRVSVLLDADGVEVSRVTAAPGRPRSRTEHEAATRALLGDR +>MOLHKGIG_00926 +MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL +GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF +DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR +>NAFOICDF_01914 +MAEPALRDIHGTPWPWPPVVSGERAAWLVFLPGAFTPVCAGELAWLGPLAVELAAEDVGL +RVVSCDAAPVLREVADRTGLPAECVLLSDFWPHGAAAARFGLLDETTGRPRRVSVLVDES +GTELVRVRPGEPGGPRTAQAHRRAAEGALGRRR +>MHAAABBN_00645 +MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL +GWIGALAEDVAVDEVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF +DAETGRPRRVSVLLDADGVEAARVVAAPGQARTRGEHEAATRDLLVDR +>LFPAFLNI_00874 +MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL +GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF +DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001364.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001364.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e2fe18e2c3133b52e8927c5dba8710b01e24203 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001364.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02016 +MEAGSTPTSTDSALLAELALAQGDLVQEWGYDDDVDFTFRDGLEDALGEELLTEEDQEPA +DAVLYWWRAEDGDVTDLADALVDAQRSLDSGPVWLMTPRKGRAGHVNPADVQEAAGTAGL +HATTGAGVSEDWAAQRLVQKRGG +>MOLHKGIG_00925 +MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA +DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL +HATTGAGASEDWAAQKLVQKRGG +>NAFOICDF_01915 +METPSDGTSTHQELLDAYGLTAGELVQEWGYDDYIDFDFRDALEDALGEELLTEEDQEPA +DAVLFWWRTDDGDVSDLTDALVDAQRSLDAGPVWLMTPRNGRPGHVSPTDVAEAAATAGL +HVTTGAGGSADWAAVRLEKRGG +>MHAAABBN_00644 +MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEGALGEELLTEDDQEPA +DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL +HATTGAGASEDWAAQKLVQKRGG +>LFPAFLNI_00873 +MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA +DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL +HATTGAGASEDWAAQKLVQKRGG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001366.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001366.fa new file mode 100644 index 0000000000000000000000000000000000000000..bff602bfe48224cdd99b9c74d9cb998f395e5151 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001366.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02018 +MPEPRSAASRPVSTEGRARLRSHLGALNTAVLQRLDATLPWYRGLTPDERSALGLVAQRA +LQGFISWFDRPKTTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER +DQAPIREHVLHYSREVAFALADVYARAAEMRGAMDSRLEAVLLDAVLRGQDPDEIRHRAT +ALGWRGDHRVMVMAGLAPGQDQPAFIPGLRRAAAKLDCDLLVGVQAERLVLVIGSVTDAQ +VVGEALTPWFAPGPVILGPVVDSLVEAHVSARHTLAGLGAAPAHPRAIRPTPAEDLLPER +ALLGDPTACEALVEGVYAPLADAGTALLDTVDAYGALGHSLEGTARELFVHANTVRYRLK +RVAEVTGWDPLVPRDAYVLQTAVTLGRLAGSRPGVAEASA +>MOLHKGIG_00923 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER +DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT +ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR +AVGEALAPWFAPGPVIVGPVVDSLVSAHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER +ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK +RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD +>NAFOICDF_01917 +MPAPRPSAPRRVSADGLARLRAHLGTFNTATLRRLDETLPWYRELTPDERSALGLIAQRA +LQGFITSFERPQTTTVDVLRDVFGQSPTELTRAISLHRALQLIRTIVDVVETGVPDAVSE +ADQPVVAEHVLHYSREIAFAIADVYARAAELRGAMDSRLEAVLLDAVLRGQEPDEIQHRA +TAFGWRGGDGVMVMAGSARDGATAAFLPGLRRDAARLQCELLVGVQSRRLVLVVGSVSDP +DAVAEALLPWFADGPVIVGPVVDSLLEAHVSAHHALAGLGAAAAHPRAGRPARSDDLLPE +RALAGDATACAALVDGVYAALADAGPSLLETVDVYTACGHSLEGTARELYVHANTVRYRL +RRAAEVTGWDPQRPRDAYVLQTAVALGRLSEGAPRL +>MHAAABBN_00642 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER +DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT +ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR +AVGEALAPWFAPGPVIVGPVVDSLVSVHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER +ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK +RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGAGSD +>LFPAFLNI_00871 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLHRALQLIRTMVDVVETRVPELLAER +DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT +ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR +AVGEALARWFAPGPVIVGPVVDSLISAHVSARHTLAGLSAAAAHPRACRPTPAEDLLPER +ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK +RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001368.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001368.fa new file mode 100644 index 0000000000000000000000000000000000000000..6fa0fb1b8b1d778da7b6b924f43d8d4c3bbaec2f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001368.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02020 +MTVTLKQHERPAASRIVSVGAYRPKNLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAGE +TVPAMAVAAGREALERAGLTGADLDAVIVSTVTFPHATPPRPPSWPTSSAPPPAPAFDVS +AACAGYCYGVAQADALVRAGTAKHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA +DEPGISPSVWGSDGERWETISFTHSQLELRDVVEQARTSGDASAITGSEEMVWPTLRQDG +PSVFRWAVWSMAKVAREALDAAGVEPEDLVAFIPHQANMRIIDEFAKQLKLPESVTVARD +IADAGNTSAASIPLAMHRLLEEDPSLSGGLALQIGFGAGLVYGAQVVRLP +>MOLHKGIG_00921 +MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE +TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS +AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA +DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG +PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD +IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP +>NAFOICDF_01919 +MTVTLKQHERPAGSRIVSVGAYRPATLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATPEE +TVVTMAVGAGREALQRAGLEASDLGAVVVATVTFPYPTPSAAAAVADALGATPAPAYDIS +AACAGYCYGVAQADALVRAGSAQHVLVVGVERLSDFIDPTDRSISFLLGDGAGAVVVSAS +DEAGIAPSVWGSDGSRWSTISPTRSLLDLRAEVEHARETGDASAIIGAEEMLWPTLRQDG +PSVFRWAVWSMAEKAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD +IAEAGNTSAASIPLAMHRLLQEHPELSGGLALQIGFGAGLVYGAQVVRLP +>MHAAABBN_00640 +MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAEE +TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS +AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA +DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG +PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD +IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP +>LFPAFLNI_00869 +MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE +TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS +AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA +DEPGISPSVWGSDGERWSTISMTHSRLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG +PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD +IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001369.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001369.fa new file mode 100644 index 0000000000000000000000000000000000000000..373e7c0d05ef31bc090218c895c3925886336897 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001369.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02021 +MASKEEILAGLAEIVNEETGLDTADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDNAQA +>MOLHKGIG_00920 +MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA +>NAFOICDF_01920 +MASKEEILAGLAEIVNEETGLETADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDQAQA +>MHAAABBN_00639 +MASKEEILAGLAEIVNEETGLDAAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA +>LFPAFLNI_00868 +MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001373.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001373.fa new file mode 100644 index 0000000000000000000000000000000000000000..44ef7b56bd0d3e70f26de9ae4eba70a292d2e2d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001373.fa @@ -0,0 +1,44 @@ +>ACLBLIBL_02026 +MTADTAHDHPVAAAQGPDTQRPDAHRPDTQRPDAQRPDTQRPDAARIARAALTRLVEPGD +ALAVHAVAALGPERALVLLTGREAIQPAERDLLAEHAGAPDTLARRWSAGLDRWAPRAAR +LDPVRDLVALHRLGGGLLVPEDEAWPAALDDLGEAAPLGLWFRGPGTLPPASRALAVVGS +REATAYGRAVTTRLAAHAVQQGVCVVSGGAYGIDGAAHRAALAAPVGPEDPDAHDGPGGA +SDRVPPTVAVLAGGLDRFYPAGHEDLLREVMAAGLLVSEMPPGASPTRYRFLQRNRVIAA +LAGAVLVVEARWRSGAQNTAGHAFGLGREVGAVPGPVTSPSSAGCHRLLQETPARLVTSE +TEALALLDGGAPAPRPGGTGGGNTAPPGDAPAPPPGGTGEGTRRPPRPPPPPRPCGSRTG +>MOLHKGIG_00916 +MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET +IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA +WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC +VISGGAYGIDGAAHRAALQAPAAPEDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM +AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG +VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGDTGGRTSARAAPEPAA +RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR +RG +>NAFOICDF_01924 +MTTAGETAQNARPDGPRVARAALTRLVEPGDDLALATVAALGPERALTLLTGAARIEAAE +RDLLADRLGQDAFARRWSAGLARWAPRSARLDPVRDLVALHRLGGGLLIPEDPAWPAGLD +DLGDAAPVGLWFRGRGTLPPLPRALAVVGSREATAYGRQVTRDVVACASAAGVCIVSGGA +YGIDGAAHEAALETAAAAGRRSGPGSHDDAAPGVPPTVAVLAGGLDRFYPAGHERLLRAV +MEEGLLLSEMPPGATPTRYRFLHRNRLIAALSGAVVVVEARWRSGAQNTAGHAHGLGREV +GAVPGPVTSPSSAGCHRLLQEGPTRLIADPAQALTLLEPPRPGEPPAASPATTTRGEASR +SPGRPTDGLTVEELLVHEALPLRRAVPVDNLTSSAGLALPTVLAVLTRLEGRRLAERRGD +LWRRAPE +>MHAAABBN_00635 +MTTYVTPAADHVAGPRRPDAARLARAALTRLLEPGDALAVQTVTALGPERALALLTGRET +IQPAERDLLADRAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA +WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC +VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM +AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG +VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQAPARSGGAGGRASTRAAPEPAT +RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR +RG +>LFPAFLNI_00864 +MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET +IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA +WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC +VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM +AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG +VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGGAGGPSSTRAAPEPAA +RPTDGLTMEEALVHEALPLRQAVPVDRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR +RG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001374.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001374.fa new file mode 100644 index 0000000000000000000000000000000000000000..7602f7d41dc13b3167c46e60cdf2302a2553f49b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001374.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02027 +MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGAGHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPE +TVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVILAFGGEPEGEAPQRRP +VRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTMLAERLP +GILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMA +ALVGGGANLARPGAVSLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYP +ARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYGQRLSGPLLDRVDLQVTVRPVQARQL +AGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGPYAVPR +AARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET +>MOLHKGIG_00915 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE +TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA +RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG +ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG +GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ +LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP +ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR +PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA +>NAFOICDF_01925 +MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGAAHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPE +TVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHLHEAILAFGGRPDASVARPSG +PSGTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTMLA +ERLPGILPPLDDRTALETAALRSLRGLEPSARGLRRTPPFEAPHHSASMAALVGGGTGLG +RPGAVSLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAAN +PCPCGFGSGTGAHCRCTSLQRRKYAARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSR +AVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGRFAVPPEARATADRAV +DRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR +>MHAAABBN_00634 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE +TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA +RRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG +ILPPLDRRTALECAALRSLRGGDARVRRRGGTAQGFDGDIDRTPPFEAPHHSASRSALVG +GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ +LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP +ASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGPYAVPRAARR +PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA +>LFPAFLNI_00863 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE +TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA +RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG +ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG +GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ +LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP +ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR +PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001375.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001375.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4432420d818fa67d37d11d98a41db0b52fd818e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001375.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02028 +MTGTAEKVGADSPGGGRGSRAHTALGRFGEDAAARWLADRGYVIADRNWRGEAGELDLVA +HHAGWWVGVEVKTRSGLAFGDPLESIDRRKLLRLHRLTAAWVRAHGEGRRAERWRVDAVA +VLVPRTGGIRFDLLQDVRP +>MOLHKGIG_00914 +MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA +HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA +VLVPRTGGIRFDLLQDVRP +>NAFOICDF_01926 +MVPLDTTTTTPAARRGSTAHTALGRYGEDAAARWLAERGYQIVARNWRGEDGELDLVARH +GPWWVGVEVKTRSGLAYGDPLEAIGRRKLLRLHRLTAAWVREAAAREGRPLRSQQWRVDA +VAVLVPRTGGVHFDLVQDVRP +>MHAAABBN_00633 +MTGTAERIGAQPPGDRRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA +HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA +VLVPRTGGIRFDLLQDVRP +>LFPAFLNI_00862 +MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA +HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA +VLVPRTGGIRFDLLQDVRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001376.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001376.fa new file mode 100644 index 0000000000000000000000000000000000000000..c956d8b8f6d2a74087698c33f112178b85f625c3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001376.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02029 +MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQSDGDVFFEIL +LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPRDELQVPPDGQLPD +>MOLHKGIG_00913 +MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL +LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS +>NAFOICDF_01927 +MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANAVTLTPHQTDGEVFFELT +LEDAWVWDVYRTARFIRRVRVLTFKDVNIEELPRDELQVPEDGGLRGDLGR +>MHAAABBN_00632 +MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL +LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS +>LFPAFLNI_00861 +MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL +LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001377.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001377.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7e88c78276fb437369e6653b32cfb38206fc8d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001377.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02030 +MTGSERAPRAGARTAVRAGLDVEAGLAAPFLAAGGTDRVLVAGMDEVGRGALAGPVVVGV +CAAWLPAEGEIPAVRDSKALTDRRRRALVPEIRAWAAAVALGEANPAEIDALGISAALGL +AGRRAWAAVCAAAGQEPVALVLDGRDDWLTRSDPDAGPAPAPRPVPPVPTMLVKAEDRCA +TVAAASIAAKVARDDTMIALHADHPAYGWAGNKGYGAAAHRAAILDHGAGEHHRRSWSLG +LPAAPADEPPTLFD +>MOLHKGIG_00912 +MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW +LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR +AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA +ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA +PAQAPPTLFD +>NAFOICDF_01928 +MSPRPPVVRAGLDVEASLAEAAIGPGASALVAGMDEVGRGALAGPVTVGVCAARVPALGV +VPAVRDSKALTDRRRRALASEIEAWAAGVVLGEASPAEIDRLGITRALALAGCRAWAGLL +AALGEEPVALILDGSDDWLRHARGGGMDDVVTGPVPPAPHMMVKAEDRCATVAAASIAAK +VGRDDAMIALSAAHPAYGWAGNKGYGAAAHRSALVELGVTEHHRRSWNLGVPGTGAEPDV +LF +>MHAAABBN_00631 +MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW +LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR +AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA +ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA +PAQAPPTLFD +>LFPAFLNI_00860 +MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW +LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR +AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA +ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA +PAQAPPTLFD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001378.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001378.fa new file mode 100644 index 0000000000000000000000000000000000000000..1507ea686a5e87624d9858f95e84b43fefbee90f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001378.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_02031 +MSRPDHRLVPPAAGHAHDSGAAPADDAARPAGPTGALLGHAVPSGAGSQALPAEPGRGPL +RAVLAVVVLTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPEPYPVRRGDVV +VFDDTKGWLADGGHVIKRVVGLPGDTVSFTPGEAALRVNGVPVAEPYLAPGDAPAQDAFE +ATVPAGRLWVLGDHRSASADSRAHRDGPGGGFVSLDDVVGRARFVVWPLDRIGGAGAAPE +AFEAVPDARGAGS +>MOLHKGIG_00911 +MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR +GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ +EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG +TDPDAFATVPDAPAPEART +>NAFOICDF_01929 +MAEAPVTPAAAGTADPAAAPAAEHPGHPLRAAAVTVAVTLALLLAVQLLLVRMFAIPSAS +MEPTLRPGDRVAVDLLVPGPLELRRGDVVVFRDARGWLAGAEAVHADPLHAAVAALGLGT +QEGHLVKRVVGLPGDRVRWSPEDARLEVNGVPVDEPYVAGPAAQEAFDVVVPDGGLWVLG +DHRSASQDSRQHQHGPGGGMVSVDDVVGRVEGVVWPLDRAGAVGPGPLAKLP +>MHAAABBN_00630 +MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR +GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ +EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG +TDPDAFATVPDAPAPEART +>LFPAFLNI_00859 +MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR +GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ +EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG +TDPDAFATVPDAPAPEART diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001379.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001379.fa new file mode 100644 index 0000000000000000000000000000000000000000..45da7307753a6ae9336e438ca56e044fa63350b4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001379.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_02032 +MSHPEPRDPRRSRGSAVSRSVAPGSGRGTTPARGSGGTAWWAWIGLTVAAAVGAAAVLRA +LTGPVYLIPSGSMEPTLHPGDRVRVDASAAGGEGVRRGDVVVFDGAGSLAPYRSVGSLER +GLEDVARSWGLGASGDAFVKRVLALPGDRLECCAPDGRLLRDGAPVDEPYLGRPVTAQDP +AADGSWTFEVPEGRMVVLGDNRSASRDSRALLGGAGGGLIPLKRVEGRAAEVVWPLDRRG +PVDASAPEAAPGAAP +>MOLHKGIG_00910 +MRTSEPRDPRRSRGSVASGAGSSPGTTAAPASGASRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD +APSGDTP +>NAFOICDF_01930 +MRAQEPRDRNRSRGSRASGEAGRPWWALVLLTLAGAVVAAALLRAFTGPVYLVPSGSMEP +TLLPGDRVHVDTAAADGAGLEHGDVVVFDGAGSLAPYRSRTALDRGLEDVAAFWGVGAAQ +DVYVKRVLALPGDTLSCCTADGRLERNGAPLDESYLGRTVDAAAPASRSTWAFEVPEGRM +VVLGDNRDVSRDSRALLGAPGGGLIPVEKVIGRVDSVAWPLDRRGDVPAGAQDGSRG +>MHAAABBN_00629 +MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLRNGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTMD +APSGDTP +>LFPAFLNI_00858 +MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLQRGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD +APSGDTP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001382.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001382.fa new file mode 100644 index 0000000000000000000000000000000000000000..b120bfaabb257c0ec995e33215a55b5fd408107e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001382.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02035 +MSPAPQDGLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGATLTVRDGGPSLPAELTVT +RARWNKQILVVGFEQSPDRNTAETLRGAQLFAAPAAPEESDEWYEDDLVDLEVRVDGRRV +GVVTALTTGAVQDLLHVALDGVDEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELASGE +AEQDDDAAASDAEADADAGREG +>MOLHKGIG_00907 +MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT +RARWNKQILVVGFEESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVDGERV +GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELATGE +DEGAADGPTDADAED +>NAFOICDF_01933 +MSPAPQPAETEGQVRVARIGKPHGIRGEVTVQLFTDDPEARFAADSRLEVRQGPPGAPAA +LTVTRARWNKAILVVGFAEVPDRNAAEALRGAQLYAAPLEKVEDDAWYEDDLLDLEVHVD +GARVGVVTGLLTGTVQDLLQVRLDATGDDALVPFVEEIVPEVDQEAGVVVVAPPPGLLEL +ASETTAGEG +>MHAAABBN_00626 +MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT +RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAVPEESDEWYEEDLVDLEVRVEGERV +GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE +DEGAVDGPADADAED +>LFPAFLNI_00855 +MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT +RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVEGERV +GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE +DEDAADGPADADAED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001384.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001384.fa new file mode 100644 index 0000000000000000000000000000000000000000..76334ebcd43d092b5b78e7016f51bb22be20b926 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001384.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02037 +MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL +SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE +PKAKESAEAETPAEEAPEAPAEDAEKSE +>MOLHKGIG_00905 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAPAAEAPAEDAEKSE +>NAFOICDF_01935 +MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE +APAESAEAEAPVEEAADAEAPAEDAEKAE +>MHAAABBN_00624 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAPAEEAAEAPAEDAEKSE +>LFPAFLNI_00853 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAPAEEAAEAPAEDAEKSE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001385.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001385.fa new file mode 100644 index 0000000000000000000000000000000000000000..2e3ac89e062573e8a08d1a68c2d0be87c1d90cca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001385.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02038 +MFNSLSDRLTATFRSLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +GEEVAQALNPGQQVVKIVNEELVGILGGETRRIRHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKAQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVFAPHPGVSSEFEAATGDPVQVA +RDGVAEANAKYHDVVIIDTAGRLGVDAELMQQAADVRAAVEPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRSEAEKMAKKFADQEDFTLDDFLNQMQQLKKMGSLKKMLM +MMPGAQGMRQQLEQFDESSIGRVEAVIHSMTPHERVAPKIINGSRRARIAKGSGVSVSEV +NGLLERFAEAQKMMKRMAAGGGMPGMPGAPGGVSRKAKGKNAKRNKVKSGNPAKAAAERK +ALEERQARAAQAQAGAVFGRDGGAGMDGFDPSSLNLPAGFEKYLKDR +>MOLHKGIG_00904 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +SAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA +RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM +MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV +NGLLERFAEAQKMMKRMAAGGGIPGMPGTPGGASRKGKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR +>NAFOICDF_01936 +MFTSLSDRLTATFRNLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +GEEVSQALNPGQQVVKIVNEELVAILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKSQGHTPLLVACDLQRPNAVKQLQVNGERAGVPVFAPHPGVSSEFEAATGDPVQVA +RAGIDEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVQPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRAEAEKMAKKFADQEDFTFDDFLTQMQQLKKMGSMKKLLG +MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIAKGSGVQVTEV +NALLERFAEAQKMMKKLAGGGVPGMPGMGPGPGRKSKGRNAKKTKVKSGNPAKAAAERRA +LEERRSRPAAGGVFGQGGTMPDMTDFDPSQLNLPAGFEKYLKDR +>MHAAABBN_00623 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +GAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA +RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM +MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV +NGLLERFAEAQKMMKRMAAGGGIPGVPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR +>LFPAFLNI_00852 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +GAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA +RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRSEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM +MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV +NGLLERFAEAQKMMKRMAAGGGIPGMPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001386.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001386.fa new file mode 100644 index 0000000000000000000000000000000000000000..466cd762d49455a02ba155b69774152fc698e972 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001386.fa @@ -0,0 +1,43 @@ +>ACLBLIBL_02039 +MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL +WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF +LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV +LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA +AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL +AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV +VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA +QAHRGGAAG +>MOLHKGIG_00903 +MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL +WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF +LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV +LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA +AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL +AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV +VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA +QAHRGGAAG +>NAFOICDF_01937 +MTETTPLDAGAVWTVTAAALVLLMTPGLALFYGGMTRAKSALNMMMMSFVSMGLIGVAWI +LWAYGMTSGDGLAGIVGSPLNDLGAVQSMADGDLISVGFSATFAIIAVALISGAVADRAK +FSTWCVFVPVWVTLVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL +VLAMMMGKRQGFGVDAAHRPHNVPFTMLGAALLWFGWFGFNSGAASDVEQLGLTWVTTLV +AAAAGMLGWVLVEWLRRGRPTSIGTASGIVSGLVAITPACAFVSPLGAVVIGLVAGAACA +LAVNLKYRWGFDDSLDVVGVHLTAGILGTLLIGLFALPETGHAGLFHGGDGSLLLAQTVA +VVVAVVFTAVVTAVIAFVLRATLGLRVSVEEEERGVDLTLHDETAYDVGFGGVPVPTDAQ +ARSTAAAE +>MHAAABBN_00622 +MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV +LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK +FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSEDGAIGARLGEALDFAGGLVVHISAGVAAL +VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGGVDELGLIWVDTLA +AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA +LAVNLKYRLGFDDSLDVVGVHLTSGILGTVLIGFFALPGEGRAGLFYGGDAGLLVAQTVA +VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR +>LFPAFLNI_00851 +MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV +LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK +FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL +VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGSVDELGLIWVATLA +AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA +LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPDEGRAGLFYGGDAGLLVAQTVA +VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001387.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001387.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3eb611de71c1843a3e7b06bee1a417caad8dc6b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001387.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02040 +MCQTGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPAPRHAAPGG +STAVLERPEAEEAPVDLVEPEVVEEVEAEPAAPELERPEAAGSRLARLRARLLKSNNVFG +KGLLALLSRDRIDEDTWDEIEETLLMADLGTEPTMVLVDRLKSRVTVEGTREPEQVRELL +REELVAMVDPSMDRRLAASRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA +ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAYEAVAEGIRLEADVVLVDTAGRL +QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD +GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD +>MOLHKGIG_00902 +MCETGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPGPRHAAPGG +STAVLERPDAEEATVDVAEPEVVEEVETAPAAPELERPEAAGSRLSRLRARLLKSNNVFG +KGLLALLSQDRIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVEGTRDPEQVRALL +REELVAMVDPSMDRRLAATRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA +ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAFEAVAEGIRAEADVVLVDTAGRL +QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD +GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD +>NAFOICDF_01938 +MITVIVISVVLALLLGVVLVGLLDRPVAPPKGTYTELRDSDDPAPAGLVADPSSAPAPEE +ALEETGRAGSHAAAPVAEPVEAAEAPERQLERPEAAGTRLQRLRARLLKSNNVFGKGLLA +LLSRDHIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVDGTRDPESVRALLREELV +AMVDPSMDRRLAATPHDGHPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFR +AAAAEQLATWGARVGVETVRSDVEGADPASVAFEAVKTGIEREADVVLVDTAGRLQNKAN +LMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKG +GIVVAIQRQLGVPVKLIGLGEGADDLAPFSAEGFVDALLAA +>MHAAABBN_00621 +MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLERPE +VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL +SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM +VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA +AAEQLATWGARVGVETVRSEKEGADPASVAFEAVELGIAEGVDVVLVDTAGRLQNKANLM +DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI +VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLTD +>LFPAFLNI_00850 +MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLKRPE +VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL +SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM +VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA +AAEQLATWGARVGVETVRSEKEGADPASVAFEAVEHGIAEGVDVVLVDTAGRLQNKANLM +DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI +VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001388.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001388.fa new file mode 100644 index 0000000000000000000000000000000000000000..a55ea6bcb465d57c6bc812d00dc38d17bc9494f3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001388.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02041 +MPSSSSRTARAPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAASFNASATAVAAVVSVFG +LTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFAQLLAFRAIGGVGSTLF +TVSAMAFLARKAPPSMRGRVSGAYASAFLIGNIVGPIVGSALAVFGYRAPFLIYGTSLVI +AAALVFFMLKDTRLADRAARDARPAMPVKEALENPSYRAALVSFFANGWATFGVRNSVMP +LFAASAFAGSGLLGWQVDGALMAGLALSVFALGNVVAVTFSSRLSDMHGRKPLILTGLLV +MAVTTGVLGWMQSPLLFLLACLVSGAGTGVLNAPQQAAIADVVGQGRRSGAVMSSAQMSA +DLGAIIGPLLAGLVVDAAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGSLPL +VRPEDARVTPREDG +>MOLHKGIG_00900 +MPSSPPAARVPLPTEIKVMVAAAFVIAIGFGIIAPLLPQYAEMFASDFANPATAVAAVVS +AFGLTRLLFAPVSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQDYTQLLLYRALGGVGS +TLFTVSAMAFLASKSPPTIRGRVSGAYASAFLIGNIVGPIVGSVLAVFGFRVPFLIYGTS +LVIAAGIVFVMLRDTRLQDRARGETRPVMPLRAALGHRSYRAALTSMFANGWATFGVRNA +ITPLFAASAFTGTALLGWGITEENRQLMAGLALSVFAAGNVLAVASSSRLSDLHGRKPLI +LVGLAVMAVFTGAIGWLESPLLFLVSCALAGAGTGTLNAPQQAAVADLVGQDRKAGPVMS +AAQMSGDLGAILGPLLVGLVVDAAGYGWGFVVTGAVIAVGALAWARAPETNLPVAPGGPR +TGSLPKVDPDVDPCRMEGRELG +>NAFOICDF_01939 +MPTTPSAARAPLPREIKVLVAAAFVIAIGFGIIAPLLPQYAERFASDFANPATAVAAVVS +AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMYLIAFAQDYTQLLVFRGLGGVGS +TLFTVSAMAFLASKSPPSMRGRVSGAYASAFLIGNIVGPIVGSVLSVFGYRVPFLIYGTS +LVIAAAIVFFMLKDTRLHDRAAADSRPVMRLREALDHPSYRAALVSMFANGWATFGVRNA +VTPLFAASAFTGTALLGWTVTQENQALMAGLALSVFAAGNVAAVTFSSRLSDVRGRKPLI +LLGLAVMAVCTGVIGWMTSPLLFLVACLLAGAGTGTLNAPQQAAVSDLVGQGRKAGPVMS +VAQMAADLGAISGPMLVGLVVDGAGYGWAFAVTGAVLAVGFLAWLRAPETNLPIVPGGPR +TGSLPKIAPEDVAPPHHREA +>MHAAABBN_00620 +MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAATFDASAVGVAAVVS +AFGLTRLLFAPVSGKLTNRLGETPVYMTGVLIVAASMFLVAFAQTFPQLLLFRALGGVGS +TLFTVSAMAFLARKSPPTMRGRISGAYASAFLIGNIVGPIVGSALSVFGYRAPFLIYGSS +LVVAAALVFFLLKDTRLADRAVRDVRPAMPVREALSNPSYRAALVSFFANGWATFGVRNS +VMPLFAATAFAGTGLLGWQVDGAMMAGLALSVFALGNVVAVSFSSRLSDVHGRKPLILTG +LLVMAVTTGAIGWVGTPSLFLIACLVSGAGTGILNAPQQAAIADVVGQDRRSGSVMSSAQ +MSADLGAIVGPLAAGLVVDVAGYGWAFVVTGAVILLGAIAWWRAPETNLPVVPGGPRTGA +LPKIEPEDARPPHREDG +>LFPAFLNI_00849 +MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYASSFNASATAVAAVVS +AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFEQLLLFRALGGVGS +TLFTVSAMAFLAAKSPPTMRGRVSGAYASAFLIGNIVGPIVGSALAVFGFRAPFLIYGTS +LVIAAGMVFVLLRDTRRADRGTGDPRPTMPLKEAFGLPSYRAALASFFANGWATFGVRNS +VMPLFAATAFAGTGLLGWQVDGAFMAGLALSVFALGNVVAVTFSSRLSDVHGRKPLILTG +LLTMAATTGVIGWMSSPALFLLACLLAGAGTGTLNAPQQAAIADVVGQGRRSGAVMSAAQ +MSADLGAISGPLLAGLVVDTAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGS +LPLVRPEDARVTPREDG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001389.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001389.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ba5650679c07ed97c3b7d58bf53f37d31014f39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001389.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_02042 +MSGSRPLDPAVVLDEAGMTYTVRSSDTGARRAGIGGMLRGVRGVRTDQVQALAPLSLIVD +RGESVGIIGTNGSGKSTLMKLITGEIHPTTGRVYATSTPVMLGVNAALVRQISGEDNIRL +GCLAMGMTTAEAAEKRDDVVRLAGLDDQALQLPLKAYSSGMASRLQFAIATSVDPDILLI +DEALNTGDAQFRARTRARIDELRARAGCVFLVSHSLTTLKQMCSRVIWIEQGILTMDGNP +EVVTGNYARYTRHRSNGADEVAERLLAEARAGVKRVAVRWAGGQRPSGVIAD +>MOLHKGIG_00895 +MSADPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR +GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG +CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID +EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR +AVTRGYNLYARAMAQGRTEEAQEILERKQSELVRERIAWSGGERPTGITAL +>NAFOICDF_01940 +MTDTTVDYALVLDRVSMTYRVPSSAADSVAALPAWRRGLARALRQPPRVPVHALHEMTLG +LEQGRTLGLVGRNGSGKSTLSQIIAGKLAPSTGRVLATATPMMLGVNAALVPAMSGRQNI +VLGCLALGMAKDEVMAKTPEIAASTGLGEAIDLPIETYSSGMSARLRFAIATSRDPEVLV +IDEALNVGDSQFRARAKERMQELKRKAGAVVLVSHDNKTILDSSNKVLWLDKGRPVMEGS +PQRVMDRYEQYNEMLAAQKVDEARAFVEDLRTTYRPRVVLPATDMHLPSVQEVEFSPRHA +L +>MHAAABBN_00617 +MSAEPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR +GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG +CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID +EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR +AVTRGYNLYARAMAQGRTEEAQEMLERKRSELVRERIAWTGGERPTGITAL +>LFPAFLNI_00846 +MPNLTGLDNIRIGLLAMGLTPAEVHDRIPQVAELADIGKSIRMPMRTYSSGMRARLRFAI +SVASQPDIIMIDEALATGDDAFRERSNQAMRDLIARSGTGFLVNHSAGVIREMCTRVVWM +DEGAIIEDGDTLDVMQHYSYFMSALRKHGEEKALEARARYETTEAERIVALKGTTGH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001392.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001392.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ea26c41f424abb65a70ab41c1ae64851ffc58b5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001392.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_02051 +MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV +ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE +STSPPGATEHMAAVIREARPDLDGATLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA +QRAKQLYETFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE +LANHHPRVDILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA +AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIATEVAQQFTGSRILVVEPHVEEL +PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGTTTEGKKVIDTRGQWR +>MOLHKGIG_00885 +MKKIETVAVIGLGYIGLPTAAILAENGVRVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA +RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES +TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE +RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL +ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA +AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP +AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL +>NAFOICDF_01945 +MMGTPPALRCRDVNARMGIQNVTQIKTVAVIGLGYIGLPTAAILAENGLTVHGVDVSPRT +VDAVNAGKVPFVEPDLADFVERNVAAGRLDASLETPKADAYIVAVPTPFQGDHAPDLSYI +EAAARGLAPQLTGDELVILESTSPPGATDHMADVIREVRPDLKDAPLDFVHCPERVLPGR +VMVELVTNDRIVGGSTPAAAERARDLYRSFCEGEILLTDCRTAEMAKLVENSFRDVNIAF +ANELSLICAEQGIDVWELIGLANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARII +RAAREINDAKPQWVIERAKAAAFDVQQKEGRPAVVAALGLAFKPNIDDLRESPALNIAAQ +LADEFSGSTVLVSEPHVDELPAKLQGKENVRFVPAEQAVAEADVVLLLVDHDAFAGLGEQ +TAGKRVIDTRGQWR +>MHAAABBN_00607 +MKKIETVAVIGLGYIGLPTAAILAENGVKVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA +RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES +TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE +RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL +ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA +AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP +AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL +>LFPAFLNI_00843 +MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV +ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE +STSPPGATEHMAAVIREARPDLDGVTLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA +QRAKQLYEAFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE +LANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA +AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIAIEVAQQFTGSRILVVEPHVEEL +PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGATTEGKKVIDTRGQWR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001394.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001394.fa new file mode 100644 index 0000000000000000000000000000000000000000..829172590f5fc30c62388d5d321ccdd0a0573063 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001394.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02054 +MSQPPAASWTPEPLPRPARSPEPPRPARRRRWPWVLGVLAAVLVVLLALGAWYAVSLART +FDDHRQTVDAGALEQAGGGEPVNVLVLGSDSRGGEGEEDMGERSDAMMLVHLPADRSQVF +VMSVLRDSWVEIPGHGEAKVNAAFDLGGYPLAVDTVEQLLGVPVHHVVEMDFQGFRGVTN +ALGGVEVCNPVAFSSGQTSPSYYPRGPVLLQDTAALRYVRERHAFDDGDVSRVQNQQRYL +AGAVERFLSPQILGNPARTTEVVATFSDHLGVDAGLTSGVVASLAWQLRGVRAGDVEMFT +VPRAGFGYSPDGDSIVELDEAKLADLRSALKDDDVQRYVAEHESEDGQDASAAGADPAPV +LALLAQPAPTPAVGEDPCAD +>MOLHKGIG_00881 +MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYTSSLG +RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ +VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYTLAVDTVELLLGVSIHHVLEVDFQGFRGV +TNALGGVEVCNPRAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVENQQR +YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM +FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP +VLTLLTGTTPAPVLGEDPCDD +>NAFOICDF_01948 +MTQPPQQPWIPPERPGGAADPLEGLRGPAPAAPPTSTPPATRRSGGGRARRRRPLRRFLA +VLGVLALLLVVALGAYGLLLARTFDGHRQTVSAAAFADPGNDGPVNFLVLGSDSRAAEDS +AETSQRSDTMMLVHVPADRRHVYVISVLRDSLVEIPGRGQRKANAAYELGGPELTAAMLD +KLLGVPVHHLAELDFQGFRGMTTALGGVEVCNPHAFSSGQKNPSFYPRGRIELKDTAALR +YVRERHAFPEGDVMRVQNQQRFVRGAVAAFLDPAVVLNPPRAVDVVAGLSDHLTVDEGLD +SATLASLAWQLRGVDRSALTMFTVPRAGYGTSPDGQDVVLLDADRMAALRDALQRDDVES +YLRAHDPEALAAGEDVQPALAAAPGATPLLTELAAAPPAGEGTLLGEDPCGG +>MHAAABBN_00603 +MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYAGSLG +RTFDDHRQTVDVGALEQAAGDGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ +VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV +TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR +YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM +FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPEKEKKAQAAGGPAP +VLTLLTGTTPAPALGENPCDD +>LFPAFLNI_00840 +MSHPPAASWTPEPLPRPESPRDDASSVARRRRRWPWVVGVLAVLLAALLGLGAWYAGSLG +RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ +VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV +TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR +YLAGAMDRFLSPEILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM +FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP +VLTLLTGTTPAPALGEDPCDD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001397.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001397.fa new file mode 100644 index 0000000000000000000000000000000000000000..2dd8b539c9c2830ff0ad4313c1f9e3a25320ce45 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001397.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02057 +MAVPKRKMSRANTRARRSQWKATAPTLVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK +GRKVADA +>MOLHKGIG_00878 +MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK +GRKVADA +>NAFOICDF_01951 +MAVPKRKMSRANTRARRSQWKAEAPSLVKTVENGRVSYRLPHQAELKTDAAGTPLFYEYK +GRKVADA +>MHAAABBN_00600 +MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK +GRKVADA +>LFPAFLNI_00837 +MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK +GRKVADA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001398.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001398.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7ebcba8892a6d751eff8e21bde0e481db8c2e47 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001398.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02058 +MDTTQRQDADSSWVIPVRDLTRGAGVQRELTAQWPAPAGVTTPLLGIPEGDPVELDLRLE +SVHEGVLVTGTADATLKGECSRCLLPLHEGITVDLQELYLTGASEDEAGEQPLVVRETVD +LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS +ETSITETEER +>MOLHKGIG_00877 +MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE +SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD +LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS +ETSITETEER +>NAFOICDF_01952 +MATTVPSGAPSPWVLSVRDLARGAGVQRELTTRLPAPAAVSMPMLGIPEGDPVDLELRLE +AVHEGVLVTGTAHADLTGECSRCLLPLHEGITVDLQELFLADPPAEGDDEQPLVEHETVD +LEPVFRDAVVTALPFQPLCRPDCEGLCADCGIRLEDAPAGHAHERVDPRWAALAALADTT +EETSITETEKR +>MHAAABBN_00599 +MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE +SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD +LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS +ETSITETEER +>LFPAFLNI_00836 +MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWRAPAGVSTPLLGIPEGDPVELDLRLE +SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD +LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS +ETSITETEER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001399.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001399.fa new file mode 100644 index 0000000000000000000000000000000000000000..9701f18ba3486e9d119420140360e3fce829c05b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001399.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02059 +MTVPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEARRAGLQDVLM +ITGRNKRALEDHFDRHPALEATLERKGDATRLAQIRESDLVGDIHYVRQGEALGLGHAVN +CARRHVGDEPFAVLLGDDIIGDGEALLARMIDVQQRLGGSVVALMEVPEEAVSAYGVAAV +EAVPGEGEDVVRVTGLVEKPAREDAPSTLAVIGRYVLASQVFDVLDRTPPGRGGEIQLTD +ALQTLADDDGEGGGVHAVVFDGRRYDTGDKLGYLQAVVEFGTRHEELGGDLRAWLKAFAA +GL +>MOLHKGIG_00876 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDTKRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF +TAGL +>NAFOICDF_01953 +MTEQSTAASPTRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEAVSAG +LGDVLMITGRNKRALEDHFDRHPALEQVLEAKGDTKRIDLIRASDLVGDIHYVRQGEALG +LGHAVGCARRHVGDEPFAVLLGDDLIGEDEGLLARMIDVQHRLGGSVIALMEVPEDAVSA +YGVAAVAPVDGEDDDVVAVTSLVEKPARGDAPSNLAIIGRYVLAPQVFEVLERTAPGRGG +EIQLTDALQTLAAGEGEGFGVHAVVFRGRRYDTGDKLGYLQAVVELGVRHPELGGDLREW +LKGFAAGL +>MHAAABBN_00598 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDAKRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVEAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGARHEDLGADLRAWLREF +TAGL +>LFPAFLNI_00835 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDATRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF +TAGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001400.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001400.fa new file mode 100644 index 0000000000000000000000000000000000000000..81baf87162147b9e3f6ea9c32c1a7fc6ca5b1480 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001400.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02060 +MRRAVCPGSFDPLHKGHVEVIARAANLFDEVVVAVSVNPAKRYRFSTEERIAMIETTLSS +LAGVTVRPMGLGLLAEFCREIGADAIVKGLRNGTDLEFEAPMAAMNRHLTGVETVYLPAD +ARYTHLSSSLIKEVHGLGGDVAELVPAAVLRGLDGEP +>MOLHKGIG_00875 +MRRAVCPGSFDPLHKGHVEVIARAANLFEEVVVAVSANPAKTYRFSVDERIAMIEATVSS +LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD +ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA +>NAFOICDF_01954 +MRRAVCPGSFDPLHKGHLEVIARAASMFDEVVVAVSDNPAKRYRFSTDERLELIRASVQG +LAGVSAEAMGPGLLAEFCREIGAGVIVKGLRNGTDLEFEAPMAAMNRHLTGVETVFLTAD +ARYTHLSSSLIKEVHGLGGDVREFVPAVVHARLEATRP +>MHAAABBN_00597 +MRRAVCPGSFDPLHMGHVEVIARAANLFEEVVVAVSANPAKTYRFSVDERIAMIEATVSS +LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD +ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA +>LFPAFLNI_00834 +MRRAVCPGSFDPLHKGHVEVIARAANLFEEVVVAVSSNPAKTYRFSVDERIAMIEATVSS +LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD +ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001401.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001401.fa new file mode 100644 index 0000000000000000000000000000000000000000..57ee49568ab9749fd0415a0f2581054ba1d4f358 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001401.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_02061 +MNADASDRTRPPRTGPAPAPATGPAPADVAGTAFVAGPWRRTAAAAGLLDDGAPVPTVFE +TMTGLAVEHGAVNLGQGFPDADGPDALLRLAAEAVLAGPNQYAPGTGDPVLRQAVAEHRR +RHWGVTEDPATQVMITTGATEGIAATVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVS +VPVEAPDFLPDPARVADAITDRTRLLIVNTPHNPTGAVYPRELLEELVTLCRSRGVLILS +DEVYDHLVYEGEHVSLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVK +QFLTYSSGPAFQRALGAYLPTEDAKRHLAGQRERYRDARDRLVAGLRAADLDPVVPAAGY +FVVVDLAPWGVTDAAEAAVRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDE +AMRRLAAAAPALDGRRPRP +>MOLHKGIG_00874 +MDGTQPTPGAAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF +PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRQAVAEHRRRHWGVTEDPATQVMITTG +ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGARHVSVPVEAPDFLPDPARVAAA +MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILSDEVYDHLVYEGEHVSLRS +VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY +LPTDGAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA +VRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA +>NAFOICDF_01955 +MSHDSPSPTDAAAAPSDVRLAGPWRAASAAAGVLRDGAPVPTVFETMTALAVEHGAVNLG +QGFPDADGPPELLALAAEAVTTGPNQYAPGTGRADLRAAVAAHRARHWGVAEDPDTQVLA +TTGATEAIAATVLALVRPGDEVITVEPFYDSHAAVVALAGGRHVTVPVHAPDFLPDPARI +AAAITPRTRLLIVNTPHNPTGAVYPRALLEELVALCRARDVLMLSDEVYDHLVHEGRHVT +LRAIPGAERIALTASSAGKSLAVTGWKVGWLTGPADLVAAVRGVKQFLSYSSGPAFQQAV +AAFLPRADDFLAGQLARHRRSRDLLVSGLRDIGLDPVVPAAGYFTVVDLAPWGVRDAAAA +ARTWTERAGVAGIPVSALCRPDGDHLRSWLRLTFCKSEDTVAEAVARLTRHAADLRAG +>MHAAABBN_00596 +MDGTQPTPGSARHDVDVDAPWRRTAAAAGLLGDTGPVPTVFETMTGLAVEHGAVNLGQGF +PDADGPDALLRLAADAVLAGPNQYAPGTGDPVLRQAVAEHRRRHWGVTEDPATQAMITTG +ATEGIASTVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVADA +ITDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLMLSDEVYDHLVYEGEHVSLRS +VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY +LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA +VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAP +>LFPAFLNI_00833 +MDGTQPTPRSAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF +PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRRAVAEHRRRHWGVTEDPATQVMITTG +ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVAAA +MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILADEVYDHLVYEGEHVGLRS +VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY +LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA +VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001402.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001402.fa new file mode 100644 index 0000000000000000000000000000000000000000..80f054dea5fe9d99f0e50eeabeee9a3d7da84f51 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001402.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02062 +MSRIIAGAAAGRPLTSVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLFAGSGALGC +EAASRGAASVLLVERERRAVAACRANAALVNRARGADVVQVRAGTVEQALAAGGEPADLI +LADPPYPLAGPALEAVLEAAAARLTPGGLIVLERAARDAPPRRPAGLEEVEVRAYGETAL +YLWQDER +>MOLHKGIG_00873 +MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC +EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI +LADPPYPVAGPPLEAVVEAAAERLAPGGLLVLERAARDAAPRRPRGLEEVEVRVYGETAL +YLWQDER +>NAFOICDF_01956 +MSRIIAGAAAGRPLRSVPGTGTRPTTDRTKEALFSWLQARDWLDGTRVLDLYAGSGALGC +EAASRGAAHVTLVEKARRAAEVCRANAAALNAVLGAPVVQVAASSVEQALALPGDSADLI +LADPPYPESGPAFHAVLAAAAARLAAGGLLVLERSARDPAPERPAGLEQVEVRTYGETAL +YFWQDEG +>MHAAABBN_00595 +MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC +EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI +LADPPYPVAGAPLEAVLEAAAGRLAPGGLFVLERAARDAAPRRPRGLEEVEVRVYGETAL +YLWQDER +>LFPAFLNI_00832 +MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC +EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAASVDLI +LADPPYPVAGPPLEAVVEAAAGRLAPGGLLVLERAARDVAPRRPRGLEEVEVRVYGETAL +YLWQDER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001404.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001404.fa new file mode 100644 index 0000000000000000000000000000000000000000..402ee4cc8f6d94685a45c643c0b0a71b032cc6af --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001404.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02064 +MSTPPRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDAGAVLARAGAAALDLARGNSGTLLAVALAGMAEPLRGRARADAFALAAAFGAADRA +ARQALSDPREGTILTVLSAASRSLARSATQAPDSPAVAADVDPAVRLGPAVTAMMADCLR +AVEQTESQLAPLAQARVVDAGAVGLLWVLEALRAAVTDTAPDEELATALHGYVEGVRPGP +EPAGEDAVEVMGTLALTPLAAADLRRRLAETGDSVILAPVGTERDEHGRVPWRVHVHVPR +AADAVELMRAAGEVQGLAVTELSGDAAGPDADGCHGR +>MOLHKGIG_00871 +MGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACPAQDDAGAVLAHAGAAALDSA +RGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRAARQALSDPREGTILTVLSAA +ARSLARSSTQAPDTPAVAGDADPAVRLGPAVTLMLADCVQAVEETESLLAPLTRAHVVDA +GAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGAHAAEAEPAAAAEAPAEGAVEVMGT +LALTPLAAAELRRRLTEVGDAVILAPLGTARDGQGRVPWRVHVHVPRAEDAIGPLRAAGD +VEGLTVTDLAGPSHGDDAAPDGCHGR +>NAFOICDF_01958 +MIRARLRGALAWLRGAEAALAQAAPRLDALNLFPVPDADTGSNMLATVRAARQAAERSAG +TDMSAVLRDAGAAALDSARGNSGTLLAVALVGLAAPLTPDAPLTTAELAAGARAADRAAR +AALSDPREGTILTVLREAATVLEAAAAGGREPAEALGSVVEAARRAVEDTEGQLAPLTRA +RVVDAGAVGLLLVLEALRAEVTRTPFDEGVVAALHGWADGPGAAGEDPQADGREAPGVEV +MCSIDLTPVDAAGLRRGLEEAGDSVILAPLSRAVDGAGRLRWRVHVHVARAEDAVALLEA +AGAPEEVAVTDLWDPAHRHPDDPAEGDAASPAPDGHGR +>MHAAABBN_00593 +MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA +ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ +AVEETESLLAPLTGAQVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE +GEPAAAAEAPAEGAVEVMGTLTLTPLAAAELRRRLADVGDAVILAPLGTARDGQGRVPWR +VHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSHGDDAAPDGCHGR +>LFPAFLNI_00830 +MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDVGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA +ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ +AVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE +GEPAAAAETPAEGAVEVMGTLALTPLAAAELRRRLADVGDAVILAPVGTARDGQGRVPWR +VHVHVPRAEDAIGPLRAAGDVEGLAVTDLAGPSHGDAAPDGCHGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001407.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001407.fa new file mode 100644 index 0000000000000000000000000000000000000000..79272e1211ae298f6b96e00812efe9e60f469e03 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001407.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02067 +MLLLFGGRSSEHPISCVTAAGVLHAADPQRWDVVPVGVARSGLWSHDELDVAAFRLDGET +LPEVPEPEAPVSLRTLPDGTVELTAEDGSSLGRVDVVFPLLHGPWGEDGTLQGMFESLGL +PYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITDRDWARDPEAALARAGALAFPLF +VKPARGGSSFGITRVSDPADLRAAVEEARRFDPKVVVEAGIVGREIECAVLDGHGSDAPR +ASLPGEIVVKHDEGDLQFYDFQAKYQDDDAAQLSCPAELPEEQTRRLRELAVRAFEAVDG +SGLGRCDFFHTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSYDALISELLDLALERGV +GLH +>MOLHKGIG_00868 +MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLDLALERGVGLH +>NAFOICDF_01961 +MTQPPETAPGRRPRVLLLFGGRSSEHPISCVTAAGVLHAADRERWDVVPVGVAHSGLWSH +GEVDAAAYALGDGELPSVPEPERPVSLRARADDAVELVGADGEDLGVVDVVFPLLHGPWG +EDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAGGLEVGPWETITDRQWRNDPE +AALERAGALDYPLFVKPARGGSSFGITKVDAPEDLRAAVEEARRFDPKVVVEAGILGREI +ECAVLDGHGAESPRASLPGEIVVKGAESGHQFYDFEAKYQDASAAQLSCPAELPEEAIER +LREQAVRAFEAVDGAGLGRCDFFYTPDGRWVVNEINTMPGFTSISMYPAMWERTGLPYGE +LISELLDLALERGVGLH +>MHAAABBN_00590 +MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGAAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGSTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLDLALERGVGLH +>LFPAFLNI_00827 +MTAIPAPEAAAGARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGGALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLYLALERGVGLH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001408.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001408.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3652f093545406e3ddf6258d723bad233824dbc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001408.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_02068 +MSDPQTVAVLGAGSWGSAFARVLGTSTSPEGARARDVVIWSRRPEVAEVVNRDHANPEYL +PGIELPACVRAVTDAFEAVRGAGVVVVAVPAQHVRETLRTLREDLAPDAVVVSLVKGLER +GTDARMSQVCTEELGLTPDRFAVVSGPNLALEIARGEPTATVVASGSSATAERIAALTAG +PTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG +GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGMSAEEAVAAMSQTAEGIKSVSAVV +HVARAHGVEMPISELMDRVVAGDVAVHRLAELLLARDLKSEGRTA +>MOLHKGIG_00867 +MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL +PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER +GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG +RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG +GDTDTMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV +HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA +>NAFOICDF_01962 +MSPAPSAGPEPAFASASAGDRAGDPTRVAVLGAGSWGTAFACVLGSSTSPAGRRAREVVV +WSRRAEVARAITEDHANPEYLPDVALPECVRAVTDAREAVAEAGVVVVAVPAQQARTVLE +GLADALAPDAIAVSLMKGLERGTDARPSQVCQEALGIGPERFAVLSGPNLALEIARGEPT +ATVVASASRATADRVAALTAGPTFRPYTNGDVVGVEIGGIVKNVIALAVGICDGQGLGDN +SKASVITRGLAETTRLAVALGGEASTLAGLAGLGDLVATCASPLSRNRSAGRLMGTGLSA +DEAVAAMKQTAEGIKSVSAVVHVARAHGVEMPISEAMDRVVAGTLDVDRLAGLLLARDLK +SEGRHA +>MHAAABBN_00589 +MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL +PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLHAVRADLAPDAVVVSLVKGLER +GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG +RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG +GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV +HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA +>LFPAFLNI_00826 +MSDPRTVAVLGAGSWGSAFARVLGLSTSPEPARASEIVMWSRRAEVAEAITERHENPEYL +PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER +GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG +RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG +GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV +HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001409.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001409.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b3538d110b412f5e5ce7010733f56dd4c066fbc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001409.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02069 +MSTVDPQTPAPAAGRPSRAARAGYVIPAAIVRPALRGLVSQVWEGTENLPETGAILAVNH +ISELDPLSVAHMVYNQGLLPTFLAKAELWKVPGFKQALQATRTIPVERSRDGGRSLAAAR +EALATGRAIIVYPEGTVTRDPDGWPMAAQSGAVRLALQTGAPLIPVGQWGIQELLPYGGR +APRPFPRKTARIRVGTPVDLDDLRGGPLTATALRAGTERMMDAITAIVADLRGEPAPAGR +WDPRTGRREPGA +>MOLHKGIG_00866 +MSGVDAQSPAAAGGRPTRTARAPYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH +ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR +EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR +SLRVLPRKTARIRVGAPVDLADLRDRPVTAGTLREGTGRMMGAITDLVAELRGEPAPEGR +WDPTAGARVAEA +>NAFOICDF_01963 +MNDGERPIAQPSRGLRRGFVAPAAVVRPALRALVRQEWLHAERIPRTGAILAVNHISELD +PLSVAHMVYNQGLLPAVLAKAELWKVPVLRRVLQSTRMIPVERSRDGGRSLAAAQAALDE +GRVIIVYPEGTVTRDPEGWPMSARSGAVRLALQTGAPLIPVGQWGMQELLPYPGFRLSPF +PRKTARVLVGEPVDLDDLRGGPLTAAVLRVGTERMMDAVTELVAQLRGEPAPAWRWDLRT +GRREGAA +>MHAAABBN_00588 +MSGVDAQSPAAAGGRPTRAARAPYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH +ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR +EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR +SLRVLPRKTARIRVGAPVDLADLRDRPVTAATLREGTGRMMAAITDLVAELRGEPAPEGR +WDPTTGARVTGA +>LFPAFLNI_00825 +MSGVDAQSPAAAGGRPTRAARAAYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH +ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR +EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR +SLRVLPRKTARIRVGAPVDLADLRDRPVTAATLREGTGRMMAAITDLVAELRGEPAPEGR +WDPTAGARVIGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001411.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001411.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf9057e5e39a18eccf8946db7330176dc967b890 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001411.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02071 +MEKFTTHTGIGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS +AGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV +ERIWKELENRPGTTVTVDLVSRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLDHQDEI +DAYERARPSYKPTTLPARTAG +>MOLHKGIG_00864 +MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS +GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV +ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI +DAYEADRPAYKPTTLPARTAG +>NAFOICDF_01965 +MDKFTTHTGIGVPLRASNVDTDQIIPAVYLKRVSRTGFEDALFAGWRQDPDFILNTEPYS +AGSVLVAGPDFGTGSSREHAVWALKDYGFKVVVSSRFADIFRGNSAKQGLVAAQVEPEDV +ERIMKQLENQPGAAVTVDLEHLTVECGGVTAAFEIDEDARHRLLHGLDDIAITLSHADAI +AAYEAGRPSYKPTTLPARTAD +>MHAAABBN_00586 +MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS +GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV +ERIWKELENRPGTTVTVDLVTRTVECGDVTAPFQIDDDTRRRLLEGLDDIAVTLGHQAEI +DAYEADRPAYKPTTLPARTAG +>LFPAFLNI_00823 +MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS +GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV +ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI +DAYEADRPAYKPTTLPARTAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001412.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001412.fa new file mode 100644 index 0000000000000000000000000000000000000000..a21433632649b7222291fdb91009702080fc7601 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001412.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02072 +MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR +PVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGIVH +VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAIT +VDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAGAR +AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPFVT +WGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSCTN +SRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM +CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT +PQEA +>MOLHKGIG_00863 +MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR +PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH +VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT +VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR +AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT +WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN +SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM +CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT +PQEA +>NAFOICDF_01966 +MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA +DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI +VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA +ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG +ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF +VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC +TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC +SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA +LENQEA +>MHAAABBN_00585 +MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR +PVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGIVH +VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT +VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR +AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT +WGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN +SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM +CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT +LQEA +>LFPAFLNI_00822 +MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR +PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH +VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT +VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR +AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT +WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN +SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM +CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT +PQEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001413.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001413.fa new file mode 100644 index 0000000000000000000000000000000000000000..dc997213414fd0c83e779037e6884d0d557dcbac --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001413.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02073 +MTAEPARAQADDDVLGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL +HRLAAALTHHRLVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRNHAD +AVVAAATRLTELIRAGEA +>MOLHKGIG_00862 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA +>NAFOICDF_01967 +MTTTPLPDAGADIGPALHVHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTLHR +LAAALTHHRLVAKDLQGRYVLGSRLAELASAAGEDRLTSAAGPVLQWLRDACGESAQVFR +RQADSRVCVASAERPWGLRDTIPVGTRMSMKAGSAAQVLLAWEDNERLVDGLVGAVFTPT +VLAAVRRRGWAQSLAEREPGVASVSAPVRGPNGKVIAALSISGPLERLSRQPGRLHAGSV +VAAADRLTELIRAGEA +>MHAAABBN_00584 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA +>LFPAFLNI_00821 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001414.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001414.fa new file mode 100644 index 0000000000000000000000000000000000000000..72b32b2a8d5d39ecbb3f552e21e5bf49ea0dcd8c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001414.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02074 +MTHPSAPAEQDRAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPEKIARLSRGEVPFH +EPGLPELLRTHVESGRLRFTTDVAEAARWADVHFVGVGTPQKVGESGADLRYVDAAVASL +AAAIDRDALIVGKSTVPVGTARRLAAMVRRVRAEAGLPGEVELAWNPEFLREGFAVKDTL +TPDRLVIGTDGPRAEQVLRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISFINA +FSEITEAVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGLDRT +MRFLAEVDDINLRRRDRVVDLAVQVLSAARDAGRGEAAAYGGKTTASGVEVLRGARIAVL +GVTFKPDSDDVRDSPALDVANRLYTAGADVRVHDPEGNANAAARFPRLDYVDSLEEAVEG +AELTLLLTEWQAFREMDPAAVGALVDARLLIDGRNVLDLAAWAEHGWTVVGLGHRFDPAA +LGA +>MOLHKGIG_00861 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGMHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASGPAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLGHRFD +PERLLRAA +>NAFOICDF_01968 +MTETAVVPAAAESEEAPARPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR +GEVPFHEPGLPELLRAHVASGRLRFTTDVAEAASWADVHFIGVGTPQKVGEAAADLTYVD +AAVESLARAIDRDALIVGKSTVPVGTARRLAARVAEIRAAEGLPGEVELAWNPEFLREGY +AVKDTLTPDRLVIGTHGPRAELLLRTVYATPLAAGTPWISTDLETAELVKVAANAFLATK +ISFINAFSEITETVGGDIGTLADAIGHDGRIGRRFLNAGVGFGGGCLPKDIRALQARVSE +LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARQGVVRSAPGGARTAPTPAGVQVLN +GTRIAVLGVTFKPYSDDVRDSPALDVANRLFTAGAEVAVYDPEGNANAAARFPRLGYVDS +LDAALQGAELVLLLTEWDEFRQMDPAAAGELVAQRILIDGRNVLDVDAWGEHGWTVLGLG +HRFDPAALNGGRPGDDAQA +>MHAAABBN_00583 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASGPAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLGHRFD +PERLLRAA +>LFPAFLNI_00820 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRVRRADASGTAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDAVGARVASRLLIDGRNVLDAAAWREHGWDVIGLGHRFD +PERLLRAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001418.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001418.fa new file mode 100644 index 0000000000000000000000000000000000000000..5d4d55980bbc360431a5259512bb37a89c0fb4db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001418.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02082 +MRIARFVDQAEPTYGVVEGPADADLSELTITALQGDPFFHGIQPTSTVHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNETPASPQFFLKPNTSVVGPGEPVTLPSWSDEVSYEAEL +AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEPAGGLRITSRLDGQTRQDGTTADMVFGVRELVAAASEAFTLLPGDVILTGTPAGVG +TVAEGQRVEAEVEGIGVLATVFRR +>MOLHKGIG_00852 +MRIARFVDQAEPTYGIVEGPADADPAELTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL +AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEPAGGLRITSRLDGETRQDGTTTDMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG +TVQEGQRVEAEVEGIGVLATVFRR +>NAFOICDF_01977 +MRIARFVDQAEPTYGVVEGPADADLSALTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNEVPSSPQFFLKPNTSVVGPDEPVTLPSWSEEVSYEAEL +AVVIGTICKDVPLSRVDDVVFGYTVANDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEQAGGLRVTSRLAGETRQDGTTADMVFGVKELVAAASEMFTLLPGDVILTGTPAGVG +TVEAGQRVEAEVEGIGVLGTHVRR +>MHAAABBN_00574 +MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL +AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG +TVQEGQRVEAEVEGIGILATVFRR +>LFPAFLNI_00811 +MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL +AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG +TVQEGQRVEAEVEGIGILATVFRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001419.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001419.fa new file mode 100644 index 0000000000000000000000000000000000000000..5fbd6078888618e14cabf72cd80c33ad3d1d9ddf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001419.fa @@ -0,0 +1,14 @@ +>ACLBLIBL_02084 +MAASGTCPTPTGGSAAEPAAARRAGDGTGPAAGSGLRAAWASARWWVRQLAGEGKYDAYL +AHHRAQHPGVEPMSEREFWRDEYAKQEANPGSRCC +>MOLHKGIG_00851 +MVAPRTTPGGAPAAEASPARRTWQAARWWVRQLSGEGKYDAYVAHHRAHHPERAPMTERE +FWRAEYARQEANPGSRCC +>NAFOICDF_01984 +MAGIWASTRWWVRQLTGEGKYDAYLAHHRAHHPGEVPMTEREFWRDEYARQDANPGSRCC +>MHAAABBN_00573 +MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV +AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC +>LFPAFLNI_00810 +MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV +AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001420.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001420.fa new file mode 100644 index 0000000000000000000000000000000000000000..fb0f5c1a1618c030316db1811de7b07e717da062 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001420.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_02085 +MSSHRSAAPAEGMAPRDPARDGGPDGLPPVEAAQRPRWTPLKIAVWVVVALVGGVAWTML +ALHRGESINAIWFVFAAVATFAIGYRFYSKYVERMIVRPDDTRATPAEYRADGRDYVATD +RRVLYGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGG +RSLGQMARDELGRIGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVALTIPIAI +FMGLYLRYLRPGRITEVSIIGFVLLMAAIIGGGWVAETDWGVALFTLDRVTIAWGIIIYG +FVAAVLPVWLLLAPRDYLSTFMKIGVIAGLAVAIVIVQPQITAPAISEFASGQTGPVWPG +SLFPFLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAV +SIDRGIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTG +GAPTLAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNV +APRFKDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAV +VLAIVAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGA +TSFGAAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATIRAFRSTEVVDHADPY +VPSRRFAPAGLIATAEEKELQRQWDALPADQRPERGH +>MOLHKGIG_00850 +MSSHRSSAAAEGAPLPATTPEDLPPTEAAGRPRWTPAKIAVWVAVALLGGVAWTMLALHR +GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL +YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG +QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV +YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA +VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP +FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR +GIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTGGAPT +LAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF +KDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLAI +VAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGATSFG +AAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATVRAFRGTEVIDHQDPYVPSQ +RFAPAGLFATAEEKELQAQWDALPAEKQPVRGH +>NAFOICDF_01985 +MSSTRSVIPTGGSAPHDARPDGLPPVEAPHEQRWTPARVAVWAVIALLGAVAWTMLALHR +GESINAIWFVFAAVSTFLIGYRFYSKYVERAIVRPDDTRATPAEYNADGRDFVATDRRVL +FGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG +QMARDELGRIGGTAAIIATLLIMVIITAILALIVVNALGDSPWGVFSVGMTIPIALFMGL +YLRYLRPGAITEVSIIGFVLLLAAIIGGGFIAETPWGAALFTLDRVTLAWAVIVYGFVAA +VLPVWLLLAPRDYLSTFMKIGVIAGLAIAIVIVQPRVQAPAFSEFAGGQAGPVWAGSLFP +FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAIMALVAAVTIDR +GVYFAMNAPTALTGGAVDSAVAWVNGLGLANADLTPDQLTTLANQVGEETVVSRTGGAPT +LAVGLAQIMGQLIGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDTLGNVFPKF +KDHNWTPGAWLATAVMVAAWGAVLVMGVTDPLGGINTLFPLFGIANQLLASIALAVVMAI +VAKRRTFKGLWIVALPLAFITVVTTVASLHKIFSPVPAVGYWAQHRAFQDALAAGKTSFG +AATTVPAMEAVVRNTFVQGTLSVLFLALALIVITSSIVATVRAFRSTEVVDHQDPYVPSR +RFAPAGLTATPAEKEIQAQWDALPADRQPVRGH +>MHAAABBN_00572 +MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR +GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL +YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG +QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV +YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA +VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP +FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR +GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT +LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF +KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI +VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG +AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ +RFAPAGLFATAEEKELQRKWDALPADRQPVRGH +>LFPAFLNI_00809 +MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR +GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL +YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG +QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV +YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA +VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP +FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR +GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT +LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF +KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI +VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG +AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ +RFAPAGLFATAEEKELQRKWDALPADRQPVRGH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001421.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001421.fa new file mode 100644 index 0000000000000000000000000000000000000000..56ace4c5ae55cd345194a124dc703053ed199ee5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001421.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02086 +MSETVFTRQPHLSPLSEEERVEILQDPGFGKVFTDHMVSIDWTWSEDGGAWHDARVEPYG +PLSLDPSASVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEEMF +LGSLKAQLEADRDWVPTGEGQSLYLRPFMFATEAFLGVRPAKEVRYMVIASPAGNYFGGE +LKPVTIWVSREYARAGRGGMGAAKTGGNYAASLLPQLEAASKGADQVVFLDQYHDDSIEE +LGGMNVFFVFDDGRLVTPELTGTILEGVTRSSILQLGRDMGLTVEERRITLAEWAEGVRS +GAIREVFACGTAAVVTPIGRLLDGDDVIESAGGTEVTLKIRAELEGIQTGRVEDRHGWLH +RLV +>MOLHKGIG_00849 +MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG +PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF +LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE +LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE +LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS +GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGADVALKIRTELEGIQTGRVEDRHGWLH +RLV +>NAFOICDF_01986 +MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG +PLSLDPSAAVLHYGQEIFEGLKAYGHEDGSVWTFRPEANAARLNRSARRLALPELPEELF +LGSLRAQLEADQAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE +LTPVTIWVSRDYARAGKGGMGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE +LGGMNVFFVHADGRLVTPELTGTILEGVTRSSILQLGRDMGMSVEERRVTLAEWAEGVRT +GAITEVFACGTAAVVTPIGRLLDGDDVIESTGGTEVAMKIRAELEGIQTGTVEDRYGWMH +RLV +>MHAAABBN_00571 +MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG +PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF +LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE +LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE +LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS +GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH +RLV +>LFPAFLNI_00808 +MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG +PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF +LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE +LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE +LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS +GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH +RLV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001424.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001424.fa new file mode 100644 index 0000000000000000000000000000000000000000..e45c7a183433b4ebf6522a3bf6ef3933fdddcf26 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001424.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02090 +MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE +AIAAAPQLKVIARAGVGLDNVDVPAATAAGVMVVNAPTSNIISAAELTCGHILATARNIA +AANRSLKAGEWKRSKYTGVELYGKKLGVIGLGRIGALVAERMRAFGMEILAYDPYVTTAR +AQQLGATLVELDQLLERADFVTIHMPKTPETVGMIGDDQFARMKDTAVVVNVARGGLVDE +DALARALDSGAIAGAGIDVFSTEPATDLAFFAQDSAVVTPHLGASTAEAQEKAGVAVAGS +VRLALSGELVPDAVNVAGGVIHEDVRPGLPLAEKLGRVLTSLVGEQSLTAVEVEIAGEIA +EHDVSAMRLAALKGVFTDIVSDQVSYVNAPMLAEQRGVECRLTTTPVSESYRNTVTLRAA +TAQGTQVSVTGTLTGPRQIQKLVGVDRHELEVPLADHLLVFTYEDRPGVIGVLGQALGVQ +GVNIAGMDVSRDDEGEALAVLTLDGALSGDTATALAAAIGASRVAEVDLSA +>MOLHKGIG_00834 +MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATQMDAE +AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA +AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR +AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE +DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS +VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIS +EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA +TAQGAQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ +GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSV +>NAFOICDF_01989 +MSAAKPVVLIAEELSPATVEALGPDFEIRHTDGADRARLLADLPGVDAVLIRSATTMDAE +AIAVAKDLKVIARAGVGLDNVEVPAATAAGVMVVNAPTSNIVSAAELTCGHILSVARNIA +PANRALKAGEWKRSKYAGVELFEKKLGVIGLGRIGALVAERMKAFGMEILAYDPYISAAR +AQQLGATLLDLDELLAQSDFITVHMPKTPETVGMISDAQFATMKDTAFIVNVARGGLIDE +DALDRALESGAIAGAGVDVFSSEPATDLAFFRHDTAVVTPHLGASTAEAQEKAGVAVAKS +VRLALAGELVPDAVNVAGGVIHEDVRPGLPLAEKLARVLRALAGERSLASVDVEVAGEIA +VHDVKALRLAALKGVFTDVVSDQVSYVNAPVLAEQRGVGGQLTTAAEAGSYRNTVTVAAV +TDEGERLSVTGTLTGPKQVEKLVGVGRHEMEVALAEHMLLFRYADRPGVVGVLGQSLGEQ +GVNIAGMDVSRDEQGSALAVLTLDAALAPGTAPTLAAAIDADRAAEVNLAD +>MHAAABBN_00566 +MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE +AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA +AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR +AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE +DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS +VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA +EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA +TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ +GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA +>LFPAFLNI_00804 +MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE +AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA +AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR +AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE +DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS +VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA +EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA +TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ +GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001425.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001425.fa new file mode 100644 index 0000000000000000000000000000000000000000..b671db9685e6eb0799689c1cdbd007d448b9ac9d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001425.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02091 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA +PEFKELRAKGEAHPIEKTGRELREMFSWLKDADDDYTEGTAAR +>MOLHKGIG_00833 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQKGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR +>NAFOICDF_01990 +MTAQKFYDDDADLSIIQGRTVAVIGYGSQGHAHSLSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDEHIAPNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEQDASGQAEALALSYAKAIGGTRAGV +IKTTFTEETESDLFGEQAVLCGGASQLIQYGFEVLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEFGDYVSGPRVITPEVKDHMKEVLADIQNGAFAKHFMDDQKAGA +PEFTELRAKGESHPIEKTGRELRQMFSWLKDTDDDYTEGTAAR +>MHAAABBN_00565 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR +>LFPAFLNI_00803 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSRSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001426.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001426.fa new file mode 100644 index 0000000000000000000000000000000000000000..40fd1e76c44df2a49bbc5c015bda0ef1bfb9ab32 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001426.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02092 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>MOLHKGIG_00832 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>NAFOICDF_01991 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTQVPGISRMTVVVDADAHLLEQ +VTKQLNKLINVIKVVELAGDSSVQRDHLLVKVRADASTRGQVVQAADLFRAHVVDVAPDS +LTFEATGTREKLEAFLEMMEPHGIRELVRSGTLALARGPRSMTDRALAR +>MHAAABBN_00564 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>LFPAFLNI_00802 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRAVAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001428.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001428.fa new file mode 100644 index 0000000000000000000000000000000000000000..032f08e94bd93a8b354e2caeccf44d1ba0219dbe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001428.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_02094 +MDTAASTPRTPSAAPDMKPRSRDVTDGMERAASRGMLRAVGLGDADFAKPQIGIASSWNE +ITPCNLSLDRLAQAAKEGVHADGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVE +TVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSTMPGHARLSDGTEKQVTI +IDAFEAVGACARGLMSEEDLLRIEKAIVPTEGACGGMYTANTMASVGEALGMSLPGSATP +PSPDRRRDDFARRSGAAVVNLLRQGITARDIMTKEAFENAIAVTMAFGGSTNAVLHLLAI +AREAGVDLSLEDFNRVGDRTPHIADLKPFGRYVMTDVDRVGGVPVVMKALLDEGLLHGDA +LTVTGRTVAENLAELAPDPVDGDVIRTMDRPMHPNGGIAILHGSLAPEGAVVKSAGFDAD +VFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPRGGPGMREMLAITGAIKGAGLGK +DVLLLTDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIAGRTLDVQVAEEELE +ARRREWTPVPPKFTTGVLGKYAKLVHSAAEGAYLG +>MOLHKGIG_00828 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG +>NAFOICDF_01993 +MDTSAADRTPQDVVTAPDMKPRSRDVTDGMERTAARGMLRAVGLGDEDFAKPQIGIASSW +NEITPCNLSLDRLAQASKDGVHAAGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADS +VETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDGTEKQV +TIIDAFEAVGACARGLMSEEDLLRIEKAIAPGEGACGGMYTANTMASIGEALGMSLPGSA +AAPSADRRRDAFARRSGEAVVNMLRLGITARDVMTKPAFENAIAVTMAFGGSTNAVLHLL +AIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRVGGVPVVMKALLDEGLLHG +DTLTVTGKTLAENLAALDPDPVDGTVIRTMENALHPNGGIAILHGSLAPEGAVVKSAGFD +ADVFEGTARVFDRERAAMDALEEGVIQAGDVVVIRYEGPKGGPGMREMLAITGAIKGAGL +GKDVLLITDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIASRTLDLLVEEAE +LEARRTSWQPVPPKFTTGVLGKYAKLVHSAAEGAYLG +>MHAAABBN_00560 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG +>LFPAFLNI_00797 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGEAVVKMIRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWKPVEPKFTTGVLGKYAKLVHSAAEGAYLG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001430.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001430.fa new file mode 100644 index 0000000000000000000000000000000000000000..6606c772a9d8dd39ea3b15d467038582ac67f479 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001430.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02097 +MSDTTQNRLQPGDIAPSFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDFRD +SLASLTAAGYVVLGVSPDPIGKIIRFAQKEGLTFSLLSDEDHAVAEAYGAWGEKKNYGRT +YEGLIRSTVVVGPDGRVTHAQYNVKATGHVARLRRTLGLDEA +>MOLHKGIG_00825 +MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD +SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT +FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA +>NAFOICDF_01996 +MTENTAAPARLSPGDVAPEFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDF +RDSLASLTAAGYRVLGISPDPIGKIIRFAQNEGLTFSLLSDEDHAVAAAYGAWGEKKNYG +RTSEGLIRSTVVVGPDGKVTLAQYNVKATGHVARLRRELGLDD +>MHAAABBN_00557 +MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD +SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT +FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA +>LFPAFLNI_00794 +MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD +SLASLTAAGYVVLGISPDPIGRIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT +FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001431.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001431.fa new file mode 100644 index 0000000000000000000000000000000000000000..1c2825857a99438bf58dca1074c45474a1b80206 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001431.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_02107 +MQPSRRALLGAGLGALGLGLGGCAGTPTPAPSASGTAPATPSGPSRLLVVGAPGRPFTRD +SARAWDSESFRIIRQVLETLLGVDPDTGAPTPRLAERHEVSADGRVHAFHLVPGLVFDDG +EPCDADAVVANIRRWAQAPAPVEGSVPMPSSFVSAFGGHEGEEGSVYAGVEARGAHEVRL +RLTSPLRHLAAALSSPAFAISSPASWERTVPVDGVETVTPAGTGPYRWATEAEVAELSRD +QPDGADVAYLVPSASHRGEEPAVRPVVVHPWGRATTRLRELRRGTADVIDVVAPGQLRPL +VEAGTQVLPRDPLAVLYVGMNLDHPRIRSQYLRQAIAYAVDRPRIAASDVFLEGTRLAHD +LVPPALGVGDEEARRYDVNPAQARRLVELSGYDGEELEFLYPAGTSSPSLPEPERVYAMV +AQDLGAIGLHITPVPVPADHDYLRAVVSRPTRALHLMGRNGAYRDPHAFLEPFARSWRAE +TGYRNPRVIQDVDAAASEQDDEARRGLFRRVVRAMALDLPALPLVYPISALATGPRVASY +PTSPQLDEPFARVRLTEG +>MOLHKGIG_00823 +MQPTRRAFLGGGLGLLGLGVAGCTTSPAAPSSAAPSSSGPGRLLVVGAPARALTRDPARA +LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD +AAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGGYAGDADSAFAGVEAHGELEVRLRLHS +PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA +SGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAG +TQVLPRDPLGVLYVGMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP +SLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL +GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR +NPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP +QLDEPFSRVRLTEG +>NAFOICDF_01998 +MDASRRSVLSLGLAGLGLGLSACGAGRATPASSSSSAASAPAVRPLVLGAPGRPLTRTPA +LAWDTESLRLIAQVLEPLLGVDQDTGAPTPLLAEHRESEDGLTHTFVLTPDLRFSDGVAC +DADAVVANLRRWSEGEPAEAVAMPSPFVAAFGGLAGEDSTAFRDATAADARTVRLRLRRR +LRHLPAALASPRFAISSPASWKRTQDVDGAPVATPAGTGPHRWADPTESVEVLEPLGGTG +PATVLVPNEHARAGLPTPPTAVVHSWGRASTRLRELRRGNADVIDVVAPGQLRPLVEAGT +QVLPRDPFSVLYLGMNLDHPLLHSLYLRQAVAYAVDRPRLASSDVFLQGTALAHDLVPPA +LGVAVEDGPRYDVDPARARRLLELAGYRGEPLEFLYPSGHAWPSLPEPERVFAMVSSDLG +VVGLRVVPVPVPADQDYRRAVLGRRGRALHLMGRDGHYRDPHAFLEPFARSARTETGYVN +AALTADVDAAASETDDERRRELHRRAGRTLLLDLPALPLVHPISALATGPRVASYPTSPQ +LDEPLAQVRLADS +>MHAAABBN_00555 +MQPTRRAFLGGGLGLLGLGVAGCTTSPAAPSSAAPSSSGPGRLLVVGAPARALTRDPARA +LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD +AAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGGYAGDADSAFAGVEAHGELEVRLRLHS +PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA +SGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAG +TQVLPRDPLGVLYVGMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP +SLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL +GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR +NPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP +QLDEPFSRVRLTEG +>LFPAFLNI_00792 +MQPTRRAFLGGGLGLLGLGVAGCTTSPAVPSSAAPSSSGPGRLLVVGAPARALTRDPARA +LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD +AAAVVANIERWASAPAPVDGTVAPPSSFVSAFGGYAGDADSAFAGVEARGELEVRLRLHS +PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA +SGATILVPSARHRGSDPAAYPVAVQAWGRASVRLRELRRGSADVIDVVAPGQLRPLVEAG +TQVLPRDPLGVLYVGMNLDHPRVRSQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP +SLGVGDEEARRYDVNPGRAREFLHLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL +GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR +NPRVVEDVDAAAAETDDDARRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP +QLDEPFSRVRLTEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001432.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001432.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c9620834ebc06854c86c5b2161d8791123d1371 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001432.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02108 +MPTPSSATTHDVVLIGGGIMSATLGVLLQRLEPTWSIALYENLDQAGLESSDPWNNAGTG +HAALCELNYAPLGKDGTVDVTKALGINEQFWTSRQFWSSLVKDGTLQDPKTFINPLPHMS +FVWGDAHADYLRTRYEAMSAQPLFAQMEHTEDPATIAEWAPLLIEGREDAGRIAASRVVG +GTDVDFGSLTRQLVTAMAGAGADVRFGHKVTGLSRGTDGRWEVSVKNKAAGTEVVDRARF +VFVGAGGGALSLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNRHMAKVYGQAAVGAPPM +SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSIRPHNLTTMLDVAKDNMDLT +KYLVAEVVKSQNKKVESLKEFYPEAEGGDWELITAGQRVQVMKRKGRFGGVLQFGTEVVT +HGDGSIGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGALKELIPSLGRTLNDDPALL +AEVSASTDAALKLA +>MOLHKGIG_00822 +MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG +HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS +FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG +GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF +VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM +SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT +KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT +HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL +DEVRTVTDAALKLA +>NAFOICDF_01999 +MWIPPDGVRRCTILALEHQEHIVSTPTSTTHDVVLIGGGIMSATLGVMLQKLEPSWSIAL +YENLDQSGLESSDPWNNAGTGHAALCELNYSPLGKDGKVDTAKAKGINEQFWITRQFWSS +LVKDGTLADPKNFINPLPHMSFVVGDAHADYLKTRYEAMSAEPLFADMEHTEDPDVIGEW +APLLMDGRTGTERLAASRVPTGTDVDFGSLTRQLVTALAAGGADVRFGHKVTGLSRGTDG +RWDVTVKNKAAGTEVRDRARFVFVGAGGGALGLLQNSGIPEIKGFGGFPVSGQFLRCTDE +KVVNQHMAKVYGQAAVGAPPMSVPHLDTRFVNGKRSLLFGPYAGFSTNFLKSGSYLDLPL +SIRPHNLPTMLNVAKDNMDLTKYLVTEVLKSNEKKVDTLHEFYPAADGSEWELITAGQRV +QVMKKKGKLGGVLQFGTEVVSHADGSIAGLLGASPGASTAAPIMVKLLERCFPAKMAGWD +AALKDMIPTLGRTLNDDPSLLAEVRSATDAALQLG +>MHAAABBN_00554 +MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG +HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS +FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG +GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF +VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM +SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT +KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT +HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL +DEVRTVTDAALKLA +>LFPAFLNI_00791 +MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG +HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS +FVWGDDHADYLRTRYETMSAQPLFAGMEHSEDPEQIRAWAPLLIEGRASGQRLAASRNTG +GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF +VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM +SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT +KYLVTEVLKSRDKKIDALHEFYPEADGAEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT +HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL +DEVRTVTDAALKLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001434.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001434.fa new file mode 100644 index 0000000000000000000000000000000000000000..31c19055759d609787a2ddc3627a052ada8c9b88 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001434.fa @@ -0,0 +1,91 @@ +>ACLBLIBL_02110 +MRIHRMRLQGIGPYAEAQDVDMDRLNDAGLFLLDGPTGAGKSTVLAALCYALYGSVPGGR +SPESLVTTLRPPGAVVPEVLVEFTVQGRRFEVVRSPRHERLKKRRSASGKDTTPTPAAVS +LREHVDGAWQEPLTRNDEVGVQVADVMHLDAAQFMQVVMLPQGRFAEFLTARSDERQRLL +RRLFGTQRFDGVEEHLKAEAERLGSRAAADAKVAASAREQLREAVAAELGEDWHAPEPFP +ATDEELVERTAERTREAVDAARAGRDAAAAEEAAARGTQAELRATGEALAAAAAWTERER +AHREGAEAAAGDRTAVAAHERAGRVLGAADRSESARAAEDRAREADGTAQAAAAEDPLSA +GWLEQARRDAAETPADDAAETSADAAALPRDAVALAERAVEEVVRAVRDRAAAERLEETE +RTEAARRTQIVAEREAAEAERSGREEGLAAVREAVEAASARLGAQADVDRRVAEAEQGLA +AAREAERHALAADAADRAREAARTGRDAAAQHRLGLLRSRYEQAAADLAADLEDGTPCAV +CGSPEHPDPAPRVGTAVTEADVAAAEEGLAAAEAVLADAETARTAAHERVRASSAAAGGR +TPAQAEEALAAARTEHAELAAVRKALAADRRRLRALETERDEAAAAETARTAEDARLQEA +ARQRHERLLELRAGIERARGDAPDLDARGALVRAARGRLEALAGAVEVRERAVAVAADAD +RALAAALREQEFEDVGAARAARLPAEDAAARTARVRAWDDEQARLAELAQSDAVRRGREL +QDQQATAPTPEDLEAAAARLLEAERSRREQDEALGRRTAVAAAVERQAALLRGVLDRSAA +LLAEHERVTGLLALVRGGGENRLKMPLASYVLAGRLEEVAAAATERLLAMTDGRYSIEYS +DDSAGRGNKGLELVVRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDT +LFVDEGFGSLDSDTLDDVLDVVDGLRSGGRTVGLVSHVERMKQEIPVRLAVTKEREGSSL +AVHVDA +>MOLHKGIG_00820 +MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR +SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS +LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRALL +RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR +DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA +AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR +DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA +ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT +ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA +EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR +DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF +DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ +TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL +DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE +LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA +DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA +>NAFOICDF_02001 +MRIHRMRLEGIGPYAEPQDLDLDPLNDAGLFLLDGPTGAGKSTVLAALCFALYGSVPGGR +TPESLVTTLRPPGAVVPQVLVEFTVQGRRFEVLRSPRHARPKKRGGGTTATQASVSLRER +VDGAWTAPLTRADEVGRQVAEVLRLDAAQFMQVVSLPQGRFAEFLTARSDDRQRLLRRLF +GTQRFDGVEDRLKECAEALGTRVAADAAEAAGARAQLLEQARLELGEDWHAPDPAPEEGE +DERLVELTRTRADAALAEARTAQQAADAAEAAARAAQDRLTADTEALRALAAWEGREREH +RQAADHVAADRSAVALHERASHVLGAATRAEQTRAAHASTAERARAAAEAVAADALAAAW +LDEAEDADAARRRADRETDALARAVRDRDALTRLEAEGTQADAERERLEDEARSAREKGK +RRAAQIAELHDTVDAAAARLGAEDEVARRLAEATERAAAAGQAAERAVAQERARAARDER +RDAQRGAAQARLDLLRSRFEQAAAELAAGLEDGSPCPVCGSAEHPDPAPRADGAVTEADV +AAADRALEAADAALAEAEQALAAASEEHRAARERAGGQDVAAAEEALSAVRAEHEALAAA +RTALATDRRALARRESEQRTADEAATARTAALARLSEAQARRTERAAELTAAVAAAQGDA +ADLDARTAHVRTATRALSALVEAGDAAARAAAVAEDAAQALAGALAEQDFADVAAARAAA +LPPDDAAARAARVRSWDVEEARLAEAAASEPLVRGRALREAGTSEPTAEEFAAAQETLRE +ATAARTARAAVVGRREALVASLERQARRLRAVLERSSELLAEHERATGLLALVRGQGENR +LKMPLASYVLAGRLEEVAAAATERLLAMTDRRYSIEYSDEATGRGNKGLELVIRDHYVDE +TRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDTLFVDEGFGSLDADTLDDVLDVV +DGLRAGGRTVGLVSHVERMKQEIPVRLEVTKSRAGSTLAIHDGG +>MHAAABBN_00552 +MRIHRMRLEGLGPYAQAQDVDFDRLNAAGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR +SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS +LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFIQVVLLPQGQFAQFLTAKSDERRVLL +RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR +DHDAEAETAAARRRAVDAHERAGRVLAAAQRASAAADAAGTASEAVTEALAHVEDEPTAA +AWLAAARADGAADAPASRQALGEAERAAEAVARAVRDRDRMRELEQEAAAAAERRAEIDR +DRAALVESRPEREAAVAAHRAVVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEV +ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT +ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRSAGEAAAGLAPEAAREALERA +ETERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR +DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETGQALTATLAEQRF +DDVDAARAARLEETEAADRTAAVQEWDAERARLAELEASEPVRRGRALAEAGVEPPTEEQ +TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL +DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE +LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA +DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA +>LFPAFLNI_00789 +MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR +SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS +LRERVDGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRVLL +RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +DTDDRLLGLAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR +DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA +AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR +DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA +ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT +ADTTVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA +EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR +DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF +DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ +TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL +DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE +LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA +DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001437.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001437.fa new file mode 100644 index 0000000000000000000000000000000000000000..0ece2e28d2176aa62aaf154aa372f0d0dbf598da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001437.fa @@ -0,0 +1,39 @@ +>ACLBLIBL_02113 +MSGVLAPVPGLDFTAIDFETANGFRGSPCALGAVRVRDGVMVERAEWLIRPPVGFDRFDP +RNVRIHGITEDRVLDAARFADVYDELAGFVGADVLAAHNAGFDVGVIESGLEVSGRDVPR +LDFVCTLVLARRVYDLASYALPSAAREAGFAPGPHHDALADAEACAAILVDVARRVLGTE +AGDGAAVAPAGARGLPEPFDVPRLMRAQGLTVNTLAQRAAGEGPESKATRQARRAQGVFD +ARVPLKDERAMPDFLRWPDEGTNPVPNPDADPGHPLHGQTVVFTGGIGMSRQTAKVRAAR +LGAQTANRVGAATTMLVVGDGFEAADLDRPAPAPGTREAVTTALAHRKTRDALRRRERGQ +HISLVSEGEFLQMLDGNWPDAAR +>MOLHKGIG_00817 +MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP +RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG +LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP +PADADVLPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGAGAESKATRQARRTEGVFDAR +VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQRAKTRAAAHG +AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRG +>NAFOICDF_02004 +MTAGIAPVRQPGLDFTAIDFETANGFRGSACQLGAVRVRDGLPASRAVWLMRPPAGFDRF +DPRNVRIHGIHADRVVDAPRFAEVYDAFAAFAGDDVLVAHNAGFDLGVIESGLEVSGRDV +PAHDYACTLTLARRIYDLPSYSLPSAAREAGFVPGRHHDALADAEACAAILVDLARRVCP +PGEATVDALLASQGLRRSRLTARAAGTGRESRATRQARTMPGLFDATIPLADDRTLPDLM +RWPDEGVNPEPAADADPGHPLYGQVVVFTGGIGMSRQEAKNRAAQRGAATANRVNGRTTM +LVVGDGVDPAELVGAPEVHGVVVDPGATDPAGRGVDPGGAVTHRKTREALQRRAKGQAIA +LVSEAEFLQMVDGAWPAGAR +>MHAAABBN_00549 +MSGGRAPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP +RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG +LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP +PADAEILPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGSGAESKATRQARRTEGVFDAR +VPLRDERAMPDFMRWPDEGVNPPPNPTADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG +AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI +ALVSEGEFLQMLDGNWPDAAR +>LFPAFLNI_00786 +MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP +RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG +LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP +PADAEILPGLTDAPAGRGVDRLMRAQGLSVSVLAPRAAGSGAESKATRQARRTEGVFDAR +VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG +AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI +ALVSEGEFLQMLDGNWPDAAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001440.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001440.fa new file mode 100644 index 0000000000000000000000000000000000000000..0690f197e01ec4ac662b45d88cf90ba58c4b874c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001440.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02116 +MKLTVIGASGSFPGPGSPASCYLVTAQGVAEDGVTPRTWRILLDLGNGSLGVLQRYIELE +ELDGILLSHLHPDHCMDLCGMHVAIRWNPEGWHRDRMPVYGPTATADRIAEAYGMDPEPG +MHEDFDFRVWRPGRTERFGPFRLTPVPVRHPIDEAYAIRVEADEPDGEGGTVTRVLTYSG +DTDACEGLVEAARDADLFLCEAAFHEGRDDGIDGVHLTGLRAGQTAAQAGAKKLLLTHLP +VWNDPQRAVLEAREAYEGPMAVAVSGLSYGV +>MOLHKGIG_00814 +MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE +DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWDRGRLPVYGPAGTADRIAEAYGMDPEPG +MHQDFEFRCWAAGRTERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG +DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP +VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV +>NAFOICDF_02007 +MKLTVIGASGSFPGPGSPASCYLVTADGPDGNGGTRPWRILLDLGNGSLGVLQRHIELEQ +IDGVLLSHLHPDHCIDLCGLHVAVRWNPEGWDAGRIPVYGPAATATRIAEAYGMDPEPGM +QEDFDFRAWEAGRTEGLGPFRLTPFAVRHPIDEAYAIRVETTEPGPDGEPVTRVLAYSGD +SDTCDGLVEAARDADLFLCEAAYHEGRDDHIDGVHLTGRRAGQMAAEAGARKLLLTHLPV +WNDPQRCAQEAREAYVGPLAVAVSGLSYGL +>MHAAABBN_00546 +MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE +DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG +MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG +DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP +VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV +>LFPAFLNI_00783 +MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE +DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG +MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG +DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP +VWNDPQRAVQEAREVYDGPLAVAVSGLSYGV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001441.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001441.fa new file mode 100644 index 0000000000000000000000000000000000000000..f52d42df18fe366605399327e31d00255a50cfab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001441.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02117 +MSAPPQARPEVSASSPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTAHAPYGPRPIAQ +VRALALGIMDELVDAGVKALVIACNSASAAVLRDARERYTGRHGIPVVEVIQPAVRRAVA +ATRSGRIGVIGTQATVGSRAYDDSFSAAPHLQVTSAACPRFVEFVEAGITTGPELLATAQ +EYTEPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEH +PHSAAGSGQDTRHRFAATGDPEHFQALARRFLGPEVGAVRRLDTVRERYPTAALAQLTPD +LIARLGAEQERET +>MOLHKGIG_00813 +MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA +LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR +TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT +APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS +AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSTAFV +PLGAEQEGVT +>NAFOICDF_02008 +MSATADTAQTGAGPSSPIGVFDSGVGGLTVARAIMDQLPHEPIIYVGDTAHSPYGPRPIA +QVRALALGVMDELVEAGVKALVIACNSASAAVLRDARERYTGRLGIPVVEVIQPAVRRAV +AATRNGRVGVIGTQATVGSRAYEDSFSAAPHLQITSVACPRFVEFVEAGITTGPELLETA +EEYVAPLKAAGVDTMVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRALVRHGLE +HPHSAAGSAAAPEHRFAATGDPEHFAALARRFLGPEVGPVRQIQEIRERYPTAALTALTP +DVLARLRAEMEEDGAR +>MHAAABBN_00545 +MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA +LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR +TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT +APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS +AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV +RPGPEQEGVT +>LFPAFLNI_00782 +MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA +LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR +TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT +APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS +AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV +RPGPEQEGVT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001442.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001442.fa new file mode 100644 index 0000000000000000000000000000000000000000..fe0e7ff709aa4cbbbceb4200cfe780b74ca6cee1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001442.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02118 +MAERFRWTRRGYTAQLEKPEVRLLRGLVKDVITLLEGRRRNVLSEADDLPADAPGAPEPS +ADVAPVPQGPEAGAGPAAGLDEADAAFWELVSGLHLSQDRVPHRAAPADPAVARLLPEAM +PQADAQERGAHRALTEDALSEGKLADARLALELLRSTRVEVPHHQAPAFGRALNDVRLVL +AARLGVETEEDAERVHAVDDWRSAEDVESTMALLYNFTTWLLETLMTEMLSELPEGADED +APGADEAGDDA +>MOLHKGIG_00812 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +ADESAPGAGDAEDEQ +>NAFOICDF_02009 +MAQRFRWTRRGYVAELEDAELRLLRGLVKDVVTLLENRQDEVAPPGSDAGTAEDAPEAGA +EPVADARPGDAVGPGEETPHDAAFWALVGGLDLVADPVAERSAPEDPAVARLLPDAMPHA +EPAERARQRALTEDALTAAKLADARRALEALRSVRVTVPHEHAVSFGRALNDVRLVLAAR +LGIETEQDAARVHAVDDWRDAQDVEATMALLYNFTTWLQETLMAEMLSELPLEGAAGPDE +EERA +>MHAAABBN_00544 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHNQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +SDESAPGAGDAEGEQ +>LFPAFLNI_00781 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +SDESAPGAGDAEGEQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001444.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001444.fa new file mode 100644 index 0000000000000000000000000000000000000000..4cfcccab94ddb567d5c9455ef77fcd422bf98fcb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001444.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02120 +MSQNPVTSAPQTPDDWRIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY +GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP +HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA +VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTSL +LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTQTGIMVTSDLD +EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG +GRKEAARRRDRRGRATAEVVGVNRGAAPDADDRPLLHRFVHAGELAAGWTGPEAVTRAAE +RHAASLRELPATVGRLQPGDPAIPTIFLED +>MOLHKGIG_00810 +MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY +GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP +HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA +VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL +LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD +EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG +GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE +RHAASLRELPASVGRLQPGDPAIPTIFLED +>NAFOICDF_02011 +MTQNASAPAPSAAPWHVPTSLMTDHYELTMLCAARRAGTAERRSRFELFSRRLPDGRRYG +VVAGTGRILEGLSRFRFSTAEVDFLADHSVVDDATLQWLADFRFSGDITGYAEGEVYFPH +SPVLQVESTFAEACILETYLLSILNYDSAVASAASRMASAAQGRPCIEMGARRIHEEAAV +AAARAAVIAGFAATSNLEAGRRYGVRTVGTAAHSFTLLHDSERAAFEAQVAALGRDTTLL +VDTYDVEQGVRTAVEVAGRALRNVRLDSGDLVQQAHEVRELLDSLGNTETGIMVTSDLDE +YAIASLRSAPVASYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASHGG +RKDAVRRRDARGRAVAELVGVNRAPAADADDRPLLHTFVKDGELQEGWTGPEAVTRAAER +HAASLAELPRAAARLQPGEALIPTIFQED +>MHAAABBN_00542 +MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY +GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP +HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA +VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL +LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD +EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG +GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE +RHAASLRELPASVGRLQPGDPAIPTIFLED +>LFPAFLNI_00779 +MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY +GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP +HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA +VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL +LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD +EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG +GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE +RHAASLRELPASVGRLQPGDPAIPTIFLED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001445.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001445.fa new file mode 100644 index 0000000000000000000000000000000000000000..e5e9d70534677ff8491d2b5f8f568a9aab1d31b6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001445.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02121 +MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG +THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDIEHLDAEFLKGLHTDAYSGFDGALG +EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESDAPGLDEWLREQGVDAITVVGIATDHC +VRATVLDALDAGYEVTVLTDLVAGVDEAASQAALHEMEAAGADLELSEGR +>MOLHKGIG_00809 +MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG +THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG +EPDAVPTGAAGERPSGTVGPYGATAVAAAAVEAGAPGLDEWLREQGVDAITVVGIATDHC +VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS +>NAFOICDF_02012 +MSEQNRALVIVDVQNDFCEGGALAVAGGADVAAAIADHVNEAREDYAAVVTTRDWHVDPV +GHFAAASLEDRDAEPDYVRTWPVHCVAGTPGAELHPGLSAEDLEIDAEFLKGQHSDGYSG +FDGHAGDPDAVRSGDEARAAAGPYGATQGAAHAADGGLGLDEWLREQDVDALTVVGLATD +HCVRATVLDGLEAGYEVTVRTDLVAGVDDAAGEAALHEMEAAGALLRAGD +>MHAAABBN_00541 +MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG +THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG +EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC +VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS +>LFPAFLNI_00778 +MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG +THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG +EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC +VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001449.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001449.fa new file mode 100644 index 0000000000000000000000000000000000000000..5783d0b06aa19f546276b4856842a2cd3088e6b6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001449.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02126 +MSEHPAEPHRTAPSSAEAPHAGPAPAEAPAVVPSAAARRRAVDAPDPDLALVTRGLTKRF +GDKTALDGLDLDVPAGSFYGVVGPNGAGKTTALSMATGLLRPDLGQAWIHGVDVWAQPLE +AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGVDADTVAARTEDLLRVMDLADAGRKLVV +DYSAGMTKKISLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV +MDLVQRMCSHVAVIAGGTLRAAGTLEEVRAGRDLEDRFVDLVGGRHEQEGLAWL +>MOLHKGIG_00804 +MTPHASEPAPTHLAAATRRRAVDAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG +VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG +AQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRTLVADYSAGMTKKVSLAAAMVHAP +DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR +AAGTLEEVRDGRDLEDRFVELVGGRHGSEGLAWL +>NAFOICDF_02019 +MRAQDAPDPNLALVTRGLAKRFGEKVALAGLDLEVPAGSFFGVVGPNGAGKTTALSMATG +MLRPDAGRVWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTGAQLITYAGLLHGLDRDTV +DVRTADLLRVMDLEEAGRKLVVDYSAGMTKKVNLAAAMVHAPDVLVLDEPFEAVDPVSAA +NIRDILHDYVGRGGTVIVSSHVMDLVQRMCSHVAVIAGGVLRAAGTLEEVRAGRDLEERF +VDLVGGRHTGEGLAWL +>MHAAABBN_00535 +MTPHAPEPAPAHLAAAARRRAADAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG +VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG +TQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP +DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR +AAGTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL +>LFPAFLNI_00771 +MTPHAPEPAPAHLAAAARRRAVDAPDPDLAFVTRGLTQRFGDKLALDALDLDVPAGSFFG +VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG +AQLVTYAGLLHGLDADTVAERTTDLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP +DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR +AADTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001450.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001450.fa new file mode 100644 index 0000000000000000000000000000000000000000..9674acb0b943e933b0a528642ced7cc0e2cbbba9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001450.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_02127 +MIPDADQRLLQQLVQLSAQVPVLLHLHVPGDASSDALYRQFADAVDAQAGRLVLARIDVA +ADPSVLQALGLGAGPAVMAVVAGQPVPLVNQEVPAETLEQLMGEILEVARQNGVAGTVPA +VAPARADAAEPAPAAPPVPPLHRAAHAALAADDLPGAVAAWEEALKDTPADPVAQQGLSA +ARLMLRTRDADAAAVRSAAADAPDDAAAQLAVADLDVLGGHVEDAFARLVRFIALHPGED +RETVRAHLVDLYTVVGVDDPRVTASRRRLAAALF +>MOLHKGIG_00803 +MTDVTAQPPSDAPSHLRGAVDLSSLGTPASAGRTAPGADAGAGGGSWVIADADQGLLQQL +VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPAVLQALGLGA +GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPAVAPARQDAGAAAA +EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAS +AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFDRLVRFIALHPGDDRETARAHLVDLYT +VVGTDDPRVQASRRQLAAALF +>NAFOICDF_02020 +MTSQPSSPSLRGAVDLSSLRTPRPAPGAQGAGAQGAGAPGEPASWAVLDADSRLLEQLVQ +LSTQVPVILVLHVPGDATSEALSTQFADAADAQAGTVVMARLDVVAEPQLLQAFGIGAGP +AVVAVVAGQPVPLANQELPQEALDGLMGQLLEVARQNGVAGRVPALAPARDGAAAPQPAP +VPPLHRRAHEALAADDLPGAVAAWEDALKESPADETARQGLSAARLMLRTRDMDAAAVRA +AAAERPDELAAQTAVADLDVLGGHVEDAFARLVRFVAAHPGEDREAARAHLVDLYIVVGS +EDPRVHASRRRLAAALY +>MHAAABBN_00534 +MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL +VQLSAQVPVLLHLHVPGDAASEALYRQFADAADAQAGRLVLARLDVAKEPAVLQALGLGA +GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDADAAAA +EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA +AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT +VVGTDDPRVQASRRRLAAALF +>LFPAFLNI_00770 +MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL +VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPTVLQALGLGA +GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDAGAAAA +EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA +AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT +VVGTDDPRVQASRRRLAAALF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001452.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001452.fa new file mode 100644 index 0000000000000000000000000000000000000000..1d0784f18a7332ae6ec31986aa751db440187186 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001452.fa @@ -0,0 +1,16 @@ +>ACLBLIBL_02129 +MADPLKELLGLDPGYSHQSGGDGGWHVRQIPSWRAVKDYTCPGCGRVIRQGQAHLVAWRS +DWIMGDEDAGADRRHWHPVCWRTRVGR +>MOLHKGIG_00801 +MPRSNRPRRSSAPRRSERGASGASRRSRPSPGRSDPLQELLGLDAGYSRQSGSDGGWHVR +QIPAWRAVKDYTCPGCGRVIRQGQAHLVAWRADWIMGDEDAGEDRRHWHPVCWRTRPSR +>NAFOICDF_02022 +MVTMPRSNRPRRSAAPRRGEGAAGGASRRSRPGPGRADPLEELLGMDPGYSHQSGSDGGW +HVRDIPSWRAVKDYTCPGCGRTIRQGQAHLVAWRSDWIMGDEDAGADRRHWHPTCWRTRA +SR +>MHAAABBN_00532 +MPRSNRPRRSSAPRRSERGASGVSRRSRPSPGRSDPLEELLGLDAGYSRQSGSDGGWHVR +QIPAWRAVKDYMCPGCGRVIRQGQAHLVAWRADWIMGDEDAGADRRHWHPVCWRTRPGR +>LFPAFLNI_00768 +MPRSNRPRRSSAPRRSERGASGASRRSRPSPGRADPLEELLGLDAGYSRQSGSDGGWHVR +QIPAWRAVKDYTCPGCGQVIRQGQAHLVAWRADWIMGDEDAGADRRHWHPVCWRTRPGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001453.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001453.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd726340012e63dc12d46b1302ba080425508f3c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001453.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02130 +MRLVIARCSVTYEGRLNAHLPPATRLLMVKADGAVLVHSDGGSYKPLNWMSPPATLHTTA +PTAEQAEQGVVEVWRVQAAKSDDRLMILIEEILADQSHELGADPGLVKDGVEADLQRLLA +EQIGLLGDGHTLVRREYMTAIGPVDILARDPEGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>MOLHKGIG_00800 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>NAFOICDF_02023 +MRLVIARCSVTYEGRLNAHLPSATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PTEEQAAAGVTQVWRVQAKKSDDRLLVLLEEVLADETHELGVDPGLVKDGVEADLQRLLA +EQIGLLGDGHTLVRREYMTAIGPVDILAKGPGGQTVAVELKRRGDIDGVEQLTRYLDLMN +RDPLLAPVTGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDADARLF +>MHAAABBN_00531 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>LFPAFLNI_00767 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PFPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001454.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001454.fa new file mode 100644 index 0000000000000000000000000000000000000000..8535b43fb90846621084d8d1b58e2b7c6841d3de --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001454.fa @@ -0,0 +1,41 @@ +>ACLBLIBL_02131 +MRPGGHARARRITPPLADHHVHGGAGVDLATSGAEDVRRWLAELRAAGASVVLGSLPALV +PADLAAALERLRPLWEDGALAGVHLEGPFLSPARAGAQHPDALCAPDSAAGRRVRALLRA +QPRGFVRTLTLAPELPGAREVAAELEAAGTVLCLGHTDAGPAEVAAALDWPRPRAAATPV +ATHLFNGMRPFHHRDPGPVPTLLAAARRGRLRLELVADGAHVAPELMELILEDPDLAAQT +CLVSDAIAATGAPCGTVHRLGPAVVHAAPDAPRLGEPAEDGQGSKATGPEDGGRAPLAGG +RRTLVEAVTALLDADLDADAVLRAAVHVPRRSLPETPAPELEDGALVWDEGRPLVALPAA +RA +>MOLHKGIG_00830 +MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRT +HGPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEV +DALAAQLTALTALCAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEVGAGH +LAMVTLAPELPGALDAVGRLAGAGVVVAIGHTDASYETTRAAIEAGARMATHLHNACRPT +HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDSMAAAGCGDGE +FPLGPLRVRVHDGVARVVGADGAAGAIAGSTATVTGSVRSAVAAGVDLDAALRAATAAPA +DALGLPDVGRLRAGSRADAVVFGPELEVRGVLHHGTWVKAAAPAAAD +>NAFOICDF_02024 +MTASALLRTTAPWVGADPGATPVRVSAVWSAGPDGALLVWAGLAERVPQELWETAVDAPA +LRLSPALTSHHVHGGAGVDLATSPAADVRSWLAAQRQAGVGAVVGSLPTLAEDALAAALD +RLRPLWAEGLLAGVHLEGPFLSPARAGAHDPALLLTPPSPAGRRVRALIAAQPEGFVRTL +TLAPELPGADALTRELTGTGVVVCPGHTDADGATTRAWLQTADDARAAATAAGLPAPTPV +ATHLFNGMRGFHHRAPGPLPALLGAARAGRARLELIGDGVHVDDEVLTAILGDPGLAPAA +CLVSDAVAATGATRGTAHRLGSLPIHAAQDGPRVGADEPTGPAEAALAGGAADLPEIVGR +LLHSDLDPDAVLRAATHVPARTLGGSHAVPVGTPETTEHAAPGGDVLVWAPDGAVTVLRS +QAAPGGRHHD +>MHAAABBN_00562 +MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVTAVGAGDPPRT +HGPVHELGDALLAPGCVDVHCHGGGGHAVESGPDAARAAAAAHARAGTTTVVASLVTDEV +DALVAQLTALAPLRAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEAGAGS +LAMVTLAPELPGALDAVGRLAEAGVLVAIGHTDASYEVTRAAIEAGARMATHLHNACRPA +HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGD +FSLGPLRARVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPA +DALGLPDVGRLRAGSRADAVVFGPELEVRGVLRHGAWVEAAAPAAAD +>LFPAFLNI_00799 +MPASVPHRPRAEQAPQAAASPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRTH +GPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEVD +ALAAQLTALTPLCAEGVLAGVHLEGPWLSPRHRGAHRAASLRAPEPEDVARLVEVGAGHL +AMVTLAPELPGALDAVGRLAEAGVVVAIGHTDASYETTRAAIDAGARMATHLHNACRPTH +HREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGEF +PLGPLRVQVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPAD +ALGLPDVGRLRVGSRADAVVFGPELEVRGVLRHGTWVKAAAPAVAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001455.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001455.fa new file mode 100644 index 0000000000000000000000000000000000000000..9cf6387cac6340b247bb1fd8bbe6947cbd046e3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001455.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02132 +MLIALAGVLAVFALSASALAVRRRALLRTSAAFPAVLQGHGRPRERVIGVYDETRLLFTG +RWMIRRERWSVGRCDLQIDRLPVAEDGRAVLELDGGRGSVTVVVDPDDAGALRAWSEAGP +SAASSFWRR +>MOLHKGIG_00799 +MQGPVLIASATVAAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL +RLTGRWRLSRERWSADRSRLQIDRLPADEAGRTVLELSAGARPVRVVVDPDDAGALRAWS +EAGPSAASSFWRR +>NAFOICDF_02025 +MRGPVLLLSGALAVFALLALAGWARHRALVRGPGRFAGVLVTDGGRRCRVVGCFRSHELV +LSHHLLPERRLWSAERWRLEVDRLPAAEAGHTRLRITDASGRSDDAVDLEVEDDVAGAVR +AWTEAGPSQAGQSWWRPPGAA +>MHAAABBN_00530 +MLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRLRLTG +GWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGARPVRVVVDPDDAGALRAWSEAGP +SAASSFWRR +>LFPAFLNI_00766 +MEGPVLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL +RLTGGWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGTRPVRVVVDPDDAGALRAWS +EAGPSAASSFWRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001457.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001457.fa new file mode 100644 index 0000000000000000000000000000000000000000..8539dc92f7cffbf50821194ad61fc1a7f7f631b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001457.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02134 +MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF +EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDVETS +SLNFEERWPIHRAAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQDHYDTAIRVKQILQKNKELQDIIAILGVDELGEEDKITVARARKIEQ +FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHIAEQAFYNVGGLDDVEREWAK +IQAEG +>MOLHKGIG_00797 +MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF +EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS +QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQEHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ +FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK +IQAEG +>NAFOICDF_02027 +MTATFTDQGTGTPTAGATGRVARVIGPVIDAEFPANAMPEIYNALTATVELAGQTRVVTF +EVAQHLGDNMVRAISLQSTDGLVRGADVQDTGAPISVPVGDAVKGHLFNVLGETLDMPIS +ELDVQERWPIHRPAPSFAALEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQEHYDVATRVKQILQKNKELQDIIAILGVDELSEEDKITVSRARKMEQ +FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK +IQAEG +>MHAAABBN_00528 +MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF +EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPAS +QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMEEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ +FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK +IQAEG +>LFPAFLNI_00764 +MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDFNGQRRTVTF +EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS +QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ +FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK +IQAEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001458.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001458.fa new file mode 100644 index 0000000000000000000000000000000000000000..f4f26f15d6cd633240c80d27c8bb68d6fbe40eab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001458.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02135 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVNASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLILSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGREYKQLWTGQTDAPAAERASEIGETLVDAFLTDTAAGGVDEIHIVFTEF +VSLVKQNPHVVRLLPLEVVEEEVAAPEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNASGLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>MOLHKGIG_00796 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKQLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>NAFOICDF_02028 +MGAQIRVYRQKIASTTSMKKIFKAMELIATSRITKARERVNQSLPYANAITRAVTAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTALHEEGKDVDVYVVG +RKAQTYFDFRGREYKQLWTGQTDAPKAERAQEIGTILVESFLTDTAAGGVDEIHVVFTEF +VSLVKQNPHVIRLLPLEVVEQDVVSPEEVLPLYEFEPDADEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNASSLIKEFTLRMNNARQAEITQELTELIAGADALNNS +>MHAAABBN_00527 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKQLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>LFPAFLNI_00763 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKKLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001459.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001459.fa new file mode 100644 index 0000000000000000000000000000000000000000..f6dcd5b8d79dd1094547647dd23e9a0604595e5c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001459.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_02136 +MAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLPSVMANELLRFE +NGIQGLAQNLDAREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDGFMGRVVDPLGQPID +DLGPIQAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQLIIGDRQTGKT +AIAVDTILNQKANWESGDVDKQVRCVYVAVGQKASTIAGVRATLEEHGALEYTTIVASPA +SDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLLRRPPGREAYPG +DVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISITDGQIFLQSDL +FNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSMFASDLDPATRR +QLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVEDVLRFEREFIDHLRRRG +SVLTDIGSTGKLEDGTVSALESEIAEFKKGFQSSEDGGVHAGHEEHRAIEQDQVAQEQIT +KQKR +>MOLHKGIG_00795 +MITKHREQGLQMAELTINADDVRNALNEFAASYEPSGTDRTEVGRVISAADGIARVEGLP +SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG +RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ +LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA +LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL +RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI +TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM +FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE +REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEEGGVRAGHEEHRAI +EQDQVAQEQITKQKR +>NAFOICDF_02029 +MITKHREQGLQMAELTINADDVRNALNDFAASYEPSDTTRTEVGRVISAADGIARVEGLP +SVMANELLRFSNGILGLAQNLDAREIGVVVLGEFQDIREGMEVQRTGEILSVPVGDGFLG +RVVDPLGHPLDDLGPIEAEGRRALELQAPTVTQRKSVHEPLQTGMKAIDAMIPIGRGQRQ +LIIGDRQTGKTAIAVDTILNQKANWQTGDVDKQVRCVYVAVGQKASTIAAVRSTLEEHGA +LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL +RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI +TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM +FASDLDPATRRQLARGERLMELLKQPQYSPYPVEDQVVAIWAGSKGHLDDVAVEDVLRFE +REFLDHLRRKDVVLGEIASTGKLEDETVSALEREIDAFKKGFQASGHDGVAAGHEEHAAI +GQDQVVQEQITKQKR +>MHAAABBN_00526 +MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP +SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG +RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ +LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA +LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL +RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI +TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM +FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWTGSKGHLDEVPVQDVLRFE +REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI +EQDQVAQEQITKQKR +>LFPAFLNI_00762 +MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP +SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG +RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ +LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA +LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL +RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI +TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM +FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE +REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI +EQDQVAQEQITKQKR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001460.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001460.fa new file mode 100644 index 0000000000000000000000000000000000000000..9427f08605af08b045afa6ebb048bb8cf78b43b6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001460.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02137 +MMTGASRDSLTASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVIKDLAGRRWSAERDLGDALETVAAHAAAAEAGRGGHAGLAAL +SGELLAFNRTVEDSHEVQRALTDQHAPVEARAALARRLLGESASPAGQLLVERAVAAPRG +VKPAAAVRQAADVVAERQRQWIAEVTVARPLGAEQQERLALGLRRAFERDLVMDVTVDPH +VVGGIRVQVGDDVVDGSMASRLNDLQRRMAG +>MOLHKGIG_00794 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL +LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAIRKAADAVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG +>NAFOICDF_02030 +MMTGASGDSLTASLESVRTVLDEGGVALARELFAALDVVDQQGALRRALTDPAWSTERRH +GVLDSLFGGRVSPGALQVLKDLAGRRWSAERDFGDALEAVAADAAAGEAARGGHAGLAAL +SGELLGFQRVFQDSHEVERALTDQRAPRESRSGLARRLLGAQASPAAVLLVERAVTDGRG +VKPATALRSYADVVATRQRQWIAEVTVARPLEDGQRERLAAGLRRAFGRDLVLDVNVDPT +VVGGIRVQVGDDVIDGSMASRLNDLQRRMAA +>MHAAABBN_00525 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL +LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAIRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG +>LFPAFLNI_00761 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAAHAAAAEAARGGHAGLAAL +SGELLAFNRTVEDSHEVQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAVRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGIRVQVGDDVVDGSMASRLHDLQRRMAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001463.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001463.fa new file mode 100644 index 0000000000000000000000000000000000000000..fdad48e76959cc5e1de878b9ea48d6c1a0e8ebf4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001463.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02140 +MLTLVLANASFVPPTISDGNLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +QLVPGKAQWLAESGYSFVRNGIAKDILGEKNFRQWVPLLFAIFFFVLLNNLFGAIPVLQL +PSFSHAGAAYGIALIVYAIWIGVGLKRHGIRYLKLAVVPSGVPSWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVIIGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>MOLHKGIG_00791 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>NAFOICDF_02033 +MLPLVLANAEFVPPSVSDAHLPDLLPWGAEYGTGFGKQMLLVLLSVVLITGFFAWAMRKP +KLVPGRAQWIAESGYAFVRNGIGRDVMGEKHFKQWVPLLFAIFFFVLLNNLFGAIPLLQM +PSFSHAGSAYAIALIVYAIWIGVGVKHHGVKYFKLAVVPSGVPGWILPLLVPLEFISNFI +VRPLTHSLRLMAVMLAGHMIVMLAGAGAAFLITQTGNPLLAGTGVLVILASVALYLLEIL +LMYLQAFVFTLLTALYIQGAIDANDH +>MHAAABBN_00522 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>LFPAFLNI_00758 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFSIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001464.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001464.fa new file mode 100644 index 0000000000000000000000000000000000000000..6aeb94a89a77418e4d263e970370ecddc199767f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001464.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02141 +MSPRTAPDAAPRSARARRRPRRRRWENRRGWWGILAWSLAATAAAVAVVCAVALAAGGPD +AAASALLGGGAVLVLSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGTVPRPD +WILPDAAAIAALVAILVWQGVEVLVFARTRRGIYAD +>MOLHKGIG_00790 +MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV +LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL +VTILVWQAAEVLVFARTRRGIYAD +>NAFOICDF_02034 +MTASARPARRRWENRAGWWGILRWCCAATAVGVLACGAVAAVLHGGPAGLSALTGGGAVL +VLSALTGATTAVAWDRARAAALPLSVGAFVVKLVLYALLLATLRMPEWMSGTAVAVGALV +GVVVWQAVEVLVFARTRRGIYAD +>MHAAABBN_00521 +MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV +LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL +VTILVWQAAEVLVFARTRRGIYAD +>LFPAFLNI_00757 +MTGAGGRRRRRRWENRRGWWGILGWSLAAAGAALAITCAAWLLSAGGEAAGSALLGGGAV +LALSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL +VTILVWQAAEVLVFARTRRGIYAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001466.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001466.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d47abff1a5cbd85cd9c82bda239cc2850c51efb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001466.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_02143 +MSAADESEPWGQALRRATGLLAEAGVDSPRVDAELLLAHVLGLGRGELLARVFAGAAGTA +GEAERFAALVARRARREPVQHLTGVAFFHGLDLAVGPGVFLPRPETELLVDAVLAELTAR +PAAATVVDLCTGSGAIAAAVSAWAQEHGRDVAVIAVELDDEAAGWARRNLEPRGVYMRQG +DALVALPELEGRVDVVVSNPPYVPEAETPVQAEARLDPARALYGGDAAGLRIPQAIAHRA +TELLVPGGLFAMEHHETQGPALLGALDADPRFTGVCVHQDLTGRDRFLTARRSCEAAAAA +EDGRMADVSDFIDVSDPAALEDAVARAREVLGDCGCVVLPTDTVYGIGADAFSPRAVAVL +LAAKGRGRTMPPPVLISDRRVLAGLAYDVPDEAEALAERFWPGALTLILKSQPTLTWDLG +ETRGTVALRVPDDAVARELLYAVGPMAVSSANRTGMPAATTAEEARGMLGESVDLYLDAG +PREDRAPSTIVDCTVTPFRVARQGAVPLEALRELVPDLLAEGEEPPVPADRLAAEPVAEA +PAPTPAPDGDDAADRAGREA +>MOLHKGIG_00788 +MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK +GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG +TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES +RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD +REA +>NAFOICDF_02036 +MSEFIDVSDPSDLTAAVERARAVLADRACVVLPTDTVYGIGADAFSPTAVAVLLAAKGRG +RTMPPPVLISDRSVMAGLAYDVPEAAEELAERFWPGALTLILRSQPTLTWDLGETRGTVA +LRVPDDAVTRELLYAVGPMAVSSANRTGMPAATTARGAEEMLGESVALYLDGGERATQEP +STIVDCTVTPFRVARQGAVSLEALRAVVPDLVAEGEEPPVPAELTTPPAAPEA +>MHAAABBN_00519 +MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK +GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG +TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES +RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD +REA +>LFPAFLNI_00755 +MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK +GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG +TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES +RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAAERIAAADDAAAARPA +DPEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001471.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001471.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c4e7340e46061cd33ed6525fb8eed741793750a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001471.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02148 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRNTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLAGDRVTRVMGIANGTTNYILDKMDSEGAG +FDEALAEAQRLGYAEADPTADVEGHDAAAKAAILATLAFGAPYTLDQVAVSGITAITAED +NEAAADAGYVIKLLAIAERARAADSAEGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVAELPALDPAEAVTSCLV +VLRVADEPGVLRRVAGVFEEQGVSIETLRQVQSDRDDAPGASLRLITHRARQRDLDATVE +ALAALDAVHEVASVLRVEGN +>MOLHKGIG_00782 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN +>NAFOICDF_02042 +MAEPTASAAQTAPAPARDALRVALLGGGTVGSQAARILTEDAAVLADRVGVRLELTGIAV +RDTAAVRDWQADPSLYTTDAEALVDGADLVIELMGGIEPARSLIRRALQVGTSVVTGNKA +LLAEHGEELYRLASETGAQLSFEAAVAGAIPILRPLRDSLSGDTVNRVMGIANGTTNFIL +DRMDTEGASFADALAEAQRLGYAEADPTADVGGFDAAAKAAILATLAFGSSYTLDQVSVE +GITEVTAEDNAAAADAGYVIKLLAIAERDTARDGTAGAILRVHPTLIPREHPLGSVRGAY +NAVFVEAENAGQLMFYGPGAGGAPTASAVMGDAVAIGQRIVRGGPARLRTPVAALPALDV +SEARTSCMVVLRVADQPGVLRRVAGVFEEHGVSIETLRQVQGADDAAGASLRLITHRARQ +RDLDDVVAELTTLDAVHEVASVLRVEGN +>MHAAABBN_00513 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN +>LFPAFLNI_00749 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGVEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001474.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001474.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab59225d09e4ceb5a0fae4dd747bf56b135b50e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001474.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02151 +MTAAPDPADREPRDLTALSDTQLQRFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV +LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH +RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP +GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV +DALTMRFRELRLVADPERTPVTDLSAHADQAPGSDDAGAPGSAEACGAAGGEIDPATLAA +LLADPARAASLTLLDVREDWERRLRRVEVPAAVADRHVPLDAVLAEPAAHAPGPDRVLVV +YCAAGARSARARDAVVAADPSAGERVLSLVGGLAAWPA +>MOLHKGIG_00779 +MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV +LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH +RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP +GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV +DALTMRFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAA +LLADPARVASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAALAPGRDRVLVV +YCAAGARSARARDAVVGADPSAGGRVLSLAGGLAAWPA +>NAFOICDF_02046 +MSRPAGEPLVPEDRAPHSLDELSDTQLQRFARHLGLDGFGPEAQLALLRSRVLVVGAGGL +GAPVLTYLAAAGVGEVHVVDDDVVDRSNLHRQVIHVETDLGRPKTASAAETMRGLHPEIR +VVEHRQRLAAANALELVGAVDLVVDGSDNYATRYLVADAGEITGVPVVWGAILRFAGQVS +VFAPGGPLYRDVFPEEPEPGDVPTCAQAGVLGVLPGIVGSLMAAEAVKLLAGVGEPLTGR +LLSVDALTMRFSTLRLVPDPERTSVTDLSAHTVPRGGADPVESGEITPAGLAALLADPER +AAALTLLDVREDWERGLARISAPAAAEDRHVRLDEVLADPAAHSPESGRTVVVYCAAGAR +SARAREAVVAAAPEAADRVLSLAGGHAAWADRN +>MHAAABBN_00510 +MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV +LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH +RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP +GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIVGSLMAAEAIKLLSGVGEPLVGRLLSV +DALTMRFRELRLVTDPERTPVTDLSAHAAQAPRPDDAGAPGSAEACGAAGEEIAPAALAA +LLADPARAASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAAHAPGQDRVLVV +YCAAGARSARARDAVVGADPSSGGRVLSLAGGLAAWPA +>LFPAFLNI_00746 +MTAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPVLTYLA +AAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEHRERLT +ATNALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAPGGPLY +RDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSVDALTM +RFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAALLADP +ARAASLTLLDVREDWERRLRRVEAPATVADRHVPLEAVLAEPAALAPGQDRVLVVYCAAG +ARSARARDAVVGADPSAGGRVLSLAGGLAAWPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001475.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001475.fa new file mode 100644 index 0000000000000000000000000000000000000000..dec84ec6a91c375346124bab32667aa6b45b66a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001475.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02152 +MAEHRTPPATPAIPPLRIGGYDLAARLIMGTGGITDLTALEGALVASGTTLTTVALRRWS +ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP +DVVETLEATELLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL +ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG +FHARRAGRIPRREHALASSPMAGRVTAEEDER +>MOLHKGIG_00778 +MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS +ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP +DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL +ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG +FHARRAGRIPRREHALASSPMAGRVTAEEDER +>NAFOICDF_02047 +MAPHDTTERRRAREASTAVPPLRIGGYELSSRLIMGTGGITDLAALEGALVASETTLTTV +ALRRWSTDARDGLIALLDRLGIDVLPNTAGCRTARDAVLTARLGREALETELVKVEVIAD +DRTLLPDVVETLDATEQLAAAGFTVLAYTSDDPAMALRLEHAGAAAVMPLGSPIGSGLGI +LNRTNLELIVSRAGVPVVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR +LALEAGYHAHRAGRIPRRLHALASSPMAGRIGGAEERA +>MHAAABBN_00509 +MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS +ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP +DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL +ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG +FHARRAGRIPRREHALASSPMAGRVTAEEDER +>LFPAFLNI_00745 +MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS +ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP +DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL +ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG +FHARRAGRIPRREHALASSPMAGRVTAEEDER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001479.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001479.fa new file mode 100644 index 0000000000000000000000000000000000000000..c3817112fad82f9d1a20628dae3e2db5fc62e79d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001479.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_02157 +MLSIAGSDSGGGAGVQADLKTIAVWGGYGMTAITAITAQNTQGVQAVHPLPVDVVRAQLD +SIAADIAVDAVKIGMLGTAELMGAVAGWLEETRPAVVVLDPVMVASSGDALTAVGDDDGR +AAWSRLLRAAHLVTPNLPELARLTGRDSTDWEAALDAAGGLAAEHEVTVLLKGGHLDEAA +AAEVPDAVVRVAGAVHEVRGPRVATRASHGTGCTLSSALATLAGAGLSWEDALERAKPWL +ADAMRAGEALAVGDASRPTWHGPVDHGHARRG +>MOLHKGIG_00773 +MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD +VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA +VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG +GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS +WDDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG +>NAFOICDF_02052 +MAPSPSTPPSSSPAAEGPAVPRVLSIAGSDSGGGAGIQADLKTIAEWGGYGMTAITAITA +QNTQGVQAVHPLPAEVVRAQLDSVASDIAVDAVKVGMLGTAELMRVVADWLEEARPAVVV +VDPVMAATSGHALTPVGDAEAHAAWGRLLRAAHLVTPNLPELARLAGRPLDSWAAALDAA +RELAAAHAVTVLAKGGHLADLTRADPEGAEAGDDPDAEGGVPDALVRPDGSVHEVRGPRV +ESGATHGTGCTLSAALATLAAGGLGWEDAIERAKPWLAQAMVAGEALAVGDRTRPTWHGP +VDHGHARRG +>MHAAABBN_00504 +MTPAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD +VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA +VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG +GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS +WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG +>LFPAFLNI_00740 +MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD +VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA +VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG +GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS +WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001480.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001480.fa new file mode 100644 index 0000000000000000000000000000000000000000..a71eca9ef99ccdfc266f33e61e7e7ea5ee86fa01 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001480.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02158 +MSPVTESSPAHRGRAEESAPLRPTSRLGIAATFIGTTIGAGYASGNEILQYFVSFGFWGG +TLALVIAGALFFLLSAIVLKMAQKLRTTDIHRLVNPTTSRVPTWFADLCITASLLGTLVI +MLAGAGAAVNTSFGLPTMVGSLLMAAVCVLSVLAGISGLVRVQAVVVPLIIVVAVGVAWW +GLANPGAPVEDVASLVTSSPLINQWWMSGILYVAFNFQLAYAVLAPIGRDSSSSGRTLVA +GAGLGAVGLVVMAGAIMFAMAAHAHLIGRADLPMVELAAMIGGWAALVYTVILLLAQFTT +AVSCLFGGVERIALLSPLRRVPGWAIAVATALAATLLSSVGFSDLVGTVYPVLGYAGIAI +IVMLIITWIAERTLVRRRAARAARA +>MOLHKGIG_00772 +MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLSITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMATVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGLVI +IVMLVVTWIVERSTVRRRAARAARA +>NAFOICDF_02053 +MSHVAQSTHENRPAQDGGNGLRPMSALGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGVLFFLLSAIVLKMAQQLRTTDIHRLVNPTSSRIPTWFADLCITASLLGTLVI +MFAGAGAALDTWLGLPAWAGAALMAAVCVLTVLGGISGLVKVQGLVVPLIILVAVGVAWW +GLTHPGAGADDVASLVTSSPLINTWWMSGILYVAFNFQLAYAVLAPIGKGSSSPGTSLVA +GAGLGAIGLVVMAGAIMAAMGAHATLIGRAELPMVELAGMVAPWVAAVYTVILLLAQFTT +AVSCLFGGVERIALLSPLRDVPGWLIAVVTAVVAVLLSSVGFSDLVGIVYPVLGYAGIAI +VAMLIATWILDRTLVRRRAARADRA +>MHAAABBN_00503 +MSHVTESSPAHPGRAEESTPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAALTVHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWAIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI +IVMLIVTWIVERTTVRRRAARAARA +>LFPAFLNI_00739 +MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI +IVMLVVTWIVERSTVRRRAARAARA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001481.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001481.fa new file mode 100644 index 0000000000000000000000000000000000000000..3f2edf4d68a8e9a4d48564461ad4369b3632c26a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001481.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_02159 +MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL +TVYRTMGPGSVPEHGLPAQRAEWIRARGDVEEYEGRDRDLLDDGRSAVRRGAASQEWAGE +RRAPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP +ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE +WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV +PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYEHYDELCEIFARYDVAFSLGDGLRPGSV +ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT +LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA +HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC +SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPTLRGAAD +A +>MOLHKGIG_00771 +MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL +TVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE +RRPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP +ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE +WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV +PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV +ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT +LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA +HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC +SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPSLRRPEG +DAVLARD +>NAFOICDF_02054 +MSASHHTPVPPQSEAVPTAEENYPTHRLGWLEDAEHGIRVPVTHVHQDDSPDGTPNPPFA +VYRTMGPGSVPERGLPAQRAEWIAARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGER +RPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDAELVRSEVAAGRAIIPANVNHPE +SEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTREW +ILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHVP +LSADRVTGIVSRGGSIMAGWCLGHHRENFLYENYDELCEIFARYDVAFSLGDGLRPGSVA +DANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYTL +GPLVTDVAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAAH +AADVAKGHPGARDRDDALSTARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFCS +MCGPKFCSMRISQDIRSEFGGESEQARIAEAGMAAKSAEFRAAGGSVYLPEPSMRRPEGD +AALAAD +>MHAAABBN_00502 +MSVSEHTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL +TVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE +RRAPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP +ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE +WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLCHV +PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV +ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT +LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA +HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC +SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPSLRRPEG +DAVLARD +>LFPAFLNI_00738 +MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNPPL +PVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE +RRPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP +ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE +WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV +PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV +ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT +LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPDRDDVKTGVITYKIAA +HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC +SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPTIRTASD +A diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001482.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001482.fa new file mode 100644 index 0000000000000000000000000000000000000000..246ef23e51cacdf79c8137cd860749b5aac7384e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001482.fa @@ -0,0 +1,29 @@ +>ACLBLIBL_02160 +MTKEHRTDHDAGDDAGPAAPVRSAAGAAEPPAGVVVGEDGRARAPWADRDPLLRAYYDEE +WGVPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREAFAGFDPDAVAGFGPERVEELL +QDAGIIRNRAKVEAAIANAQAVVGMRDEPWTPLHPGSPGAGPGWDGPGDRPDRGLAGLVW +AHQPAATPRPGTVAEVPSASDESRALATALKARGCRFVGPTTCFALMEAAGIVDTHLLSS +WRRGASGIWE +>MOLHKGIG_00770 +MSAHHADDGLPAPVSTLAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW +GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREVFAGFDPDAVAAFGDAEVEALLA +DPGIIRNRRKIEAAVANAQAVVGMRGERFAPLHPGAPGAGPAWHGDGDRPARGLPGLVWA +HQPAATPRPETVAQVPSTSDESRALARALKAHGCRFVGPTTCFALLEAAGIVDTHLLGSW +RRGASGIWE +>NAFOICDF_02056 +MDEENSEAAGLVLGADGRARAAWAAADPLLRDYYDAEWGLPVTDERGLFERLTLEAFQSG +LSWRTVLAKRPRFREVFAGFDPDAVAAFGAVEVEALMADAGIIRNRRKIDAALANARAVV +GIRDEVFAPLHPGSPGAGPAWDGEGDRPGTGLPGLVWAHQPAQTPTPRTIGEVPSASPES +TALAKALKARGCRFVGPTTCFALLEAAGVVDTHLVSSWRRGASGIWA +>MHAAABBN_00501 +MSAHHADDGLPAPVSTLAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW +GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREVFAGFDADAVAAFGDAEVEALLA +DPGIIRNRRKIEAAIANAQAVVGMRGERFTPLHPGSPGAGPAWHGDGDRPARGLAGLVWA +HQPAATPRPETVAQVPSASEESRALARALKAHGCRFVGPTTCFALMEAAGVVDTHLLGSW +RRGASGIWE +>LFPAFLNI_00734 +MSAHHADDGLPAPVSTPAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW +GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFWEVFAGFDADAVAAFGDAEVEALLS +DPGIIRNRRKIEAAIANARAVVGMRGERFAPLHPGAPGAGPAWHGDGDRPARGLPGLVWA +HQPAATPRPETVAQVPSTSDESRALARALKAHGCRFVGPTTCFALLEAAGIVDTHLLGSW +RRGASGIWE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001484.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001484.fa new file mode 100644 index 0000000000000000000000000000000000000000..54ec287ec9abbd8c9aa9931c29bac17685e8316c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001484.fa @@ -0,0 +1,121 @@ +>ACLBLIBL_02163 +MTETPTPPAAASSAPAIVFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMC +LALGLGEAGVIGHTQPRRIAARSVAERIAEELGEDIGRTVGYQVRFTAQTSKATRVKVMT +DGILLAEIPHDPQLRRYSVVIVDEAHERSLNIDFLLGYLRTLLPQRPDLKVIITSATIDP +ERFARHFGRALAEGEEHEDAVPADDGGLVVPAPVIEVSGRTYPVEVRYRPLTGEPSPDDP +EDDSDDAAETRDPLDAIGEAVLELAAEPPGDILVFLPGEREIRDAADHLSGVVASSKRLA +GTEVLPLFGRLSMAEQHRVFGRAAAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISR +YSHRTKVQRLPIERVSQASANQRAGRSGRTSPGIAIRLYSEEDYLSRPEFTDPEILRTSL +ASVILQMLSLGVAATPADVQGFPFVQPPDGRQVSDGATTLTELGALHPPRPSGAKDGHDG +GRGRGGRAPEPGTITPIGRRLARLPVDPRLGRMILESGERGCVREVMVLAAALTIQDPRE +RPVEQREAADELHRRFADENSDFSAILNLWAYLQEQQKELSGSQFRKLCRREHINWLRVH +EWQDLVRQLRQLAKDVGVAVHAGPVDPVGQHEAVHRSLLTGLLSQIGSYDERRREYAGAR +GTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEAAGGLVKRTYNEPH +WSRRAGAVVAREKVTLFGVTLIPDRSVKYGRIDPELSRELFIRHALVEGDWRTRHRFFAR +NRAALEEVDALETRLRRRDLRIGDEDLFAFYDARVPANVVSERHFDAWWKKARQERPDLL +DLDVAALLTADAEDLDTDAFPTVFPYPLSGGDVDLDLEYTFDPTGASGTDGVTVSVPVLL +LNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKQLVPAPDVARQLVADLDAHADPLADE +LTEALSAAVRRVRGIVVEPGLWAPDAVPAHLRMDYRVVDARGAVMGAGQDLAALQARLAK +ANRSAIAARLAGTDDPANARPGPGRQGGRRDGGGNDGGAGRRGSGRGVRGRGRDGTGRPE +AGAQGAGGAAAAFAERHGLTSWSIGTVPRRITTDPGARGPAITGYPALVPETTAEGGPAA +GLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVAD +CSQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTRLVEQVLSRAAEVRRRLKGS +VSLAMAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILVRLDRLDAGGHLQRDG +QHMAVVQRLEDEFDAAVQAHRARFSGVPVPADLERVRWLIEELRVSFFAQELGTAVSVSE +KRVRQALAQAARA +>MOLHKGIG_00766 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT +TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA +TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII +TSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVV +AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT +GTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDGIAIRLYSEEDYLSRPEFTDP +EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA +GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE +LHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ +LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSA +LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR +EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL +ETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTAD +AEDLDTDAFPTTFSYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW +LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPEALSAAVRR +VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA +GTDDPASARPGPRGTGRGGRAQADARAGAEGRRRPEGPGRSGATPAFEERHRLTSWSIGT +VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT +LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD +RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA +ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG +TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA +>NAFOICDF_02059 +MTDFPQPPAAAPVITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLAL +GLGGAGVVGHTQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGI +LLAEIPHDPDLRKYSAIIVDEAHERSLNIDFLLGYLKRLLPRRPDLKVIITSATIDPERF +ARHFGTEDEPAPIIEVSGRTYPVEIRYRPLTEEPSPDDPDDDADDHAETRDPIDAVGDAV +LELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSMAEQHRVFG +RAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASAN +QRSGRSGRTSDGIAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMD +FPFVQPPDSRQVTDGAATLTELGALHADAPTRGGGRGRGKGAGNRSAAGTITDIGRRLAR +LPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAADELHARFADDRSDF +SAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPG +PVDPVGKHDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAA +ELVETSRLWARAVARIEPEWIEEVAGDLVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVP +ERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDELETRLRRRDLRVG +DEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTA +FRYPLPGGDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTA +LIKALPKAVRKNLVPAPDVARLLVEDLDAHADPLRDELPAALSSAVRRVRGAVVEPELWR +LDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARLAGTDDPRNARPGQ +GAGRGRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLTSWTVGEVPRQITT +APGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRY +VLDHLDNKEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLI +DTVFAVTALVEQVLSRAAEVRRRLKGGVSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQL +QHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAHRSRFPGTPVPAEL +ERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG +>MHAAABBN_00496 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT +TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA +TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII +TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV +AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT +GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP +EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA +GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE +LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ +LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSA +LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR +EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL +ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD +AEDLDTDAFPTTFAYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW +LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR +VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA +GTDDPASARPGPRGTGRGGRAPADARAGAEGHRRPEGPGRSGATPVFEERHGLTSWSIGT +VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT +LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD +RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDSVSLALAPALSDVKAHLEQLVFPGFVA +ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG +TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA +>LFPAFLNI_00730 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT +TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTTQTSKA +TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII +TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV +AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT +GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP +EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA +GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE +LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ +LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYVGARGTRFAVFPGSA +LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRTYNEPHWSRRAGSVVAR +EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL +ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD +AEDLDTDAFPTTFTYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW +LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR +VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA +GTDDPASARPGPRRTGRGGRAQADGRAGAEGRRRPEGPGRSGATPAFEERHGLTSWSIGT +VPRTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSADDQAAWHRAGVIRLLLAT +LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD +RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA +ATGWERLQHLPRYLQGILTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG +TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001486.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001486.fa new file mode 100644 index 0000000000000000000000000000000000000000..f2a7f54647bada28f9ef2084e7fc5f84cec61d66 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001486.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_02165 +MWGIDDGDTVVVYDDDRGLSAARAWWLLRHAGLRDSMLLDGGLAAWRAGGLPLQPGEVIP +MPGSARTSWGRMPVVDTAGAEAMASGGLLLDARAAERYRGETEPIDPVTGHIPGARSLPT +AGSLAEDGRLRPAEELAARFDAVGVDDETPVAVYCGSGVTAAHAVLTLAVAGRPGVALYP +GSWSAWIQDPSNAVAVGPDPHGEPGRD +>MOLHKGIG_00764 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQARVVPAPTAAPSSSHDAGGDPDADTDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPEGPAYAQPGRCRPNRVILLDVRFRATAG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSMLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPDGASGRD +>NAFOICDF_02061 +MKDSTEGRPPSPASSPAADAPTDQTPLAELAEDATAPDPAAAEPPSLVDVGVLAGWLGLT +PAEPVPAPPPGPVFDRRVDPGRVILLDVRYAVAGAGGSGHDAYLRGHLPGAVFVSLPNQL +AGHAGPRQGRHPLPDPVQFAHSLRMWGIDDGDTVVVYDDDRSLAAARAWWLLRHAGLRDS +VLLDGGLGAWRAAGLPLQPGEVIPQPGSVHPSWGRMPVVDTDGAEAIAAGGLLLDARSAE +RYRGEEEPLDPVAGHIPGARSLPTSGNVAADGRLLDPAALAARFEDAGLSDEVPAAVYCG +SGVTAAHQVLALAVAGRHGVALYPGSWSAWIQDPDRPVATGPRPEGD +>MHAAABBN_00494 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDADIDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFRATGG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPDGASGRD +>LFPAFLNI_00728 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDADIDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFRATGG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNAPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPYGASGRE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001487.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001487.fa new file mode 100644 index 0000000000000000000000000000000000000000..08cf1baa19708d1e9aa46ea4434c7bc6ada10f22 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001487.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02167 +MSAPDPGPRVVRPRATRQKAAVDRALETIPDFVSAQELHARLQEEGERISLATVYRTLQQ +QLEDGQVDVLRREDGESVYRRCEARGHHHHLVCRLCWSTVEVTAPPVEAWAARIAAEHGF +TEAEHTVEITGVCADCAATRAADAG +>MOLHKGIG_00763 +MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT +LQQQLDDGLVDVLRRDDGESVYRRCEDEGHHHHLVCRSCWTTVEVTAPHVEAWATAVAAE +HGFTDADHTVEITGVCARCRTEGRTRGA +>NAFOICDF_02062 +MSETPGRPSEAPAPRGRSTRQKAAVDGALDAAEDFVSAQELHARLRDAGERVSLATVYRA +LQQRLDEGTVDMLRREDGESVYRRCAAEGHHHHLVCRVCWTTVEVTAPGVEEWAARMAAE +HGFSDPDHTVEITGVCAECRAAGRG +>MHAAABBN_00493 +MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT +LQQQLDDGLVDMLRRDDGETVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE +HGFTDADHTVEITGVCARCRTEGRTRGA +>LFPAFLNI_00727 +MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT +LQQQLDDGLVDMLRRDDGESVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE +HGFTDADHTVEITGVCARCRAEGRTRAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001488.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001488.fa new file mode 100644 index 0000000000000000000000000000000000000000..d0fd293bdcae8946a9ce54886e8f31d18bb99054 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001488.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_02169 +MDWLIEPFLLGFQQRALVGGLIAAALCAVVGTWLVLRGMSFFGDAFVHGVMPGIALSVVL +GFDAHLGAALAALVMLAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISLSDSYTGSLT +AILFGDALGVTWEGIVRQAVIAALVLVLALVLYRPLMALSFSPAKARSLGMRPRLTHALL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALAVLLGAAGVTIGLVLS +YHLGTAASATMALVPIAMFFVVLAGRAGLRALRSRRVRADRRRAVVETPSRRSVSP +>MOLHKGIG_00761 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQRERETPVVALPGAEVAR +>NAFOICDF_02064 +MDWLIDPFLLGFQQRALLGGLIAALMCSAVGTWLVLRGMSFFGDAFVHGVLPGIALAVLL +GGSPHLGAALAAVLMMGGISLVHRTTTLKEDTAIGLLFVGMMALGVVIISLSSSYTGSLT +AILFGDALGVTPENLLVQAAIGVVVVVLALVLYRPLLALSFSEAKSQALGMRPRLTHTLL +LVLIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALSAGIGALSVVAGLVLS +YHWGTAASATMALVPVVLFFVVLLGRSAVQAAAGRRRRTRGAASAPTPAGDDDAESRRET +EGSPAR +>MHAAABBN_00491 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAPR +>LFPAFLNI_00725 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001491.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001491.fa new file mode 100644 index 0000000000000000000000000000000000000000..ffb44a681d5ff7755327bff9143c35164827bd65 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001491.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02172 +MEWLLLILGFALVLGTGFFVAVEFSMIAIDVPTVQRMVDEGDKGAEPLLRCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLIDPVLLDVGVPESVVGTVSLVVAMVVATLLSMLIGE +LIPKNMAIAEPMTIGRALARPQLLFSTVFKPAILVLNGFSNGVLARFGIEAKEEISGARS +PEELSSLVRRSAQLGTLDEQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQPLPEVVD +LARRTGFSRFPVIGESSDDIRGVVHVKKVVAVPRERRADLEAGSLMTEVIRVPETVHLDQ +LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDKVTPGVLQTAAGRWYF +PAELRPDEAQAQITSLSVPEDGAYETIGGFIMARLGRLAAVGDVVSVDGGTLSVERMDGR +RVERVRFDPAAAADKEARA +>MOLHKGIG_00758 +MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE +LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS +PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD +LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ +LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF +PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR +RIERVRFDPAAEDEETRA +>NAFOICDF_02067 +MEWILLILGLLLVLGTGFFVMVEFSLIAIDAPTVQRMVDDGDRSWEPLLTCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLVDPLILAVGLPQSVAGPVSLVVAMAAATLLSMLLGE +LVPKNMAIAEPLRLGRALARPQLVFAAVFKPAILVLNGFSNGVLHRMGLEAKEEISGARS +PEELSSLVRRSAQLGTLDEQTATFLDRTLRFAERTAADVMTPRIRMETVGEDDGLLDVVE +LARRSGYSRFPVIGESPDDVLGVVHVKKAVAVPMDRRADLTAGALMTDVIRVPETVHLDQ +LLAELREASLQLAIVVDEYGGTAGVVTLEDVVEEIVGEVSDEHDRVTPGVLQTASGRWYL +PAELRPDEAHAQIKALDVPEDGAYETIGGFVMARLGRIPAVGDVVPLDVGTLTVERMDGR +RVDRVRFDPRPVTEEARA +>MHAAABBN_00488 +MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE +LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS +PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD +LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ +LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF +PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR +RIERVRFDPAAEDEETRA +>LFPAFLNI_00722 +MEWLLLILGLLLIAGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE +LIPKNMSIAEPMTIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS +PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQALPEVLD +LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ +LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF +PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR +RIERVRFDPAAEDEETRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001492.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001492.fa new file mode 100644 index 0000000000000000000000000000000000000000..4acacc27f0f5e96e53620ee2fa3647e2915b39f2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001492.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02173 +MRFLTSPTVDLTYNDVFLVPSHSEVTSRLDVDIAPDDGTGATIPLVSANMTAVTGRRMVE +TMARRGGLGILPQDIPVEVIAEVVRRVKSAHPVADTALTVGPQDTVLDLLHLVDRRNHGA +VCVVDADGGLLGVVRPRDCEDVDRFASAASVMQPASVTLTPAELGEAGGADGGQALRAAF +DRLNAAGQDMAPVVEPAAGSAAPALRGVVTAAGLLRSSLFTPSLDDAGRLRVGAALGVNG +AVGDKAAALVEAGVDVLVVDTAHGHQQSMLDALAAVRALDAPVPVVAGNVVSADGVRDLV +EAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECSAAARDLGARVWADGGVKHPRDVA +LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA +RKAMFEEGISSSRMYVDPRRPSVEDLIDTITSGVRSSLTYAGAQDLAQFRERAVVGVQSA +AGYEEGRPVASSW +>MOLHKGIG_00757 +MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE +TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA +VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPAVTLTLAELGGTDGAPDKDALRAAF +ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING +AVGEKAAVLVEAGVDVLVVDTAHGHQQTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV +AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA +LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA +RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA +AGYEEGRPVASSW +>NAFOICDF_02068 +MRLMHEPAVDLTYNDVFLVPSHSEVGSRTAVDIAPDDGTVGSVPLVSANMTAVTGRRMAE +TLARRGGLGVLPQDVPVDVVAKTVAAVKAAHAVADTALTVDAHATVLDVLHLVDRRAHGA +VCVVDDDGRLLGVAGAEDCGDVDRFASVVSVMRTPSVLLSPADLEGPDAPRAAFEVLHAA +GRPLAPVVEDPVADRPVLRGVVTGQGLVRSSLAAPALDASGRLQVGAALGVNGDVGSRAA +ALLAAGADVLVVDTAHGHQRVMRDALAAVRALDPEVPVVAGNVVTAEGVRDLVAAGADVV +KVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAAREVGARVWADGGVKHPRDVALALAAGA +SQVMIGSWFAGTLESPGDLVQGSDGRRYKESFGMASARAVEHRTRDEDAFSRARKAMFEE +GISSSRMYVDPRRPSVEDLVDGITAGLRSSLTYAGAANLAQFRERAVVGVQSAAGYEEGR +PVPASW +>MHAAABBN_00487 +MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE +TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA +VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPVVTLTLAELGGTDGAPSKDALRAAF +ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING +AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV +AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA +LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA +RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA +AGYEEGRPVASSW +>LFPAFLNI_00721 +MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE +TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA +VCVVDAHGGLLGVVRPQDCVGVDRFASATSVMHPPAVTLTLAELGGTDGAPSKDALRAAF +ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING +AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV +AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA +LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA +RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA +AGYEEGRPVASSW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001493.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001493.fa new file mode 100644 index 0000000000000000000000000000000000000000..9e2d290fb18e025b82a61d82aad30b0627500c1a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001493.fa @@ -0,0 +1,110 @@ +>ACLBLIBL_02174 +MLRKRRYTVPELTSDRLAQEFPGNERLVAEIYRKYRADSGSVDRQWAQIFARLEASAPAP +AEKAPAQAAAKAAPKAEPQAEAKVTEPKAKPAPARGAQPKETSTSTGPKVKKTPAAQAVP +SEPADPSKDAAKEEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDVPAKVLIDNRVVI +NSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLP +RPDGSRSLVVPNVKAAETLDFRGFWQAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGT +VHSVPRLSKGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSG +EFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQDLQVNPEEQVGKVARVQQLIHAYRD +RGHLMANVDPLEYSMPYHPDLDIREHGLTLWDLDRQWPTGGFGGASTLTLRKILGVLRDA +YCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIG +QKRFSLEGGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYGQVFREFE +GATPGGTSGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRL +DLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTP +PTQARSAVYSTDVAKTIQAPILHVNGDEPESVMHVAELAFEYRQRFNKDVVIDLVCYRRR +GHNEGDDPSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFA +ETHEGSASSGGEGIRPAEDRDQAPEAPETTAISAETLRAIGQAHIDVPEGFTVHPKLAAL +LERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDE +WAPLKNLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFINGAQTIID +EFISSAEQKWAQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPTTGANHF +HLLREQAYARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDPKKVTRVQL +VSGRLYYDLLARRNKDGDETTAIVRVEQLYPLPLDELRAALEAYPQAEVVWVQDEPANQG +PWPFMALNLLPQLDREVRLVSRPASASTSAGTKGRHDQELSTLLDAGFAR +>MOLHKGIG_00756 +MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA +KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT +ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART +RGGKVSFTHFIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA +LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL +SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH +GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN +VDPLEYSMAYHPDLDIREHGLTLWDLDRKWPTGGFGGAGSLTLRKILGVLRDAYCRTIGV +EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE +GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA +SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP +DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVVVNNQVGFTTPPTQARSA +VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD +PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP +ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM +AVDGGIDWGFAELAAFGSLLMERVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLRHL +SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD +QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA +YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGGFQPVIPDAGVDAKDVTRVLLVSGRLYY +DLLARRQKSGDTSTAIVRVEQLYPLPLDEIRKALRAYPVADVTWVQDEPANQGPWPFMAL +NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR +>NAFOICDF_02069 +MPELTSDRLSQEFPGNEDLVAQIYRKYREDQGAVDRQWAQIFARLEASQPQPEPAAAAPK +ATSSATAEPAPAVKPAVKRGAATPADPQAAAKKSGPTDVSAPAQRKRSVSEAVPSEPARD +AAAGASEKQDKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKLLIDNRTVINSHLART +RGGKVSFTHLIGYAVVRALKAMPSMNTLYEERDGKPTMVEPAHVNFGLAIDLPKPDGTRA +LVVPNIKAAETLSFRQFWEAYDDLVKRGRANKLTMDDYAGTTVSLTNPGGIGTVHSVPRL +SKGQAAIIGVGALTYPAAFQGAAESTLNSLAISKTITLTSTYDHRVIQGAGSGEFLKLIH +GYLLGEDGFYDDVFHDLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN +VDPLEYRMPTHPDLDIREHGLTLWDLDREWPTGGFGGADTLTLRRILGVLRDAYCRTVGV +EYMHIQNPAERAWFQDKLERPYEKPSREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE +GGESLIPLLDSILGDAADEGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA +SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVARAKQDRLEAAGESG +AAFPVLPILVHGDAAFAGQGVVTEVLNLSQLPGYRTGGTIHVVVNNQVGFTTSPAEGRSS +VYATDVAKTIQAPILHVNGDEPESVLRVARLAYEYRQRFHKDVVIDLVCYRRRGHNEGDD +PSMTQPRMYTLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETHAAET +GQAVATTGLEPARDRDAARPAPSTTAISPDTLRRIGDVHLEVPEDFTVHPKLSQLLEKRA +KMAVDGGIDWGFAELAAFGSLLMEGVPVRLSGQDSQRGTFTQRHSVFHDRVTDETWTPLN +HLSESEAPFWVYNSLLSEYAVLGFEYGYSVERSDALVLWEAQFGDFINGAQTMIDEFISS +AEQKWSQNSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSHGANHFHLLRE +QAYSRPRRPLVVFTPKQLLRLKAAADPVEAFTQGGFRKVIGDASVDAAQVERVILVSGRL +YYDLLARREKSGDTSTAIVRVEQLYPLPAEEIRAELAKYPGAQVRWVQDEPANQGPWPFM +ALNLLPQLDREVTLVSRPALAATSAGTKGRHDEELSTLLDTAFGA +>MHAAABBN_00486 +MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA +KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT +ATTTADEKQEKATVLKGMAKAVATNMDASLSVPTATTVRDLPAKVLIDNRVVINSHLART +RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA +LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL +SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH +GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN +VDPLEYSMAYHPDLDIREHGLTLWDLDRQWPTGGFGGASSLTLRKILGVLRDAYCRTIGV +EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE +GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA +SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP +DSFSVLPILVHGDAAFAGQGVVAEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA +VYSTDVAKTIQAPILHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD +PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP +ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM +AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITDETWAPLKHL +SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD +QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREQA +YARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDVTRVLLVSGRLYY +DLLARREKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL +NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR +>LFPAFLNI_00720 +MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAAAAEAEPKAAA +EAEPKAAARAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKAKKTPAAQAVPSEPADT +ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART +RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA +LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL +SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH +GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN +VDPLEYSMAYHPDLDIREHGLTLWDLDREWPTGGFGGASSLTLRKILGVLRDAYCRTIGV +EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE +GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA +SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP +DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA +VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD +PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERAFAETHEDAP +TSGDEGIRPAEDRDAAPKAPASTAISAEMLRAIGQAHLDVPEGFTVHPKLAALLERRAKM +AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLKHL +SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD +QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA +YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDATRVLLVSGRLYY +DLLARRQKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL +NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001495.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001495.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff0f43ffaa909f8db22dc430267f96b4c2e21ec7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001495.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02176 +MTADQHGRECRDAQEDTLERLYQYLDGALTPEEIDQVRAHVEDCEDCRHQQELEQFIRTA +VRRSCQEKAPEQLRTTILTRITQLSTTRVTWR +>MOLHKGIG_00754 +MTADQHGHECRVAQDASLERLYQYLDGALTPEDIEQVRAHVAECPDCRHQKELEELIRSA +VRRCCQEKAPAQLRATIMTRITQISTTTVTWG +>NAFOICDF_02071 +MSQDGDCRGCNDGEDRLEQLYQYLDGALTPEDIDQVRAHVDQCPDCHHQQELELIIRSAL +RRSCQEKAPAQLRATIMTRITQVSTTTVRRAG +>MHAAABBN_00484 +MTVDQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA +VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG +>LFPAFLNI_00718 +MTADQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA +VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001496.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001496.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a9a64c8860a8c76d02d617bd4e439ab944eb4d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001496.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02177 +MTTALMARPDRDVDWRVMSTDNNLPEIARPADAPEHDRADIDVAAEDEQQRRARFERDAL +EFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY +RKRQRQPLEADSPEVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAIPEEFRL +AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAERGIKAQPKKTGRG +AAKKTETSTKEATR +>MOLHKGIG_00753 +MSAALLTHPSRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL +EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY +RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL +AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR +GGTKQTETSTKEATR +>NAFOICDF_02072 +MAATLLERPVLTGSRGAAVDWPAMSTQNSTPEIARPADAPALDLPGIDVDAESEAQRRAR +FERDALEFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN +TYINLYRKKQRQPLEADTDTVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAI +PEEFRLAVYFADVEGYAYKEIAEILDIPIGTVMSRLHRGRKQLRERLTDYAGERGMGPKG +RTAQETSTQEEKR +>MHAAABBN_00483 +MSAALLTHASRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL +EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY +RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL +AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR +GGTKQTETSTKEATR +>LFPAFLNI_00717 +MSAALLTHPSRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL +EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY +RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL +AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR +GGTKQTETSTKEATR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001497.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001497.fa new file mode 100644 index 0000000000000000000000000000000000000000..599828622f80e1fb1f2d1576e06d3c0918ca2858 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001497.fa @@ -0,0 +1,47 @@ +>ACLBLIBL_02178 +MTRPTPAPEDPSEHPSERPVEPLAGDVVAWPAPAARGPVRGTVRLPGSKSLTNRHLVLAA +VADGPVTLRGALVSRDSALMRAALESLGARFEDLPDGGLRVHPLPLGKPLEGEVEVDCGL +AGTVMRFVPFVAALRPGRVRFDGDAGARVRPMAPVIDALRRLGVAVHEEGEPGLLPFTVH +TPPDAATVAGGPRATEDGAPVPEAAVDAGASSQFLSGALLAAAAMPRGLRLRHTGATVPS +PEHVGMTVAVLRSLGVRVEQPDATSWTVAPGGIAAHEAAIEPDLSNAGPFLAAAAVTGGS +VTVPDWPTRTTQIGDRWRRILPAFGASVALTVDRTDRSRAALTVTGGTRPDGTPLVTGAR +DVADTAELAPTVAALALLAEGPTRLTGIGHLRGHETDRLAALAAESARFGVEVDEQADAL +GFPGTDASGPLTPAAAQTYHDHRMATFAAVVGLRVPGTAVVDVATTAKTMPDFPAMWASL +VAPAAGADEAGAL +>MOLHKGIG_00752 +MTRPTRAAAHSPAPRPDAAETWPAPVARGPVRGEVRLPGSKSLTNRHLVLAALADGPCVL +HGVLESRDTALMRTALTALGARFEPLSDGGLRVHPMPVGEPLAGDVAVDCGLAGTVMRFV +PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVNEEGEPGRLPFTMTTRADAATV +APDGDVPEVAVDASGSSQFLSAALLAAAGMPRGLRLRHTGQTVPSPEHVAMTVGVLRALE +VDVAETGPGAWTVAPGRIPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD +RWRRILPQFGASVALTVDRTDRSRGRLTVTGVVQDDGAPRITGAGEIADTAELAPTAAAL +ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGITVDEEETSLGFPGTDASGPLSPAA +LETYHDHRMATFAAVVGLRVPGTGIVDVATTAKTMPDFPALWTALVAPGDAAEEAR +>NAFOICDF_02073 +MTAPGPAAPSPTTPPCASAASRTPASAWPDPWPAPAAAGPVRGTVRVPGSKSLTNRCLVL +AAISAGPSVLHGVLRSRDTDLMRTALTALGARFEDRADGAVVVQPLPVGVPLEEPVAVDC +GLAGTVMRFVPAVAALRPGTVVLDGDAGARVRPMAPLLDGLAQTGTRVEFLGAEGFLPVR +LTTGEELGAEAAIDSSASSQFLSGLLLSAARRPAGLTLRHTGAQVPSPEHVAMTVQFLRE +HGVHVDTLEEGAWRVHPGAPAGVESAVEPDLSNAGPFLAAAAVTGGEVSVPDWPAATTQI +GDRWRSILPAFGAEVSFTPDPTDDARGTLTVRGGVDEAGRPRIAGAGELAGTAELAPTAA +ALALLASGPTHLTGIGHLRGHETDRLAAIAAEAGRFGVRVEESADALAFPGSDSSGPLRP +AEARTYHDHRMATFAAVVGLAVPGTAVQDVATTAKTLPDFPALWTALVGGEPAHDRPERD +EVR +>MHAAABBN_00482 +MTRPTRAATHSPAPRPDAAETWPAPMARGPVRGDVRLPGSKSLTNRHLVLAALADGPCIL +HGVLESRDAALMRTALTALGARFEPLSDGGLRVHPMPVGEPLAGDVAVDCGLAGTVMRFV +PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVVEEGEPGRLPFTTTTRADAATV +APDGDVPEVAVDAAGSSQFLSAALLAAAGMPRGLRLRHTGEAVPSPEHVAMTVGVLRALE +VDVAETGPGAWTVAPGRIPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD +RWRRILPQFGASVALTVDRTDRSRGRLTVTGAVHDDGAPRITGAGEIADTAELAPTAAAL +ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGITVDEDETSLGFPGTDASGPLSPAA +LETYHDHRMATFAAVVGLRVPGTGIVDVATTAKTMPDFPALWTALVAPGDAAEEAR +>LFPAFLNI_00716 +MTRPTRAAAHSPAPRPDAAETWPAPVAHGPVRGEVRLPGSKSLTNRHLVLAALADGPCVL +HGVLDSRDAALMRTALTALGARFEALSDGGLRVHPMPVGEPVAGDVAVDCGLAGTVMRFV +PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVNEEGEPGRLPFTMTTRADATTV +APDGDVPEVAVDASGSSQFLSAALLAAAGMPRGLRLRHTGQTVPSPEHVAMTVGVLRALE +VDVAETSPGAWTVAPGRVPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD +RWRRILPQFGASVALTVDRTDRSRGRLTVTGAVHDDGTPRITGAGEIADTAELAPTAAAL +ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGVTVDEGETTLGFPGTDASGPLSPAA +LETYHDHRMATFAAVVGLRVPGTGIVDVATTSKTMPDFPALWTALVAPGDAAEEAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001498.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001498.fa new file mode 100644 index 0000000000000000000000000000000000000000..5d0fbc6427634aca3cd27ba7eac1e36ad35c0074 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001498.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02179 +MGRRVDPGAWDESDVRVRPSKRGTRPRTKERPKHEDAVVGMVTTVDRGRYTVVLPERLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARVVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALMAHYESL +DLEVMTSGAAVFEAETGDTALDGALVARVAERLQGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTDDDGVPLADTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCAHTADSPGCGLDGWVAAGHAGPSGAARLASLRRLLGNRLGPAGAED +SASSED +>MOLHKGIG_00751 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEVGMVTTVDRGRYAVVLPERLDE +RITAMRARELRRTPIATGDRVAVVGDLSGEEGTLARIVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGVPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED +>NAFOICDF_02074 +MGRSLDPSAWDESHVRVRPSKRGTRPRTKQRPQHEDAQTGLVTTVDRGRYTVVLPGRAHA +PVTAMRARELRRTPIATGDRVDVVGDLSGDEGSLARIVRVQERDTVLRRSADDSDAVERV +VVANADTLMVMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAELVAHYEAL +DLEVMTSGASRFEAESGDTDLDDGLVERVAERLAGHTAAFVGPSGVGKSTLLNALTGAGR +ATGHVNAVTGRGRHTSSSALAMSLPGPDGEPVPDTWVVDTPGIRSFGLGWVEPDRVVEAF +EDLAGGLEGCPRGCTHLADSPGCGLDAWVAEGHAGEAGPARLASLRRLLGNRTTAEAGGS +ASSED +>MHAAABBN_00481 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAQVGMVTTVDRGRYAVVLPDRLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIIRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED +>LFPAFLNI_00715 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEIGMVTTVDRGRYAVVLPDRLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001500.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001500.fa new file mode 100644 index 0000000000000000000000000000000000000000..755a68f6b0e7164ce9b6a6d9f86a332bec211314 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001500.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02184 +MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDVYEAGLVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRIRNRRAGVA +>MOLHKGIG_00745 +MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA +>NAFOICDF_02082 +MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA +>MHAAABBN_00476 +MGKNSKGKATKQPAPGERQVIANNKKARHDYTILDTYEAGIVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA +>LFPAFLNI_00710 +MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001502.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001502.fa new file mode 100644 index 0000000000000000000000000000000000000000..7489eebf0fd9666d16dbe0a1f1f0a2625329a203 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001502.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02186 +MALDKTVATAAEAVADVPDGASLAVGGFGLSGNPIQLIEALLEQGAADLSVVSNNCGVDG +WGLGILLGAGRIRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGTQVAEGGLPMRYDAEGNVVKSSAAKPTDTFVLGEGYVSQDPAEEQTYVLEQSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDEVHLPGV +FVHRIVEVGTDIEKRIEKRTVRAAGEES +>MOLHKGIG_00743 +MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG +WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQAPDEPETYVLERSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV +FVHRIVEVGTDIEKRIEKRTVRASGEGRA +>NAFOICDF_02084 +MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGAMDLSVVSNNCGVDG +WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGIQVAEGGLPMHYDADGTVVKSSQAKPTDTFVLGEGYLNQAPGEPETYVLERSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV +FVHRIVEVGTDIEKRIEKRTVRASGEEQA +>MHAAABBN_00474 +MALDKTVATPAEAVADVPDGASLAVGGFGLTGNPVQLIEALLEQGATDLSVVSNNCGVDG +WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGI +FVHRIVEVGTDIEKRIEKRTVRASGEEQA +>LFPAFLNI_00708 +MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG +WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV +FVHRIVEVGTDIEKRIEKRTVRASGEEQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001503.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001503.fa new file mode 100644 index 0000000000000000000000000000000000000000..bf4836e4617abfd5d7439de431f9f856ad4b56b6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001503.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02187 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALECAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLVRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAYAEEKGLTILATVGALGQTAGPDSSQLH +SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>MOLHKGIG_00742 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>NAFOICDF_02085 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSQGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGS +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTVLATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>MHAAABBN_00473 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>LFPAFLNI_00707 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARTGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEIPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001504.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001504.fa new file mode 100644 index 0000000000000000000000000000000000000000..1dc1dba78863b7e1dfcce2e50bdadb9e6b44b40e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001504.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02188 +MTMRAARWHGKKDIRIEEIASPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDQDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVRRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVLKEIDLRGTIAYA +NDHADTIRMVEDGTVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL +>MOLHKGIG_00741 +MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA +NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDRGFETLIHHNETAVKILVSPTGQGL +>NAFOICDF_02086 +MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVALIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA +NDHADTIRMVEDGAVDLTPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL +>MHAAABBN_00472 +MTMRAARWHGKKDIRIEEIDSPSAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA +NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL +>LFPAFLNI_00706 +MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA +NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001505.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001505.fa new file mode 100644 index 0000000000000000000000000000000000000000..80c7930292ac5d43ed318f1207543e9042e61be1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001505.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02189 +MADTDFSAEIDSLRHTLASIEQVSDIDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS +HRQADLKRITSLESRIEDLETMVELAAEEDEPSLLDDANDELASIRKSLEELEVVTLLSG +EYDPRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF +EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLQRKA +EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDAFVDAGI +RWRAEQAKAAQED +>MOLHKGIG_00740 +MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS +HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG +EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF +EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA +EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI +RWRAEQVKAAQED +>NAFOICDF_02087 +MADTDFSAEIDALRHTLASIEQVSDVEKMTAEVAELEKEAAAPDLWDDPEAAQKVTSKLS +HRQADLKRIKSLADRIDDLETMVELAAEEDEPSLLDDANVELTSIRKALEELEVVTLLNG +EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQKGWSTKVMDTSYAEEAGLKSATF +EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLVRKA +EEDAKKKEMAGDIKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDDFIDAGI +RWRAEQVKAAQED +>MHAAABBN_00471 +MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS +HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG +EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF +EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA +EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI +RWRAEQVKAAQED +>LFPAFLNI_00705 +MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS +HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG +EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF +EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA +EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI +RWRAEQVKAAQED diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001506.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001506.fa new file mode 100644 index 0000000000000000000000000000000000000000..d1ac950db080b9a1950af210a91b156e3bc15ddb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001506.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02192 +MRALSALRRDDGQTTVLTVGLCALLIGLMLVMLAATTVQLQHRRLQSLADGAALAGAEEL +GFRLGEDPGVVLDDGDVAASAAAHLDAVDAASSVHGLGGMAAGVADDGATVTVRLDAEVD +LLAAAGPFAGMLPLSVPIQATGDSRTSLSR +>MOLHKGIG_00738 +MRRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE +ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR +ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR +>NAFOICDF_02091 +MTRRHRSRPQRRPDRRHGAHERGEITVLTLGLSAIVVGLLLVVLSATLVLIQARKVQSLA +DGAALAGAEQLAFQLDADPRVVLEPGSVQASVNEHLDAVGARESVPGLESVSAQVAGDGA +TVVVRARAKVTLVPSGAGWLADLIPASVPVSAEGSSRTVLTR +>MHAAABBN_00469 +MSRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE +ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR +ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR +>LFPAFLNI_00702 +MRRPLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAVAGAE +ELGFRLGEDPGVVLSDGDVAASASAHLAAVGAREAVPGLGGMSARVAEDGTTVVVTLDAR +ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001507.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001507.fa new file mode 100644 index 0000000000000000000000000000000000000000..74d94e5f9cc482c5067c8356740582090997445b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001507.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02193 +MPIASDVRDERGSATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAAKVVVSG +TEGRSAAQAHAAVRLTLADFGIDYGAYELDLGCSAGDCVSLDPGEVVQARVDVEVPIPLT +PADWSLAPVTVGSDARQAVPRF +>MOLHKGIG_00737 +MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE +ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT +PAAWSLTPVTVGSDARQTVPRF +>NAFOICDF_02092 +MPSATDARHGPTHAPWRGTDLADDVGSATVEFLGLSLILLIPLAYLMLFVSQVQAAAFGA +LASADQAARVMVSGEGGNPGQAEGTIPLTLADYGFDAADAEWSVACDVGGCGTLEPGEVV +DVTVAISLDPPLLPDGWVSVDIATVDSHSRARMPRF +>MHAAABBN_00468 +MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE +ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT +PAAWSLTPVTVGSDARQTVPRF +>LFPAFLNI_00701 +MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE +ADHPSAGAAHATLELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVAVPVPLT +PAAWSMTPVTVGSDARQTVPRF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001508.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001508.fa new file mode 100644 index 0000000000000000000000000000000000000000..605260fb7d86f7f0859e4e424354f0034464a3fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001508.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02194 +MTAGSGAAAAAPRRRRPRWRDDRGAAVAESTMVMTLVVLLFAALLQAGLVIHTRNVMIDA +ASAGARYGALADRVPEDGVQRARELLAAGVPGQSGARIVAEPTSQDGVPVLRVTISSSLP +GVGFLPGPIPVEVSGHAHRL +>MOLHKGIG_00736 +MPRGAAHGAQAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI +DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS +LPGLGFLPGPIPVEVSGHAFRQ +>NAFOICDF_02093 +MEPAARPAVQGRPGPDRRAGDRGSVVAENAMVTALLVLLFAAVLQVGIIVHVRNVMIDAA +SAGARYGALADRDPAEGAARARDVLSASVPGQSGAQVRSEPTTVGGVPVVRVTITSSLPG +LGFLPGPVPIEVHGHAFRY +>MHAAABBN_00467 +MPRGAVHAVPVPRGVHMGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI +DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS +LPGLGFLPGPIPVEVSGHAFRQ +>LFPAFLNI_00700 +MPRGAAHDAPAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI +DAASAGARYGALADRNPEDGVQRARELLSTGVPGQSGADVAAELTSQDGVPVLRVTVSSS +LPGLGFLPGPIPVEVSGHAFRQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001509.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001509.fa new file mode 100644 index 0000000000000000000000000000000000000000..8644d94add7038daaf02fb48600754c62493a8cf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001509.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02195 +MLHHHVISILTALRGLLHDDVRDDRGDVPGWVMITLMSAVLVAALLTLALPALTDLFDQA +ISQVTQGE +>MOLHKGIG_00735 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA +ISQVSQGG +>NAFOICDF_02094 +MLTNAYLTVVSALTSLLHDDARDERGDVPGWVMITLMSAALVVALLGLAMPALKAMFDQA +ITQVNNAAG +>MHAAABBN_00466 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA +ISQVSQGG +>LFPAFLNI_00699 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALEGLFNQA +ISQVSQGG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001511.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001511.fa new file mode 100644 index 0000000000000000000000000000000000000000..2242e4fccce1410e40737a014703759b6125adf3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001511.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_02219 +MSASLLWAALLGLTLGAGLLLIAVAQPLGWRPTLEQRVEPQLRHHTPASRLLEDEEAGAS +PWGAWGRILDPVLRAGVGWLHRLSPAGETLERKLAAAGMTVSAADFRAQQVLSAAAGAGI +ATAFSVALALAGRIPVVTGVGFVIVGGMAGYLLRDQLLSLRVQRRRAAILTEFPSVAELF +ALSVGAGESAAGALERIATTARGELAGEFRATLAEMRAGSSLSAALKSMGRRVQLAPVER +FIGGILIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPIVTR +>MOLHKGIG_00734 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGTWGRILDPVVQAGVGWVQRISPGGAALDRKLAAAGLAVTSTDFRAQQVLSGAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLREQLLSLRVRRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRTTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF +>NAFOICDF_02095 +MSGGLLWGIALGLVMAAGVWLIVTAQPWGWRPSLEERIEPQLRHHVPASRLLADGRATST +PWGTWGRLLGPSLAGATRGLQRLSPAGESLTLKLQAAGSELSVMDFRAQQVLCAVIATAA +GTVLSVLLTLAGAVPVVSGVALVVAAGLSGYVLRDQMLTWAVARRRTAILTEFPSVAELF +ALSVGAGESATGAMERIVRSARGEMAGEFDRTLADVRAGASLSSALKAMGRRVQLEPVER +FIGGILIALDRGTPLADVLRAQAQDVRELGRRELMESAGRKEIQMMVPLVFGILPLTVVF +AIFPGLALLRLSF +>MHAAABBN_00465 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGTWGRILDPVVQAGVGWVQRISPGGAALDRKLAAAGLAVTSTDFRAQQVLSAAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLREQLLSLRVRRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRTTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF +>LFPAFLNI_00698 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGAWGRILDPVVQAGVGWVQRISPGGVALDRKLAAAGLAVTSADFRAQQVLSAAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLRDQLLSLRARRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRVTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001513.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001513.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcd137cca80e2ff57f36baabf6105f5ed3487e3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001513.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02221 +MDAVRILEDEIREVVRRQGIDPQREHARVIALIQDAAADYESRAEVSALPDLEDPAAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARAGRSELTGIVLTEEEVHDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFISRARRLEDLVRSGSLT +PTAARFLDAAVDVGMNVLVSGATQAGKTTLLNCLASSIGARERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRSFVVPTVATCIDVVVHCERDWDGRRRVLEVLTVGA +RVEDGVIETSTLFQRDSAGDLRLNEAASLEFDAFARRGVDVHELVGLR +>MOLHKGIG_00732 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR +>NAFOICDF_02097 +MDAVRMLEDELRELVRRRGVDPRVEGHRIRTMIAEATLDYESRSLVSSLPPLEDPEAARQ +ELFDRIAGLGPLQRLMDDPTVEEIWLNAPDQVYCARAGRSELTGIVLSEEQVRDLVELML +KSSGRRLDLSMPFVDASLPDGSRLHVAIPDITRRHWAVNIRKFISRAHRLDDLVRSESLT +TPAARFLDAAVDAGMNILVSGATQAGKTTMLNCLSASIGARERVITVEEIFELQIPVRDV +VGLQCRQPNLEGTGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSASDALTKLCTLPLLAGENISRNFVVPTVATCIDVVVHCERDREGRRRVREILTVGS +RVEGGVIETSTLFRRDAHGDLVLNPSADLEFEAFARRGLDPRDLVEVR +>MHAAABBN_00463 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR +>LFPAFLNI_00696 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDTGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001514.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001514.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5011bc7484d0c88097b152d6d0c8f8d56a58066 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001514.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02223 +MAQILLFHHALGLTDGVRALAAQIEAGGHTVHTPDLYDGALFTDVEEGIAHVESLGGFDV +IAERGMRAAAQHPQASVVAGISMGVVAAHKAAQAVPAFRACIDIAGIVPLDAFAPLWQPH +TALQVHLATRDPWVMDEDLPLARSVAATEEDPDKPAVLFEYDTDAHLFMDSSTDGHDPAL +TEVLVRRIHELLA +>MOLHKGIG_00730 +MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI +GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT +ALQIHLGTRDPWALEGDLATARSYAATAEHPDRPADLFEYDTDRHLFMNSSTADFDADLT +AVLVRRIHELLA +>NAFOICDF_02099 +MAQIILFHHARGLTEGVLALAEQIEQASGHHVHTPDLFGGAVLPTVEDGLAHLQQIGQDE +VMTRAMHACAEHKEASVVAGISMGVMPAWKAAQTAPGFRACIAMSSALPLDAYARLWQPH +TSLQIHLAAQDPWVKDEDLPLARTYAATAEHPDRPADLFEYETASHLFMDSSTDQYDARH +TEVMVERIRELLA +>MHAAABBN_00461 +MAQIVLFHHALGLTDGVRALAEQIAGGGHTVHTPDLYDGRTFATVDEGVAHAQHIGFEEI +GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGALALDAYAPLWQPHT +ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT +AVLVRRIHELLA +>LFPAFLNI_00694 +MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI +GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT +ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT +AVLVRRIHELLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001515.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001515.fa new file mode 100644 index 0000000000000000000000000000000000000000..31607afc3c2acf66cb5ab807b108187152ccdc54 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001515.fa @@ -0,0 +1,46 @@ +>ACLBLIBL_02226 +MGFIARFPHTAAGVILTLHVALTLDLGYGQAGLAAAAMTLGIAVGSPWRGRVVDAKGLRR +ALLPSVIAEALIWPLVPWLPFWLMLVAVFFGGVFALPIFSVVRQGLGVLTHGRDRQTAFA +LDSIITETIFMVGPALGAVVAATWSSALGLTIVGLSSALGGVLLMWFNPPTRSSQLAVVG +PETEDPYTEDEDREEAVAQTVHGAPMHVEMTAPSLATGALPVVTEAIPLVTGALPVIAAD +GSGPATPTPGLTRAERLRLWRARHFAWVGPEALGVLVVSMAAGLVMVGTEVTMVAELEHA +GMAGSVGVVYAFWCGASAVGGLFYGAWGRQVHPYLLMGLLALLTLPMAFVDGLWALALAA +IPSGLFTAPTLASASSRLSTLVPEERRGEAMGFYGSAMTAGAAMGAPLSGVFIDAIHPAA +GYVFAGLAGAVLVLAAALVTLARRRRVGGTSA +>MOLHKGIG_00729 +MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL +GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS +VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG +GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL +PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA +AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA +VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG +AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA +>NAFOICDF_02100 +MDFRAYGRLLQDPRIRNLLAVGFIARFPHTAAGVILTLHVAVTLGLGYGQAGLAAAAMTL +GIACGSPWRGRAIDRDGLRRALLPSVVAEAVIWPVVPWLPFGFLLVAVFFGGLFAVPIFS +VVRQGLGVLTHGADRQTAFTLDSIITELVFMVGPALGAVIAATGSTALGLTVVGLSGALS +GALLMWFNPPTRSTQLAADGPSAGDPFTEEEDREQALSQAVHTAPVRATVAAADLATGAL +PVVTEAVPIVTGSLPVIAADGSGPVSPAPRAGRHDDGRAADGLTRDERWRLWRVRHFGWV +TPEVLGVLVVAMAAGIALVGTEVTMVAELEHAGQEASVGVVYAFWCGASALGGLFYGAWG +RQVHPYLLGALFALAVAPMAFVDGLWALAWASVPSGLLTAPTLAAASSRISLLVSEERRG +EAMGYYGSAMTAGSALGAPVVGLVIDGVGPGAGYVGAAGAAVVMIGAAAILTAARRRRSP +ARG +>MHAAABBN_00460 +MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL +GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS +VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG +GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL +PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRSHFSWVGSEVLGVLVVSMA +AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA +VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVEEERRGEAMGFYGSAMTAG +AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVARGRRSA +>LFPAFLNI_00693 +MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL +GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS +VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG +GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL +PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA +AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA +VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG +AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001516.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001516.fa new file mode 100644 index 0000000000000000000000000000000000000000..81b090ef1032a486335e84ce13e3430725fac90a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001516.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02229 +MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD +VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV +TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA +LDLIRAKDRRRNN +>MOLHKGIG_00728 +MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD +VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV +TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA +LDLIRAKDRRSNG +>NAFOICDF_02102 +MTTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLLV +CDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRVE +GDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIAL +DLLRAKDARRND +>MHAAABBN_00459 +MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD +VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV +TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA +LDLIRAKDRRSNG +>LFPAFLNI_00692 +MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD +VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV +TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA +LDLIRAKDRRSNG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001517.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001517.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea7088f232d05c7cfc3bf73a35c6628a7a7ada6c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001517.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02231 +MQFGVFTIGDVTQDPTTGTTPTEHQRIKDTVRIAQHAAQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAMTTDLQLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIPLAVENYNLLYRLWHEETVDWSGKFRSPLQNFTLTPQPLDGVAPFVWHG +SIRSAEIAEQAAYYGDGFFYNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEQFSSMTPLTVGSPQQVIERTLGFRDWVGDY +QRQMFLIDHAGLPTDTVLKQIDIFGEEVLPVLRKEFAALKPDDVPEAPTHEFLVERARRG +EAPVPGGKEGSQAQIDRAAAAEKRAAAKAGEGA +>MOLHKGIG_00727 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ +>NAFOICDF_02103 +MQLGIFTIGDITADPTTGTTPTEHQRIKDTVTIARHAEQAGFDVFATGQHHNPPFVAPGN +PPTLLSHLAAVTETMTLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTLGRGNTGPVY +PWFGKDIRQGVNLAVENYNLLYRLWHEETVDWSGQFRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGFFHNNIFWNKEHIIRMVRLYRQRFEHYGHGKAHQAYVGLGGQA +YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEDFTSMTPLTVGSPQQVIERTLSFRDWVGDY +QRQMFLIDHAGLPTDTVLKQIDLFGEEVLPVLREEFAALKPDDVPEAPTHEFLVERARRG +EAPVPGGREGSPAHAAREAARAKQAEQQKKKEDAR +>MHAAABBN_00458 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ +>LFPAFLNI_00691 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001519.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001519.fa new file mode 100644 index 0000000000000000000000000000000000000000..1fdc278e3bb15231e69d5d219aefe238fc8467ca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001519.fa @@ -0,0 +1,23 @@ +>ACLBLIBL_02233 +MNSSSTPTPEPSETARHAWRAYFEATQMLSEMLERGLKKDSGMSLADYNLLLLLYEAPEG +RLRMGELASGMVFSPSRITYQVKTLVARGLIERRAAECDRRGFEAVLTDEGRTAFRRAAA +GHARQVDELFLSHLEPGEAETLERIFTRLGGRLEGLC +>MOLHKGIG_00725 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR +LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL +C +>NAFOICDF_02105 +MTSSSTPAAEPTGPRAARHAWRAYFESTQMLQDQLERGLKAECGITLADYNLLLLLVESD +GGRLRLGELASRMVFSPSRVTYQVKSLVARGLIERRRVECDRRGFEAVLTDAGRTAFRRA +AVVHARQVDELFLDLLQPGEAEVLGRVFTRVGTALESRCAGRAAPSEPCGAQASNSADA +>MHAAABBN_00456 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR +LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL +C +>LFPAFLNI_00689 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVLERR +LKQDCGMSLADYNLLLLLYESPEDRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLVDLAPGEAESLTRIFSRLGRRLEGL +C diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001520.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001520.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4d489435585c3cade458ffdc0eb0a9b2615fbdb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001520.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02234 +MRTRTLTGVATAALGAVVVAGAGPALAQTVITQGSALSAPAGACSLTIVDDATAYTAAHC +GAGQWEVGSPVLDAEGVQIGTVSGLPGTSGVDVVRVALAEDVEVVGEWSTRPAASVEVGE +TVFTHGSSVPLGAPNSLSHTQTFDAATVCDDAYSDQMALDVASTYPGDSGGAVYDAQQRV +VGVISGVAPVTFDEEGNVVGCDAQSLSSIMVPVESLDAVGQETAAPAAVEPAAAEAPATE +VTETPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIRAELIERAEAEAAAEAP +AEQPAAEAPVAEAVVAGTEDVVAAPAEGVAYGTQVMAETSQGGFASVTVTAYDADGTVLG +VDGLDLTGEYRAWMPVPAEVPAGGSVVVTVVDAAGDATDTQVTLGGQLIG +>MOLHKGIG_00724 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE +TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA +APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD +GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG +>NAFOICDF_02106 +MKKTTLTGATTAALGAVVVAGAGSALAATPLTQGAALSVPAGECSITLVSDTTAFTAAHC +GAGQWTVGSAVHAADGARIGSVSALPGSTGVDVVKIALDEDVDVVGDWSTRPAASVKPGE +TVYTQGSSVPLGSPNSISDPETYDIAETCGDVYTDQVSLDAATTRPGDSGGAVYDAKQRV +VGVVSGLAPVSFDEEGRAVGCDAASLSTIMVPAESLKAVAAAPAKATAPAPTVGKHGVIL +KAPTAPAAKAPAAEKKAPAAKAPAAEKKAAPAPTLGKHGVSAETATAGTTTLKVAPEDGI +DFRTRVQATTKTGGFSYMAVTAYDAAGKQIGHLHLHSDGQPMTWINTPAQVPAGGHIEVQ +LKDAAGQPTDATVTLGGVPVN +>MHAAABBN_00455 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE +TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA +APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD +GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG +>LFPAFLNI_00688 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE +TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA +APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD +GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001522.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001522.fa new file mode 100644 index 0000000000000000000000000000000000000000..1711c1a17fd59513568c449301fc6f81abd57737 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001522.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02236 +MTPNPAAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQRAGAEWIHLVDL +DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPAWT +ARVIERFGDKVAVGLDVRGTTLAARGWTQEGGDLWEVLARLEDAGCSRYVVTDVTKDGTL +KGPNTELLAQVCARTDKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ +ALAVAGGATVEQARAEQPGPVAE +>MOLHKGIG_00722 +MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA +AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR +VIERFGDRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG +PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL +AVAGGATVEQARSEQPGPVAP +>NAFOICDF_02108 +MTETTPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQDAGAEWIHLVDLDA +AFGRGDNRDVLRRVVDEIGVKIELSGGIRDDASLENALAMGAARVNLGTAALEDPAWTAR +AIERFGNRVAVGLDVRGTTLAARGWTQDGGDLWEVLARLEEAGCARYVVTDVTKDGTLRG +PNRELLARMCAATDKPVVASGGISSLEDIAALAAMVPQGVEGAIMGKALYAGRFSLEQAL +AVAAGATVERAREQHPFQAAP +>MHAAABBN_00453 +MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA +AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR +VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG +PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL +AVAGGATVEQARSEQPGPVAP +>LFPAFLNI_00686 +MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA +AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR +VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG +PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL +AVAGGATVEQARSEQPGPVAP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001523.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001523.fa new file mode 100644 index 0000000000000000000000000000000000000000..6f289073b4239fa1d1ce1f6eec64990291892562 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001523.fa @@ -0,0 +1,10 @@ +>ACLBLIBL_02237 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVAR +>MOLHKGIG_00721 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA +>NAFOICDF_02109 +MPYWSVLYLGLGGILLGAAWSMRTQKAPTWAVVIALVLAAMAVAAAFLTV +>MHAAABBN_00452 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA +>LFPAFLNI_00685 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001524.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001524.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ce9768f90ee51fabf3c9abe998f39801db53bcd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001524.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02238 +MARPTSVPGVRPSVAVLDYGSGNVHSAVRALERAGADVELTRDPEAVQSADGLLVPGVGA +FASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERAEGMGEWPGVVEA +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLRWEFDQTISAMRPPQVTWAH +HGADFVAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>MOLHKGIG_00720 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>NAFOICDF_02110 +MASPTSVPGVRPTVAVLDYGSGNVHSAVRAVEHAGARVELTKDPDAVLGADGLVVPGVGA +FASVMEALRSSGGTRWIGRRVAGGRPVLGICVGHQVLFEAGVEHGVRTEGMGEWPGVVEP +LPAATVPHMGWNTVRPAEGSALFAGIEDERFYFVHSYAVQSWEFDQGNEAMRPPQVTWSH +HGADFIAAVENGPLSATQFHPEKSGDAGQALLRNWLETL +>MHAAABBN_00451 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>LFPAFLNI_00684 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPAEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001527.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001527.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee49c4a5d106424e218bc3a700214ac8af592009 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001527.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02241 +MTLMTAQFAGSPAAARRRPAAIRLTRRGRLLLRGIPVMAAAAAATLAVAFLLGVLLSPAA +VSADTAAPATQTVTVMPGDSLWTIATTIAPEEDVYEVIAAIDELNGLEGRAPALGEELFI +PATR +>MOLHKGIG_00717 +MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA +VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV +PATR +>NAFOICDF_02113 +MTAVTAVLSRTHQLTSVRARPTRAVAASTRAAARTSGVRLTRRGRLLFRGLPVILSVAAA +TVAAAFFAGVLFSPPAVSADTPAEELQTVTVMPGDSLWTIARDVAPEADRRDTMRRIDEL +NGLEGRDPELGQELYVPPTR +>MHAAABBN_00448 +MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA +VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV +PATR +>LFPAFLNI_00681 +MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA +VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV +PATR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001528.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001528.fa new file mode 100644 index 0000000000000000000000000000000000000000..6f8d15161941fb4a82dc620bec66312676f65c94 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001528.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02242 +MATTDEQPAPLTDRQRRIVQTIRDAIAEHGYPPSMREIGDAAGLASLSSVTHQLGRLEQH +GYIRRDPGRPRALEVLLDVDGTPLGEAAPPAAAAPSGLPAIPAWHTGAEDADTVPVPWVG +RIAAGGPVLAEQQVEDVMAVPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQETAE +NGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRAL +>MOLHKGIG_00716 +MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL +ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRVTAIPAWHTGADEADSVPVP +WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE +TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL +>NAFOICDF_02114 +MATSPTPPPGGAQPLTDRQRRIVRTIRQAIAERGYPPSMREIGDAAGLASLSSVTHQLGQ +LERFGYLRRDPGRPRALEVLRDEDGAAAVADAAPGAPEIPSWHTGASEDATVEVPWVGRI +AAGGPILADQQVEDVMAVPRRLTGEGDLFMLRVVGDSMVDAAICDGDWVVVRRQETAENG +DIVAALLDDEATVKTLRRRDGHTWLLPQNTAYEPILGDHATLMGRVVTVLRAL +>MHAAABBN_00447 +MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL +ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRISAIPAWHTGADEADSVPVP +WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE +TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL +>LFPAFLNI_00680 +MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL +ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPTAAPSSRVSAIPAWHTGADEADSVPVP +WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQD +TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001529.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001529.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f970eda30876f166694d14d0c9239d4d01f1eea --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001529.fa @@ -0,0 +1,65 @@ +>ACLBLIBL_02243 +MSGAGTEGTTPAGEGAQPRTDHEREALRLLDAAVEATGGQQRAGQREMVLQVARALESRR +HLLVQAGTGTGKSLAYLIPALQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDEL +PREPVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGLLGSAADGTGGPSSLLGK +EVMYLRAWADQTETGDRDDLDVPVTDRAWRQVSVSAIDCLGASRCPMAEECFSERARADA +ADADVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAAT +SLRKHTTVAVEDLMEAGAGLDRAFTDAPSGLLAAGPDEVQEQALNAVLAAARQCLSDLGQ +DKDKEADADGGRQMARSRVLEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGD +ESDPPQLFVAPISVAGKLREGLFGKATTVLTSATLTVGAGERRFDSVAGDVGLAGPDAPR +FEALDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASGGGALGLFSSRRAA +EDAAAEMRRRLGPKATVLCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLV +AIDRIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVHDRGVVA +VLDSRLATERYGGYITSALPDFWRTTDRAVVLGVLGRLAETGS +>MOLHKGIG_00715 +MSGGAEEVGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL +VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE +PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGMIGSATDGAAGPSSLLGKEVM +YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA +DVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR +RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD +KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD +PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA +LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA +AAEMRRRLGPKTTILCQGDATLSALVRQFSEEPDTSLFGTMSLWQGVDVPGNSLRLVVID +RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD +PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD +>NAFOICDF_02115 +MTDSTTGPAGAVPTTDREEEALRLLDVVVEATGGQQRAGQREMVLQVARALESRRHLLVQ +AGTGTGKSLAYLIPALQHAMDQEDPVVVATATLALQAQIMKRDAPRLVQALAGELPREPV +VALVKGRSNYLCRHKVDGGYPGDEGEETLFEVADDGGLIGSGEDGEPSSPLGKEVMYLRA +WADVTETGDRDDLEVPVTDRAWRQVSVNAVDCLGATRCPLAEECFSERARADAADADVVV +TNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLRRHTS +VAVEDLAQAAAGLDRAFTDTPSGLIQGGPDDVQEQALTAVLSAARQCFSDLGKDKEGEAD +AGRQMARSRLLEVVEVAERMLAAHPEADFPEVLWATRPGRFEPGSGWQPGDEADPPQLYV +APISVAGRLREGLFGKATTVLTSATLTVGQGERRFDSVAGDVGLAGPDAPRFTALDVGSP +FDYPRQGVLYVARHLPKPGRTASPESLDELEALLRASNGGALGLFSSRRAAEDAAEHMRR +RLGRGHTVLCQGDATLSALVRQFADEPDTSLFGTMSLWQGVDVPGPSLRLVVIDRIPFPR +PDDPLSQARTRDVARHGGNGFMRVSATHAAVRMAQGAGRLVRSVEDRGVVAVLDSRLATE +RYGGYITSALPDFWRTTDRAVVRGVLERLAREAH +>MHAAABBN_00446 +MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL +VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE +PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM +YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA +DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR +RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD +KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD +PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA +LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA +AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID +RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD +PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD +>LFPAFLNI_00679 +MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL +VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE +PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM +YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA +DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR +RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD +KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD +PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA +LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLSASRGGALGLFSSRRAAEDA +AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID +RIPFPRPDDPLSQARTRDVARNGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD +PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001534.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001534.fa new file mode 100644 index 0000000000000000000000000000000000000000..30b73eeb0399757544123f92216d907f82fac508 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001534.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02250 +MRAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDIGTAKVTEAEREG +VPHHLLDVLDVGQEASVAAFQSAARGVFEDVRSRGRTPILVGGSGLYVRAALDVLEFPPT +DPEVRAAVEAELAERGEAALRAELAAVDPESAAKVADARRLVRALEVHRITGRPFSAFMP +RREHDPSVAPVVQIGLSLERAVLHERIEARVERMLAAGLLDEVRALDVPGPDGLRQGPTS +ARAIGYAQMLAVLDGTLTPEQAAEQTVVATRRFARRQETWFRADPRVHWVDALAPDVVAQ +ALAVVAGS +>MOLHKGIG_00707 +MPAAASRPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER +EGVPHHLLDVLDVGQEASVAAFQSAVRDLFAQIRARGRTPILVGGSGLYVRAALDVLEFP +PTDPALRAELEARAQREGLAGLRAELASLDPVSAERLQDARRIVRALEVCRLTGRPFSAF +MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAEGLLDEVRRLDVPGPDGLRQGP +TASRAIGYAQMLAVLDGELTEAEAADQTVVATRRFARRQETWFRADPRVVWLDAQDEDVV +AEALAVVAGDAT +>NAFOICDF_02122 +MSAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER +EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLEFP +PTDPALRAELEARAQREGLTGLRAELAALDPASAERLRDARRIVRALEVCRLTGRPFSAF +MPERTYAPEVAPVVQLGLRLDRAELHQRIAARVERMLAGGLLDEVRRLDVPGPDGLRQGP +TASRAIGYAQMLAVLDGELTAAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV +AAALAVVAGDAT +>MHAAABBN_00441 +MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER +EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP +PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF +MPERTYAPEVAPVVQLGLRLDRSELHQRIAARVERMLAEGLLDEVRRLDVPGPGGLRQGP +TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV +AEALAVVAGGAA +>LFPAFLNI_00674 +MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER +EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP +PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF +MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAGGLLDEVRRLDVPGSEGLRQGP +TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDIV +AEALAVVAGDAT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001536.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001536.fa new file mode 100644 index 0000000000000000000000000000000000000000..9408169223dc8ccf66999f9b61b4f3492d9e1e1c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001536.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_02252 +MTRARRDAGGGAARRSERNGRSGAASGASAFDDARDTDAARMWLELAGVPEADAPAAARS +VDEPPAAPTDGPDDPPLATAENGSSAAPSGPAAAPDEAGPPDLGSLLGRASDLPSPAPGA +AARVLPWSADARPERGGRGARGTSSEARRARRRTARLAAADVASAPEAASTPEEANARED +ARPRRRPGPAPLPAEPREREEAAREVVLRQLALGPRSRGQLEAKLADREAEPELIARVLD +RFEEVRLVDDAAFAEVWVRSRHRSKGLARRAIGHELRQKGVDRDVAAEALEAIDGEDERA +AALELVRRRLRGRRVPAGNGPHARAERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLGELE +E +>MOLHKGIG_00705 +MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAS +DAARDAAPARDAGAPAEDVPDPAPGAAPDLGALLTRASDLPSPAPGAGPRSLPWSGREDT +RADTERRGRRRAPAKRSGRTRPREDGRAPAEPAPQTDRPRRRPGPAPLPTAPREREEAAR +EVVLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRS +KGLARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEAR +AERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE +>NAFOICDF_02124 +MPEDPREREEAARQVVLRQLAMGPRSRRQLERKLADREAEPELVERVLDRFEEVSLVDDA +AFAEVWVRSRARGKRLSRRAISRELHDKGVDRDVAEEALAAIEPEDERQAALELVRSKMR +GRPAPAADGPEGRAERDKVTRRLVGMLGRKGYGPGLAFGVVKEVLAELDEA +>MHAAABBN_00439 +MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA +RDAVPARDAGTPAGDGSDPAPGAAPDLGALLTRASDLPSPAPGAGPRALPWSGREDTRAD +TERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV +VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG +LARRALGHELQQKGVDREIAAEALEAIDGEDERTAALDLVRRRLRGRTVPGGASPEARAE +RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE +>LFPAFLNI_00672 +MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA +RDAVPARDAGTPAGDVPDPAPGVAPDLGALLTRASDLPSPAPGAGPRTLPWSGREDTRAD +IERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV +VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG +LARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEARAE +RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001537.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001537.fa new file mode 100644 index 0000000000000000000000000000000000000000..bc1d7273f58f456b82f40635fb5cf46b054bb10d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001537.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_02253 +MSKTPDREKALEAALAQIDKQFGKGSVMRLGDQTQTPVEVIPTGSVAMDVALGIGGLPRG +RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTDALLVSQP +DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKIT +GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG +NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG +QGKENARRFLKDNPDLAQEIEERILTKLGIGVDPEAEADEAPALTAVPGDTAAG +>MOLHKGIG_00704 +MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG +RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP +DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT +GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG +NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG +QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG +>NAFOICDF_02125 +MSKASATEKVATEREKALEAALAQIDKQFGKGSVMRLGERSQAPVEVIPTGSVAMDVALG +IGGLPRGRVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTD +ALLVSQPDTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMS +QALRKVTGRLHQTNTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLK +EAGSPVGNRTRVKIVKNKMAPPFKQAEFDILYGEGISKEGSLIDMGVEEGIVKKSGAWFT +YDGDQLGQGKENARRFLKDNPDLADEIEHRIFTKLGIGADPQAEDDAEGETPALQAVAGD +VAAG +>MHAAABBN_00438 +MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG +RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP +DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT +GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG +NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG +QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG +>LFPAFLNI_00671 +MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG +RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP +DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT +GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG +NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG +QGKENARRFLRDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001538.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001538.fa new file mode 100644 index 0000000000000000000000000000000000000000..4256e3ed279f1c6faf923cd17251bea2ca8863bc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001538.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02254 +MRVSEFQRLMDEEFGPGRAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCELHDIPE +ERRLGRDVPPKR +>MOLHKGIG_00700 +MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ +ERRLGRDVPPKR +>NAFOICDF_02126 +MTEFQRLMEDEFGPARAGLVADSLHLPGFDATASEALAAGADPKDVWRAVCDLHEIPAER +RLGRDVPPTR +>MHAAABBN_00437 +MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ +ERRLGRDVPPKR +>LFPAFLNI_00670 +MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ +ERRLGRDVPPKR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001539.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001539.fa new file mode 100644 index 0000000000000000000000000000000000000000..99f547415248a6fab5b0b3c1d29412cd556a9815 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001539.fa @@ -0,0 +1,17 @@ +>ACLBLIBL_02255 +MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE +DLTDAADPSLGTLAGR +>MOLHKGIG_00699 +MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD +IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR +>NAFOICDF_02127 +MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA +DMAEDGAADVAPLAVR +>MHAAABBN_00436 +MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD +IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR +>LFPAFLNI_00669 +MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD +IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001540.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001540.fa new file mode 100644 index 0000000000000000000000000000000000000000..83b4cf87f9ae87d9bd214591f9ac789c9d4a2fac --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001540.fa @@ -0,0 +1,22 @@ +>ACLBLIBL_02257 +MAAQETVRALAGAGLTVATAESLTAGLVAARLADVPGASAVLQGGVVAYQNSVKAGLLGV +PADLLERVGAVDPEVARRMAEGARAGLGADVGVATTGVAGPEPHQGRPVGTVWLGVAVPE +RLTAALDGLGGERRGAATAIPLALDGDRRAIREATVAAALAALTRLGAPVGERATGEGAA +GEPCAGA +>MOLHKGIG_00697 +MAGAQDVVHALAHAGRTVATGESLTAGLLAARLADVPGASAVLHGGVVAYQNAVKTGLLG +VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP +DADANALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAVRGH +>NAFOICDF_02128 +MSTGVGAVAAEGEAADPARAAVRALTTAGLTVATAESLTAGLVAARLADVPGASAALQGG +VVAYQNHVKAGLLGVDAGLLTARGAVDPEVARQMACGARRAAGADVGVATTGVAGPEPHQ +GKPVGTVFVGVAVPAELAPALAGLDGEPGAGEAAPGEAGSGGSEAGVAAAAFALTLPGNR +AEIRAATVETVLDLLAALGTTGRGMPDEAPALS +>MHAAABBN_00434 +MAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGLLG +VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP +DADASALDVFGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAGRGH +>LFPAFLNI_00667 +MTTAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGL +LGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLA +VPDADASALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTHLLAGPGH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001541.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001541.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b91b5320e6db25366cc603fd4f5a171de36faad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001541.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02258 +MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV +LTGLEYVKDAWILRRDALAAPRGA +>MOLHKGIG_00696 +MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRGA +>NAFOICDF_02129 +MNAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMYTD +KLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGITAM +RFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTVVT +GVEYVRDAVRLRADWLASHPEARR +>MHAAABBN_00433 +MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRGA +>LFPAFLNI_00666 +MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001544.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001544.fa new file mode 100644 index 0000000000000000000000000000000000000000..83af47baad0db70490b173c27182ba0b47edbfec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001544.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02261 +MSAVRSASAPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDGGADGLVVTGTTGE +TSTLTDEENLAMFRTVVEAVGDRAKVVAGTGTNDTAHTLELSRRAKETGVDGLLLVTPYY +NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHSDLDLYSGDDGATLPLMALGAVGVVSVAAHVAPGLYRKLVDAVHAGDLAAA +REHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQASADELSDIRADLAE +AGITF +>MOLHKGIG_00693 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATRDELSVIRADLAE +AGITF +>NAFOICDF_02131 +MTDARRTVNPSELPFGTVVPAMVTPMDQDGAVDLQAAAVLATHLVDQGADALVITGTTGE +TSTLTDEENLAMFRTVVEAVGERARVIAGTGTNDTHHSLELSRRAAEIGVHGLLLVTPYY +NKPNQAGIRRHFETIADGVDLPIMLYDIPGRSVMPIQPETLVALAAHPNITALKDAKGDL +QSTTTVLAHTDLHVYSGDDGATLPLMAMGAVGVVSVAAHVAVPGYRALVDAVHAGDLRAA +RDAHFALDPVQRGIMSHVQGAVAAKTVLAGQGIIPTAAVRLPLVAADDAELAAIRADLAE +AGISF +>MHAAABBN_00430 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGS +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE +AGITF +>LFPAFLNI_00663 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAVLAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETIIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE +AGITF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001547.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001547.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2348c3a17c7db2aae13b601665bd23bfdda4b99 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001547.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02266 +MAGMSIHREIPLDFTGVLADEGHGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR +DESPEGYGSTHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL +PMAVEVLTDMLTSSLLDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP +IGGTPETIRAVTREHVAGHYARWYRPDELVVTAAGNLDHDEVCRLVLAALQASGWELAPG +ALPAPRRAVDTEGAAASRVLTGTHTVAKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG +GGMSSRLFQEVRERRGLAYSTYSFSAGYSDAGYWGLYAGCQPDRVDEVSALMEAELDRMA +AEVVTEEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLERVRAVDAA +QVRAVAARLAAGERARVVVAPA +>MOLHKGIG_00689 +MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES +PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA +VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG +TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP +APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM +SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD +VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR +AVAARLAAGDRARVVVAPA +>NAFOICDF_02135 +MAGMTVQREIPLDFSGVLAEDRGAVVCRSVLPGGVRVLTESMPDQRSVTVGYWVAVGSRD +ESPEGYGSTHFLEHLLFKGTPTRTAMDIASAFDRVGGESNAGTAKESTVYHAHVLDEDLP +MAVEVLTDMVTSSLIDADELETERGVILEELAMDADDPVDVAHERLAAVLMDGHPLGRPI +GGTPETIRAVTREHVVAHYRHWYRPQELVITAAGNLDHDDVCRLVLDALERSGWDLAEGA +APAPRRTADAAGAGAVLAGTHTVAKQVEQANVIVGGQSLSTTDPDRFALGVMMSVLGGGM +SSRLFQEIRERRGLAYSTYSFSAGYSDGGYFGLYAGCQPERVDEVAALMEAELERMAAAE +VTAEELDRAHGQICGGTVLGMESTGARMSRLGRAELVTGEFVDLSASLARVRAVDAGRVR +AVAARLAAGERARVVVAPA +>MHAAABBN_00426 +MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES +PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA +VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG +TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP +APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM +SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD +VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR +AVAARLAAGDRARVVVAPA +>LFPAFLNI_00659 +MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES +PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA +VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG +TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTPGALP +APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM +SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD +VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR +AVAARLAAGDRARVVVAPA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001548.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001548.fa new file mode 100644 index 0000000000000000000000000000000000000000..88bf8e98b841e6d6db49a402777531a26ecb867a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001548.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_02269 +MEGPEITFAEAVIDNGAYGKRTIRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASVSTQLSGLPFSGPIGGVRMALVDDGAGKRQWVAFPKH +SQLQDAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGASAPTEEVVAEGLEAAKP +FIRALCEAQADLVKRAGKDPVDVPVFKDYEDDAFEAVEKLATDRLTEIFSIGDKQTRESA +SDAYHVEVMDELAGEDKPFAERRGEIAKAYGSVTKQVVRQRILKDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYLHHYNFPPYST +GETGRVGSPKRREIGHGALAERAMVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT +AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGAFVSLTPGKDGLLHVSELRKLNEGKRVDDVEDVLGVGQKVQVEITK +IDDRGKLSLSPVVAESDADAETADAIESSQTEA +>MOLHKGIG_00688 +MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH +SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP +FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA +SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST +GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT +AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK +IDDRGKLSLSPVVAESDALAETADAIESSQIEA +>NAFOICDF_02136 +MEGPEITFAEAVIDNGRHGTRTVRFETGRLAQQAAGSAMVYIDEETSMLSATTVGKHPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFTKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALLDDGSGQRQWVAFPKH +SQLEDAVFNMAVAGRVAGDDVAIMMVEAEAGENAWTLVKERGAQAPTEEIVAEGLEAAKP +FIRALCEAQADLAARAGKAPVEVPVFKDYEQDAYDAVEKIATDRLTEIFSIADKQEREAA +SDAYHLEVIEELAGEGKDFAERKGEVAKAYGSLTKQIVRRRILKDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYMHHYNFPPYST +GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAHVAGIAMGLVSAEVEGQTQYAALTDILGAEDAFGDMDFKVAGTSEFVT +AIQLDTKLDGIPASVLAGALTQAREARLHILSVLEAAIDQPDELAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGAFVSLTPGKDGLLHISELRKLNEGKRVEDVEDVLGVGQKVQVEITK +IDDRGKLSLAPVVADEDAAAGESREEDEEA +>MHAAABBN_00425 +MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH +SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP +FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA +SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST +GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT +AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGGSAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK +IDDRGKLSLSPVVAESDALAETADAIESSQIEA +>LFPAFLNI_00658 +MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH +SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP +FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA +SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST +GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT +AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK +IDDRGKLSLSPVVAESDALAETADAIESSQIEA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001549.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001549.fa new file mode 100644 index 0000000000000000000000000000000000000000..4dcf49c0f96158bd19eac1873b1a3d6af17b1634 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001549.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02270 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK +>MOLHKGIG_00687 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK +>NAFOICDF_02137 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK +>MHAAABBN_00424 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK +>LFPAFLNI_00657 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001550.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001550.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a44b7e3d990e1b3509afc2238258f6d6c5dd7d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001550.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_02271 +MTTASPPPPPPRGRLAPAAAPTPPGRRLDLPIIGAEYPQLLRTPRSRWWHPLLSAGLVLG +SVLVLLAVLTLPMMLALVSEVGWDVFASADPADLARVEEALFSAPMMLLNNLMLAAFIGI +AVLAVAVCHPVAARFVHSVQGRIRWRWLLRAHLVLLPLFLVYVLGTWALDGAPTAPRAED +WVWLVVMAFLLTPLQAAGEEYLFRGWLLLAIGSWFRRPLPAIVLAAAVSAVTFSLAHGSF +DPWILLDLSVFAVAAVLLTWRTGGLEAAVALHVVNNVVVIVFGTLAGTVNESFVDVETTG +SPLATLVSAAVIALSTALLLWQARRAGIARTVPVSVGARP +>MOLHKGIG_00686 +MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG +LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA +LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGAWALDGAPTAPRAQDWVWLLV +MAFVLTPFQAAGEEYLFRGWLLLAVGTWIRRPVVAAAVTAVLSAATFSLAHGSLDPWILL +DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL +LSVAVVAVATALLLWQARRAGIARTVPVTVGARP +>NAFOICDF_02138 +MRTPRARWWNPLASFGMVLLGVGVLTVLLTVPMALVLFQQLDPGELWSAEGPSEASLELA +LFSAPMVLLNNLLLAALTGVALLAVLVAHPVKARFLHSVEGRVRWRWLLRAHLVLLPLFL +VYVLGTWALDGARVAPRPEDWGWLLAMALLVTPFQAAGEEYLFRGWTMLALGTWIRRPGV +AVAVTAAVSAVAFALAHGSLNPWILLDLGVFAVAAVLLTWRTGGLEAAVALHVVNNVVIL +AFGTVTGLATESYVTASTQGDPLATLVSAAVTALATVLLLWQAKRAGVARTVPSAVGARP +>MHAAABBN_00423 +MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG +LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA +LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGTWALDGAPTAPRAQDWVWLLV +MAFVLTPFQAAGEEYLFRGWLLLAVGTWVRRPVVAVAVTAMLSAAAFSLAHGSLDPWILL +DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL +LSVAVVAVATALLLWQARRAGIARTVPVTVGARP +>LFPAFLNI_00656 +MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG +LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA +LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGAWALDGAPTAPRAQDWVWLLV +MAFVLTPFQAAGEEYLFRGWLLLAVGTWIRRPVVAAAVTAVLSAATFSLAHGSLDPWILL +DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL +LSVAVVAVATALLLWQARRAGIARTVPVTVGARP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001552.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001552.fa new file mode 100644 index 0000000000000000000000000000000000000000..40802566ee568080cebb30a4483d52c4ca9fa2bf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001552.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02279 +MLVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARERDALAVAVTFSPHPRS +VHRPDEPHVDILGPQQRAVLLSETGLDALLMQRYTLEFADQSPEEFVLSMFVRGLNAAVV +VVGHDVRFGRGNVGDFAEMVRLGALHGFEVEAVEEHPAEIGDEPERRCSSTWVREALAAG +DVAQAAAILGRHHTLDGEVVHGFARGRELGFPTANLAPEAEGMIPADGVYAGWVHDVQGE +AWPAAISIGSNPTFEGVSRVVEAHVIDRPEERVEDFDLYGQHIEVEFVQRLRGMVAYEGV +EKLVAQMTQDVEQARAILAATPSDR +>MOLHKGIG_00684 +MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA +VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV +VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG +DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG +VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV +EKLVAQITQDVDEARAILATTPSDR +>NAFOICDF_02140 +MLVWNSMAEVPTDLPRTVVALGNFDGVHRGHRAVLERVVEIAHERGQLAVAVTFTPHPRV +VHQPGLEHVEILSPEQRAVRLDETGIDALFLQHYTLEFAAQTPEEFVTSMFVRGLNAAAV +VVGRDVRFGRDNAGDFAEMVRLGGVHGFDVVAVEDLPAEDGDGERRCSSTWIRELLAAGD +VAHAAEVLGRNHVVAGAVVHGFARGRELGFPTANLEADAAGMIPADGVYAGWVHDAHGSV +WPAAVSIGSNPTFEGVSRVVEAHVIDRPEEPVEDFDLYGQQIEVEFVERLRGMVAYEGVE +KLVAQMHQDVDQARAVLAAAPQPAGRV +>MHAAABBN_00421 +MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA +VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV +VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG +DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG +VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV +EKLVAQITQDVDEARAILATTPSDR +>LFPAFLNI_00654 +MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA +VHQPEVPHVDIISPEQRVVLLEEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV +VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG +DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG +VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV +EKLVAQITQDVDEARAILATTPSDR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001553.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001553.fa new file mode 100644 index 0000000000000000000000000000000000000000..bc1b7ad90e4b67db06ffd762992f0238021027ad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001553.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02280 +MARTRTASGAARPGAAAPARNQGLGRIIVMVYAVFALSATARSLFQILTDVEAAPVAYSL +SAFAATVYIVATLALARSGARAWAVALGAVLVELIGVVGVGLWTVLDPGLFAEETVWSRF +GAGYGYVPLVLPVVGLAWLLAHRPSRPTAEEMAR +>MOLHKGIG_00683 +MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV +ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV +LPVVGLIWLLTHRPARPAEAGAL +>NAFOICDF_02141 +MVEQHPVADDGAPARPRRNQGLGRIIVMVYAVFALSASARSLFQILDHFWVAPFAYVLSA +FAAVVYIVATLALARSGPTAWKVAVAAVGVELAGVVGVGLLTVLDPQLFADATVWSRFGA +GYGYVPLVLPMVGLAWLLSHRPSREGRVR +>MHAAABBN_00420 +MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV +ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV +LPVVGLIWLLTHRPARPAEAGAL +>LFPAFLNI_00653 +MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV +ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV +LPVVGLIWLLTHRPARPAEAGAL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001554.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001554.fa new file mode 100644 index 0000000000000000000000000000000000000000..ddf220c85d220259467d9974a31fef31f79d6c8d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001554.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02281 +MILDAWFWAGLVIGAVSLAVCVAMTAIRRHPADSSILSVAAVELFLLVYAVAAAVRQLGG +EGLNGPGWEFWGYVVTALLVPVIAVAWAVTDKTRWSNLVLAVVGPTVVVMLHRMQVIWFG +QW +>MOLHKGIG_00682 +MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG +DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG +QW +>NAFOICDF_02142 +MILDAWFWTGAVVGGLSFVVCLAMTALRRHPADSSIVSVAAVELFLLVYGVVGAFRQLGG +QPLNGPTWEFWGYVLTALLVPVIAVAWAVTDKTRWSNLVMAVAGPTVVVMLHRMQVIWFG +QW +>MHAAABBN_00419 +MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG +DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG +QW +>LFPAFLNI_00652 +MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG +DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG +QW diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001555.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001555.fa new file mode 100644 index 0000000000000000000000000000000000000000..4623fb4a3c9c63cf1522c1a0a2071ed9a557c024 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001555.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_02282 +MDKPQGWTSHDVVGRLRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY +TATIRLGQSTVTDDAEGDVVQTRLANAVTPERVAEQVAALTGPILQAPSAVSAIKVAGRR +AYDRVRAGEDVALQARPVTVHEFTVHEMRRLDGGRLVDLDVTVRCSSGTYVRALARDLGE +ALETGGHLTALRRTAVGPFDVADALTLEELAEGFVMTGLSEAAAGLFPVRELTEDEAREL +AFGRAVAPTGSGEALVAGRAPDGRVVALISDVRRRGADVAKPQLVFAPAEGPGQGGTA +>MOLHKGIG_00681 +MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY +TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR +AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE +ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL +AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA +>NAFOICDF_02143 +MNARTAHAPTPDAPGTEASGVVLVDKPAGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATG +LLVVGVNKATRLLTAITGTDKEYTATIRLGQSTTTDDAEGEVVQTRLANAVTPERVAEQV +AALTGDILQVPSSVSAVKVAGRRAYDRVRAGEDVQLDARPVTVHAFEVEDFRRLDGGRTV +DLDVTVRCSSGTYVRALARDLGEALDTGGHLTALRRTAVGPFRVEDAVDLDALAERFVMT +ELSAAAAGLFPVRELTAHEAAELSFGRAIDPSGELAAAAGASGKAADGLVAGRTPDGTVV +ALLQDGRRSGRDVARPHLVFAPAEGQGKEEAR +>MHAAABBN_00418 +MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGADKTY +TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR +AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE +ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL +AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA +>LFPAFLNI_00651 +MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY +TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR +AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE +ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSKAAAGLFPVRELTEHEAHEL +AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001560.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001560.fa new file mode 100644 index 0000000000000000000000000000000000000000..d206d7f4c054ceea54171005060c668065a1b5c6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001560.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02287 +MVAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPVQALATNKMGSVFGTATSAITYRRRL +RQDLSTALPMAAVAFVAALAGAVVAASLPAGVIRPVILVALIAVAVFTAVRPGLGKTAGV +GPERRTAVARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKIVNLATN +LGALAFFIPAGHAVLGLGLLLGAANLVGGYVGARMAIARGTGFIRVVYLVVVAALIVKVG +ADTLAPLLL +>MOLHKGIG_00675 +MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL +RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV +GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN +LGALAYFVPSGHAVLGLGLLLGAANLMGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG +ADTLAPLLR +>NAFOICDF_02149 +MELFGPVELSVGIVLLVLAAGFSAGWIDAVVGGGGLLQLPVMLLVPGLSPVQALATNKMG +SVFGTAASAATYARRVRPDLRTALPMAAVALLCSLGGAVVATVLPAAVIRPVILVALVGV +ALVTALRPQWGLTQGLKHAGTAHALRALAVGAVVGFYDGVLGPGTGTFLILGLVGVLGYD +FLQASAKAKIVNLATNVGALAFFLPAGHVVLGLGLLLGAANLTGGYVGARMAISRGTGFI +RTVFLVVVCALILRLAWDVFAPLLG +>MHAAABBN_00412 +MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL +RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV +GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN +LGALAYFVPSGHAVLGLGLLLGAANLVGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG +ADTLAPLLR +>LFPAFLNI_00645 +MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL +RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV +GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN +LGALAYFVPSGHAVLGLGLLLGAANLMGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG +ADTLAPLLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001561.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001561.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a4bc5674135f8345bd262c305f226db5c0cc54e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001561.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_02288 +MALRMSTLFLRTLRDDPADAEVASHRLLVRSGMIRRAGFGTFTWLPLGLRVLRRVEQIVR +EEMDAIGGQEVHFPALLPKEPYEATGRWDEYGDGIFRVQDRKGADLLLAPTHEEMFTLLV +KDHYSSYKDLPAYLYQIQTKYRDESRPRAGLLRVRDFVMKDSYSFTVDDAGLDEAYEAHR +AAYERIFARLGLETVPVEATAGAMGGSRSEEFLHPCAIGEDTFVESPGGYRANVEAVTTV +APAPLDEAAMAALPAPEVKETPVSTTIAALVDVANELAPRAEGVWTAADTLKCVVLTAVL +DGDERRQFVVAVPGDREVDLKRLETTVAPALGLSGEPGVEAATEEDLRRHPSLVKGYIGP +GAGPDGGAPVLGAESVSGLPFLVDPRIAAGTAWITGANADQRHVFGLVAGRDFGWDGVVE +ATVVRDGDEAPDGSGPLTARRGIEMGHIFQLGRKYAEALDLKVLDQNGKQVVVTMGSYGI +GVTRAVAAIAESHRDEKGLVWPRAVAPADVHVLATGKGAEVFEAAEQIVAGLEAAGLTVL +FDDRPKVSAGVKFGDVELIGLPTSVVVGRGLADGVVEVKDRATGEARSVPVAEAVDAVVA +EVRDGR +>MOLHKGIG_00674 +MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR +EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV +KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR +AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV +APAPLDEAAMAVLPAAEVKDTPVSTTIAALVDVANRLAPRDGEPWTAADTLKCVVVTAVV +DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP +AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFTWDGV +LEATAVREGDQAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY +GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT +VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV +LAEVRDGR +>NAFOICDF_02150 +MALRMSTLFLRTLRDDPADAEVASHKLMVRAGYIRRAAPGIYTWLPLGLKVLAKVEQIVR +EEMDAIGAQEVHFPALLPREPYEATGRWEEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV +KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR +AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV +APAPLDEAAMAALPAAEVKDTPASTTIAALVDVSNELLPREDRPWEAADTLKCVVLTAVV +EGGERRQFVVAVPGDREVDLKRLEASVGPALGLVGEPDLEAATAEDLKRHPSLVKGYIGP +GAGPDGTPVLGAEDSVSGLPFLVDPRIAAGTVWMTGANADQKHAFGLVAGLDFTWDGVVE +ATVVREGDPAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDENGRQVVVTMGSYGI +GVTRAVAAIAERYHDEKGLVWPRAVAPADVHVVVATKGEDGVQAALDLAARLEERGLTVI +VDDRPKVSPGVKFKDAELVGVPTAVVVGRGLADGELELKDRATGASRAIALDSAVDEVLA +EVRPQG +>MHAAABBN_00411 +MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR +EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV +KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR +AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV +APAPLDEAAMAVLPAAEVKDTPVSTTIAALVDVANQLAPREGEPWTAADTLKCVVVTAVV +DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP +AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFMWDGV +LEATAVREGDEAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY +GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT +VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV +LAEVRDGR +>LFPAFLNI_00644 +MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR +EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV +KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR +AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV +APAPLDEAAMAALPAAEVKDTPVSTTIAALVDVANRLAPREGEPWTAADTLKCVVVTAVV +DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP +AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFTWDGV +LEATAVREGDEAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY +GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT +VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV +LAEVRDGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001564.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001564.fa new file mode 100644 index 0000000000000000000000000000000000000000..987ea2966e430c7a9bafc0c93be73ca88308b31f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001564.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02291 +MSAVEVLWYVLGVVAVALGLAVSIALHEVGHLMPAKLFGVRVTQYMIGFGPTIASWRRGE +TEYGFKAVPLGGYVAMVGMLPPPRPGQEPRTASTGFVQQLGRMADDARTQAAAELTAADE +GRQFIQLPVWKRVVIMLGGPFMNLLIALGVTALLVTTVGTSQPSTTAAEVYRCVVTTDEQ +QARAAEGGGQDCRPGDPVAPAHEAGLRPGDTVTSFDGRPVDDWDALSGLIRERAGQPTAI +EWERDGEPHSATITPRLTQRPVTDAVGRPERAPDGTALTEEVGFIGMGSQIETVQQSPLA +AGPVVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALQEA +ELADKAALLLSLVAGVNVALMVFNLIPLLPLDGGHVAGALWEALRRGWARLRGRPDPGPF +DLARMLPLTYAVAGLMLVMGVVLIVADIVEPIRLF +>MOLHKGIG_00671 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI +EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD +AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA +TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF +DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF +>NAFOICDF_02153 +MSAVEALWFVGGVVVVALGLALSIALHEVGHLVPAKLFGVRVTQYMVGFGPTVASWRRGE +TEYGIKAFPLGGYVAMVGMLPPPKGGTVARTGSTGFRARAGRMADDARAQAAEEITAADE +GRQFIQLPVWKRVVIMLGGPFVNLLIALALTAVLVSTLGVARPSTTADEVFQCVVSQSEQ +QSRAADGGAAQDCRPGDPAAPAYEAGLRPGDRVVSFDGRDVGSWAELSTAIRARAGQATA +IAWERDGTRTESTLTPLLTERPVTDALGVPERGADGGVKTEPVGFIGLASRQETVTLAPW +EAVPLVGRQAQGVVGVILALPQRLWDTAVAVVTPAPRDPNGPMSVVGVGRIAGEAAALDT +ASPADKAALLLSLVAGVNVALLVFNLIPLLPLDGGHVAGALWEGLRRGWARLRGRPDPGP +FDLAVMMPLTYVVGAAMLAMGVLLIVADIVKPVQLF +>MHAAABBN_00408 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI +EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD +AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA +TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF +DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF +>LFPAFLNI_00641 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI +EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD +AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA +TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF +DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001565.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001565.fa new file mode 100644 index 0000000000000000000000000000000000000000..a888dfc452d1f6b8da34c8add674978a839ea445 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001565.fa @@ -0,0 +1,44 @@ +>ACLBLIBL_02292 +MTHGSLTDYTLPAAGAPSASNAHDDGAPRAVALIGSTGSIGTQGLDVIAQDPARFRAVAL +SGGANTGLLAEQAVRFEVQAVGSATATEDELRAAIADAAARLGLKPAPRPALFTGPTAAE +RIAAWKGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP +VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALAEVTPAQALAHPTWDMGRVV +TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHPQSVVHSMVEFTDGSTLAQASPPDMRL +PIALGLAWPARVPGAAAGCDWTRAATWAFEPLDEDAFPAVRAAKEAAAASPTHMAVFNAV +NEEAVDAFHDGRIRFDAIVDTVRAVVGEYEPARVLGAAGHGHVAQDLTVEAVLAAEDWAR +TAARARW +>MOLHKGIG_00670 +MTHGSLTDYTLPAPAPAHDGGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN +TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP +GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS +ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS +LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL +CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD +AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR +W +>NAFOICDF_02154 +MTHGSLTDYTFPADHGPGASDGACRAVALVGSTGSIGTQGLDVIAQAPERFRAVALSGGA +NTALLAEQAVAHGVEAVGSAAASEEELRAALADAAARLRRPDPRPALFTGPEAAARIAAW +EGADTVLNGITGSIGLAPTLAALRAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEH +SALAQALRGGTAGEVRRLVLTASGGPFRGFSAAQLAEVTPAQALAHPTWDMGRVVTTNSA +SLVNKALEVIEAHLLFDVPLERIDVVVHSQSVVHSMVEFTDGSTLAQASPPDMRLPIALG +IGWPHRVLGAAAGCDWTQAAQWTFEPLDEAAFPAVSLAKEAAASSDTHMAVFNAANEEAV +DAFHGGRIRFDQIVETVRAVLGEYRPDGVLAAAGADPDELTVEAVLAAEDWARAAARGRW +>MHAAABBN_00407 +MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPTRLRAVALAGGAN +TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPSPRPVLFTGPCAAEQIAAWP +GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEHS +ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS +LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL +CWPRRLSGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD +AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR +W +>LFPAFLNI_00640 +MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN +TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP +GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS +ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS +LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL +CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD +AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR +W diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001566.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001566.fa new file mode 100644 index 0000000000000000000000000000000000000000..e2ce80b0965053b36d736b6349e8f7e460ab6cb4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001566.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02293 +MSALTPLLQAAPEAVGSPAVNIGIFLAFVVVTLVIVIRASKTSSSSADYYAGGRGFSGTQ +NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA +DVLSFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIAIVGV +LMIVYVLIGGMKGTTYVQIIKAILLIAGAGVMTVWSLAMFGFDFNAMLGAAVELNPEGEA +ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG +AFYLFTLVLGYGAGALIGPERIMAAPGGQNSAAPLLAFELGGSILLGVISAVAFATILAV +VAGLAITAAASFAHDVYGSVIAKHQLTPNEEVRIGKITVVVIGLLAIVGGIAAQGQNVAF +LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGAPTSMI +PGADFAIFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH +>MOLHKGIG_00669 +MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ +NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA +DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNINDRAGQALVIVIVGV +LMIVYVLIGGMKGTTYVQIIKAVLLIAGAGIMTVWTLALFGFDFNALLGAAVEKNPKGEA +ILEPGLQYGASALTRLDFVSLGLALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG +AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV +VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF +LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI +PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH +>NAFOICDF_02155 +MSTFALPLAAAVGDPVVNIGIFVAFVAVTLVIVIRASKKNASAADYYAGGRGFSGTQNGT +AIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMADVL +SFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNITDKGGQALVIVIVGVLMI +VYVLVGGMKGTTYVQIIKAILLITGAGVMTLWSLALFGFDFNAMMGAAVQLNPQGEAILE +PGLQYGKNFTTRLDFLSLGLALVLGTAGLPHVLMRFYTVPTAKEARTSVVWAIVLIGAFY +LFTLVLGYGAGALIGPEKILAAPGGVNSAAPLLAFELGGSILLGLISAVAFATILAVVAG +LALTAAASFAHDVWGSVIAKEPLTPEEEVRIGKITVVVIGVLAIVGGIAAQGQNVAFLVA +LAFAVAASANLPTILYSLFWRGFTTRGAVWSMYGGLIASIVLIVLSPVMSGAETSMIPTA +DFAVFPLKNPGIVSIPLAFVLGWLGSVTSKDVEDPDKQAEMEVRSLTGVGAEKPVAH +>MHAAABBN_00406 +MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ +NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA +DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV +LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA +ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG +AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV +VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF +LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI +PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH +>LFPAFLNI_00639 +MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNTSSADYYAGGRGFSGTQ +NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA +DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV +LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA +ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG +AFYLFTLVLGYGAGALIGPERITAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV +VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF +LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI +PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001567.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001567.fa new file mode 100644 index 0000000000000000000000000000000000000000..95c45f83b1dd22846a2b3c7f25cfccac7dd47587 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001567.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02294 +MSSSEPTAPAPTAAQFRAAQQSEEFTELRSTYRSFAFPMTVAFFVWYLVFVIAGAFFPEF +MSIRLGGNITLGLVLGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGGAPET +PEATR +>MOLHKGIG_00668 +MSSSEPTAPVPTAAQFRAAQQSEEFTELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP +EATR +>NAFOICDF_02156 +MSTGPHTPPAPTPAQFRAAQDSPEFRELRRTQRSFAFPMTVTFFVWYLLFVILGAFFPQV +MAVRLGGNITLGLVLGLLQFVTTFAITFAYVRFSNRVLDPRAAALRERLEREAAGAAPET +PEVAL +>MHAAABBN_00405 +MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP +EATR +>LFPAFLNI_00638 +MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAPENP +EATR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001568.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001568.fa new file mode 100644 index 0000000000000000000000000000000000000000..64457c83923ee4cecace3261ad06e3796e02bddb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001568.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02301 +MPAAVDPSAPAASAAAPTSRVAAKARRREDLLAAAARLFAARGFDAVRLEDIGAEVGISG +PAIYRHFAGKAAVLVAILATASQDLLEGALATEREHDAGEDALRALIAFQTDFALAQRDV +IRVQDRDMSALPEDERAAVTGTQRAYIDVWARQLRVVHPSEDQATAVFRAQAVLGLINST +PRSVRRTAADRAARRATLVAMAWAAATAPGPAADRP +>MOLHKGIG_00662 +MPAADPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP +AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI +RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPREDQATAVFRAQAVLGLLNSTP +RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED +>NAFOICDF_02157 +MPHAPDTAAPGPTGTPRERAKARRRAELLAAAARLFAAHGYEATRLEDIGAAAGISGPGI +YRHFAGKAAVLVEILSSASLFLLDGAEAVAARGLSGAEAVHDLIAFHTDFALANRDVIRV +QGRDMSSLPPADGAEITRVQRRYIDLWGAQLRRLHPGEDHATARFRTQALLGLINSTPFS +VRRSRADRGARRDALIGMAWAAARTPGGTARPEPPVVP +>MHAAABBN_00399 +MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP +AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI +RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP +RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED +>LFPAFLNI_00632 +MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP +AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI +RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP +RSVRRTAADRAARRATLVAMAWAAATAPGPLPGGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001576.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001576.fa new file mode 100644 index 0000000000000000000000000000000000000000..3276c5ce0db7b33b9548597d709ff43d8da6a284 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001576.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02310 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKAEKFITLGDVVLRAAVASGAADVESLLASEHEGRT +LGDHVIEEGALLGEKVAVRRLARVEGALVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA +AHDIAVHTAAYSPTYLSREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLEDQPFAKDPKQTVGKVASDAGTKVTGFARFRVGN +>MOLHKGIG_00653 +MANYTAADIKALRERTGAGMMDVKKALDEADGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASEHEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAYVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA +AHDIAVHVAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN +>NAFOICDF_02167 +MANYTAADIKALRERTGAGMMDVKKALDEANGDADKAVEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFISLGDVVLKAAVASGAADVDSLLASDHEGRT +LGDYVTEEGALLGEKVAVRRVARVEGAHVDAYLHKTSKDLPAQVGVLLAVDADSDAAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIAEESARAEGKPEQALAKIVEGRLTGFFK +EGVLVDQPFAKDPKTTVGKVASEAGTAVTGYARFRVGN +>MHAAABBN_00390 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN +>LFPAFLNI_00623 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001577.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001577.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd141f329bc211963f83a32ca66e6b5621573e44 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001577.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02311 +MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET +VAHGGTILFVGTKKQGQEVIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI +DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMSKTPSAVWVVDTKKEHLAVDEAKKL +GIPVVAILDTNCDPDEVTYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQSAAE +PMAEWERELLEQHNAQQAEQAEAPAEAQAQAEEASAEAPAQAEEASAGAPAQAE +>MOLHKGIG_00652 +MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET +VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI +DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL +GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE +PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAERAEAPAAEAAPQGE +>NAFOICDF_02168 +MSVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLTYIDRAYEFVKQT +VAHGGTILFVGTKKQAQEAIAEQATRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEAI +DFEDVAGSTHTKKELLLLNRELEKLQGNLGGIRDMARTPSAVWIVDTKKEHLAVDEAQKL +NIPVVAILDTNCDPDEVAYPIPGNDDAIRSVTLLTRIVADAVAEGLIARQGGKSGDSSAE +PMAEWERELLEQHNAEQAAQAEAPAAEAAESEAPAAE +>MHAAABBN_00389 +MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET +VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI +DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL +GIPVVAILDTNCDPDEVPYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE +PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAAPQGE +>LFPAFLNI_00622 +MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET +VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI +DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL +GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE +PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAEQAEAPAAEAAPQGE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001578.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001578.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3bde3de045103083d8bb20999c1aed25505c77b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001578.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02312 +MTARSPAPRRARPAASPHRLLAVLLLCVLGLALAFALGPGIGAATPSSIRAEDGPTADAR +LAVAATPARAWTAPAAGVRPGDVLRPFAAPERPWGRGHRGVDLAVSPGAAVLAPAAGTVV +FAGTVVDRPVVTLEHADGTRSSLEPVEAAAPVGARLERGAPLGTVADAPAHCAVPCVHWG +VRVPDGWRFGDATFDRYLDPLVLIGWSGPSVLWPHAAPPPAGPAPARE +>MOLHKGIG_00651 +MTPRTHLPRPLPRPHIAGCVAAALLAWLVLASGVGGLDAVPRATSAPSGRDALLLVAASP +AGPGSTAAPVAWHAPVAGAAPDDVLRAFVAPERPWGRGHRGVDLAVPSGAAIRAPAAGRV +VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW +GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP +>NAFOICDF_02169 +MNEASTPPPRLRAAAVLAVALLATASAARAEDAPAAPPVTGALLAPTPGAGPSDVLRGFA +GPERPWSRGHRGVDLATSSGLVTAPAAGTVRFVGSVAGRGVLTLAHPDGTLSSFEPVTSD +LTAGQAVAAGQEVARVQEGAAHCPVRCVHWGVRREDAWAVGAARFDRYLDPLLLLGWSGP +SVLWPVGDAG +>MHAAABBN_00388 +MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALEMGDLGPASRATPAPSTRDALLLVAASP +AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV +VFAGVVVDRPVLTLEHADGTRSSLEPVEADVAVGAVVDAGDPVGRLAGAPPHCPRACVHW +GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP +>LFPAFLNI_00621 +MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALGMGDLGPVSRATPAPSTRDALLLVAASP +AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV +VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW +GVREPDGWRVGEAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001579.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001579.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3700ae2ed605802d14eaafdf8eb05ea5c950923 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001579.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02314 +MSVTSSRAASRRAPRTAAASLALALGAGALAGVGSVTAAETAQAVETTYTVRAGDGWWVI +SQRTGVSMSTLQSLNGMTSATMLHPGMVLKTSGTAAPAPAPAPSASTYTVLAGDGWWIIS +YRTGVSASVLQSINGMTSSTVLHPGMVLKTSVVASSAPAPAPAPVTNGKQAAVDFVRSTV +QNPSSYYLWGGNGPYGFDCSGLTQQAMAKAGISIPRRAGDQYNAAKSYVPISQAQPGDLV +FYANQSTGRIYHVAMYMGGGQLAHALNEDAGLLFTSTTIMKSDMLAVAARY +>MOLHKGIG_00649 +MSVTSSHAAVRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETAYTVRSGDGWWII +AQRTGVSMSRLQSLNGMTAATVLHPGMVLKTSGTATPTPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASILQSINGMSSSTMLHPGMVLKTTSVSTSSAPAVAPAPAPASKQAAVDYVR +SAVRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPG +DLVFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY +>NAFOICDF_02171 +MPEALLTPARRPRAAAASLALALGAGAGVTAGAAVIAPQAVAAETYTVQAGDGWWIISQR +TGVSMATLMQLNGMTSADMLHPGMVLKTSGTVTAAAGTYTVKAGDGWYAISRATGVPVST +LTSLNGMTITSMLYPGMVLKTTGTPASTAPAPAPAPAPVVRQSSKQAAIDFAVAKVNDPN +TYYAWGGNGPYGYDCSGLTKAAFAAAGITIPRVSHDQYVNAPAYAPLSQAQPGDLVFWAN +QSTGRVYHVAVYIGNGKVAHALNTTDDLVITSTDVMTSNRLAVVGRY +>MHAAABBN_00386 +MSVTSSHAASRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII +AQRTGVSMSTLQSLNGMTAATVLHPGMVLETSGTATPAPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASILQSINGMTSSTMLHPGMVLKTTSVSTSSAPALAPASAPASKQAAVDYVR +AAVRNPSSYYAWGGNGPSGFDCSGLTQQAMAQAGISIPRRAGDQYLAAKSYVPISQAQPG +DLVFYANQSTGRIYHVAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY +>LFPAFLNI_00619 +MSVTSPHAAARRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII +AQRTGVSMSTLQSLNGMTAATVLHPGMVLKTSGTATPAPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASVLQSINGMTSSTMLHPGMVLKTTSVSTSSAPAPAPAPASKQAAVDYVRSA +VRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPGDL +VFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001582.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001582.fa new file mode 100644 index 0000000000000000000000000000000000000000..71b1c0221fbcce45ed16a0f70aacb963dc1f393a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001582.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02320 +MTTPEKKDAAAATPVQDSQLAHDDPRTRHPKLDAPEQRQEEPGLDVKTEPVPDIGLDSYR +GLGRLEGRKALITGGDSGIGAAVAVAYAREGADVAIAYLPEEQPDADRVLAAIEAAGRTA +VALPGDLMDAGYREGLVEEAATALGGLDILVNNAGKQIISESLEDLTDQQVLETFQVNIL +SMFTLSRAALTHMGPGSTIINTTSVQAYNPNPMILDYAATKAAINNFTKGLAQQLGERGI +RVNAVAPGPVWSVLQVSYGQPKEKLPVFGHDTPTGRGGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP +>MOLHKGIG_00642 +MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRVDKQRQPEPGLDVKTDPVPDIGLDSYR +GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA +VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM +SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI +RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSNPIGRAGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP +>NAFOICDF_02183 +MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDSYR +GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA +VALPGDLMDVDYRASLVDEAAQRLGGLDILVNNAGKQFISDDLVDLTDEQVHETFQINIM +SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI +RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPLGRAGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP +>MHAAABBN_00379 +MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRIAKQRQPEPGLDVKTDPVPDIGLDSYR +GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA +VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM +SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI +RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP +>LFPAFLNI_00612 +MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDAYR +GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA +VALPGDLMDADYRAALVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM +SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQVGPKGI +RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001584.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001584.fa new file mode 100644 index 0000000000000000000000000000000000000000..43f9900e4cb3d92a9355e52c35a8070a52d2407c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001584.fa @@ -0,0 +1,24 @@ +>ACLBLIBL_02333 +MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR +LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQMILDSQHTQHKAIWEDL +IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV +HESEAKPNG +>MOLHKGIG_00168 +MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR +LADRWERQLEIACGKPTAEATSMERLTAYILTCSTAASRAEFQMILDSQHTQHMAIWEDL +IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV +HESEAKPNG +>NAFOICDF_00676 +MAKTTEQLLDDAIAVLRRGGVVTIDSVASEAGMSKAGVVHHFSSKEALMVGVVNRVMDLW +EGQLAATIGEVTDPVERLRAYVDFEVLSDFDGGDLALLADVKLRDTLAAQWRERLRPWFG +EDAPGDAGQKAALQSARLIADGAWTDQALGLLSMTGEQRALVRGIAQRLIDEGVQK +>MHAAABBN_00359 +MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR +LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQLILDSQHTQHKAIWEDL +IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV +HESEAKPNG +>LFPAFLNI_02011 +MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR +LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQMILDSQDTQHKAIWEDL +IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV +HESEAKPNG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001586.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001586.fa new file mode 100644 index 0000000000000000000000000000000000000000..47b4833d80a81809b3f788652d557db93b422ead --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001586.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02350 +MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASASGS +ASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDDDA +KWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTDQT +VDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG +>MOLHKGIG_00584 +MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDASGS +ATSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDDDTTWE +VDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTLDE +MDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH +>NAFOICDF_02245 +MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT +SASASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDDDTTW +EVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDGVTLD +EMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH +>MHAAABBN_00317 +MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT +SASASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDDDTT +WEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTL +DEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER +>LFPAFLNI_00585 +MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDASGS +ASSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDDDTTWEV +DVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDGVTLDEM +DLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001587.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001587.fa new file mode 100644 index 0000000000000000000000000000000000000000..410dfea75d3aca291f70bf17dcbdc099e33029cc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001587.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_02351 +MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY +HCFGCGEHGDVISFLMELEHTTFTETVERLAARVGVELHYEDGGTGPDKAETGRRRRLLE +ANKVADEFYRRALGSAEAQTGRDFLTQRGFTQEHAEQFGLGYAPQGWSHLLDHLRQKGFR +DEELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP +LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKMA +RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTYVAVEPSGMDPCDLRMQQG +DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAAPIVAGIKDAVLRPGYERE +LAGWLGLDPNAVHRAVAAAGRGQRRGGGSEPRREPERGPEPDQAPGQGRGPAPEGPSVGP +QGRHGEAAAPAPQVLVPVDPRDPVARCERESLEVVLQHPTLLSAEQWTALYAARFTIPQY +AAVHHGVKVAGSSGATPQRWVDAVRYAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIM +NRLFALQIVHRKEELLGRLQRLGPDGDPAEFTALNSELMELEARRRALRADD +>MOLHKGIG_00583 +MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY +HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE +ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHATQFGLGYAPQGWSHLLDHLRQRGFR +DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP +LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA +RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG +DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAVPIVAGIKDAVLRPGYERE +LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPQGRHGEAAAPAPRIVV +PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT +PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL +GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD +>NAFOICDF_02246 +MVRMAGLIVRKDIDLVRERADLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGV +GTYHCFGCGEHGDVISFLMEMEHTTFTETVERLAARAGVELHYEDGQGPDRAETSRRRRL +LEANKLADEFYRARLAAPDAQPGRDFLTGRGFTQEHAEQFGLGYAPQGWSALLDHLRQQG +FRDDELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGNTIGFGARKLFEDDPGPKYLNTPE +TPLYKKSQVLYGIDLAKRAIAKERQLVLVEGYTDVMAAHLSGVETAVATCGTAFGADHIK +IARRLISDDGTGGEVIFTFDGDAAGQKAALKAFDEDHRFLAKTFVAVEPNGLDPCDLRMQ +QGEEAVRALIASRRPLFEFAISAGLKDYDLNTVEGRAGALRHAAPIVAGIKDSVLRPGYE +RELAGWLGMDPNVVSRAVAQELRGRRRGGPSGGSAERTPAPERAPEGANAGQAPGEEPAA +PRPALIVPVDPRDPAARRERESLEVVLQHPTLLSAEQWTAFYQARFTIPQYAAVHHAVKV +AGTAGATPSRWVDAVRDAAPGEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFSLQIV +HRKEELLGQLQRLGPEGDHDEFMRLNAELMELETRRRALRADD +>MHAAABBN_00316 +MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY +HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE +ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR +DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP +LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA +RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG +DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE +LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPTGRHGEAAAPAPKIVV +PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT +PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL +GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD +>LFPAFLNI_00584 +MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY +HCFGCGAHGDVISFLMELEHTTFMETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE +ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR +DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP +LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA +RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG +DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE +LAGWLGLGPNAVHRAVAAAGRAPRRGPEPEARPTPASDGQAVGPTGRHGEAAAPAPRIVV +PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKVAGSAGAT +PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL +GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001590.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001590.fa new file mode 100644 index 0000000000000000000000000000000000000000..ded538a8b393396d96bb3520253dbe7f04cfc168 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001590.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02358 +MAEGWAGPAHQPVLFGPQGRPPYAGRAVQTPGYTPWDRERWLPEPPKSSYRSDFERDRAR +VLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGRSLGCDPDLVDTACLSH +DLGHPPFGHNGEKALDALSADVGGFEGNAQTLRLLARLEQKKLFEDGSSAGLNLTRAALD +AACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFREGVSGSRKSMEAQVMDLADDIS +YSVHDVEDGVVNAAFQLKWLAIPEHRERVVETTRQWYLPLTDPAEVDEALARLEATDVWV +SEMDGSRRALAAMKDMTSQLIGRFCTAAFDATRQVFGNEPLTRHGADVVVPAETETEIAV +MKGIAAAYVMASEQRQPLYARQRELLAELVELLDASGDRYLEPMFAFDWREAADEAARRR +VVLDQVASLTDSTALEWHHTLVQGAEFTRVWI +>MOLHKGIG_00575 +MAEPTTPEPAAGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYPPWDRERWLPE +PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR +SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF +ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT +RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA +EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH +GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATGDRYLEPM +FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI +>NAFOICDF_02249 +MAEPQPTLFGPADRPPYAGRPVPTPGYTDWDRRRWLAEPPKSSYRSDFERDRARVLHSAA +LRRLGAKTQVVAPDLDDFSRTRLTHSLEVAQIGRELGRSLGCDPDLVDTACLSHDLGHPP +FGHNGEKALDAVAEAAGGFEGNAQTLRLLARLEQKKSFPDGSSAGLNLTRAALDAACKYP +WVREDAPLRPDGKRSRKFGVYADDLPVFEWFRQGVHGARKSMEAQVMDLADDISYSVHDV +EDGVVNSAFQLRWITEPGERRARVLETTRDWYLPGGDLEEIDAALTRLESQDVWMGEMDG +SRRALAGMKDMTSQLIGRFCTAAFDATREVFGNEPLTRHAADVVVPAHTEHEIAVMKGIA +AAFVMTSEQRQPLYARQRDLLTELVDLLMTTGDRYLDPMFAADFQDAADDAARARVVIDQ +VASLTDSTAIEWHRTLVRGETFQRVWL +>MHAAABBN_00307 +MAEPTTPVPAAGTPAAPSSHWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE +PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR +SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF +ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT +RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA +EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH +GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLEATGDRYLEPM +FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI +>LFPAFLNI_00576 +MAERTTPAPADGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE +PPKSSYRSDFERDRARVLHSAGLRRLGDKTQVVAPDADDFARTRLTHSLEVAQVGRELGR +SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF +ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT +RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA +EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH +GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATEDRYLEPM +FAFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001593.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001593.fa new file mode 100644 index 0000000000000000000000000000000000000000..c74507737fc7768181d0338e840e1f95f472f164 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001593.fa @@ -0,0 +1,33 @@ +>ACLBLIBL_02373 +MNECCNRDIRYENPLYMAEAAATADLLAGGRLELGVSRGSPEAAKDGQAQFGYELADGQT +WAGVTRKRGRRFLAAVRGEGIATPDLASGWAHSSAPLRIEPHSPGLADRIWWGSGSAGSA +VEAAKDGYDMLSSTLLLQDDGRPFHVQQADQIAGYLEAYEAAGHAGTGRTAVTRSAFVIQ +DHEDELYFGRDRNSRESAGMLDGGRARSGPTYAGSAEEVAEKLAADDAVQAADWVLFANP +NQLGPEYNAKIFAGWAEVWRLLGWDR +>MOLHKGIG_00572 +MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP +FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALD +GQAQFGYALDEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL +ADRIWWGSGSVGSVAGAATDGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG +PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD +DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA +>NAFOICDF_02253 +MTTKNLGFLNFGHWIHRPRVGRRPVEPDAKQAIDDVVQMAVDAEAAGLDGAWIRIHHFQR +MFSSPFPILTAMAAHTERIHLGTGVIDLRYENPLYMAEAAATTDLLAGGRLELGVSRGSP +EAARDGQAQFGYELADGQTWSDVARERGRRLLAGVRGEGIATPDLSSGWAHSSAPLRIEP +HSPGLADRIWWGSGTVGSAVEAAKDGYGMLSSTLLLQDDGRPFHVQQADQIARYLEAYEA +GGHTTPARTAVTRSAFVIQDHEDELYFGRDRHSRDSSGHLDGGAARSGPTYAGSAEEVAE +LLAADDAVQAADWVLFANPNQLGAEYNAKLFAGWAEVWRLLGWDS +>MHAAABBN_00296 +MRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALDGQAQFGYALDEGQTWADVTRER +GRRFLSAVRGEGIATPDLTSGWAHSSQPLRIGPHSPGLADRIWWGSGSTPSAVEAGRDGY +NMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHTGPGRTAVTRSAFVIQDREDELYF +GRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAADDAVAAADWVLFANPNQLGVEYN +AKIFAGWAEVWRLLGWDA +>LFPAFLNI_00573 +MTRKHLGFLNFGHWIHRPGTAPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP +FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLLSGGRLELGVSRGSPEAALD +GQAQFGYALAEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL +ADRIWWGSGSVGSVAGAAADGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG +PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD +DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001594.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001594.fa new file mode 100644 index 0000000000000000000000000000000000000000..63d76dc3c7688a51bd51726782a99886879db956 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001594.fa @@ -0,0 +1,38 @@ +>ACLBLIBL_02376 +MSGAYDDDAGALFDSAAVSGGEVVLRPWRAGDDLALLQVWGDPANVQQHQDRAMLAEDAE +RPWRRALVAEDAGVPVAAGVVYASSLHPQRLWLYVETAAPERRRGIGRALVAALRGLAAE +AHAAGTVPTAALKARFAKDALVPGTAVEEGVDTEAVRAQTAALAAGTEAFLAAEGFTPVQ +RSRRVAVAPGAIGLPDVRDEDRPDGVVLEEASTGSVELTQAVAAFYDAVHAWDPSTMSVG +AAQQLLLGPATGASGAVVLRDAPKAEGGRIRAFAVSYTPERQEAPADVLVGWDPELSEED +ALQSVADLLALLVAQHPVQVEVDEAMAPLERIVDGLIGGNAARTLVDTYVFVDDAA +>MOLHKGIG_00567 +MDLPAGVTLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAPDADTPWRHTLVAEDDGVPV +GAGTVVAQALHPRRLWLYLEVAPTARRRGIGSALLGALRDAVEQAHAAGQVTTTHLKTRF +AVASRVAVATGRSADAAEATAPAAGEEAGEAHAAQVAGTEAFLVAAAFSPVQRSRRVAVA +PGSIALPPLRDEDHPEGAVLEDAATGSVELTRAVAAFYDAVHGWDPAQMSVGAAQQLILG +PATGASGAVVLRDAPREEGGAVQAFAVSYTAERQDAPADVFLGWDPELPLDQAQLAAGQL +LAMLVAQHPVQVEVDEAMTALEPILDGLIAQRAAATLVDTRIWATDPA +>NAFOICDF_02260 +MSPRHDDDAPALTAAVSGGEVVLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAADADSP +WRRTLVAEEDGVPVGAAVAFAQPLHPGRLWVYGEVARTVRGRGVGRALLEALRGLVAAAH +EAGAVPTTELKARFAVASRVPVGGGEVVEAAPGEAPEAGAAGAEAHAAQVAATERFLVAA +GFTPVQRSRRIAVAPGVIALPALRDEEHPEGRVLEEISTGSVELTRAVAAFYDAAHAWDP +SQMSVGAAQQLILGPQTGAAGAVVLRDAPREEGGTIQAFAVSYTAERQDAPADVLLGWDP +SLGLEEAQLAVGDLLALLVAQHPVQVEADEAMTALEPILDALLAKRAAGTLVDTRVWATD +PS +>MHAAABBN_00292 +MTGAAGAAGHDDGGALFDSAAVAGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA +EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG +LAAEAHAAGAIPTTALKARFAKDALVPGVSGADPQTDAEGPAGQPPVDTEAVRSQTAALA +AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA +FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA +PADVLVGWDPELGEEDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART +LVDTYVFVDDAPGA +>LFPAFLNI_00570 +MTGAAGAAGHDDGGALFDSAAVGGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA +EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG +LAAEAHAAGAIPTTALKARFAKDALVPGVTGADPQTEADGATGRPPVDTDAVRSQTAALA +AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA +FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA +PADVLVGWDPELGEKDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART +LVDTYVFVDDATGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001595.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001595.fa new file mode 100644 index 0000000000000000000000000000000000000000..fb6c86a7fb3810fac3f2bf8e9857888e520196f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001595.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02377 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHKRHRQDHLLEAFEAKKGRPSASMD +EIVCPDCGTKGAWTEPQMFSGLVKTFLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDTWVEACWDWFID +LGIDPENLRRLDVPEEERAHYSDGTIDLEYRFGFGGGDGWGELMGVANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGTDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQALAAELRALWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMSQERVALSQVKSYLLERLVK +>MOLHKGIG_00566 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAGQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPTTQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK +>NAFOICDF_02261 +MAAKSPLDNVINLAKRRGFVFQAGDIYGGSRSAWDYGPLGVELKENIKAEWWRTFVRSRE +DMVGLDSSIILPRQVWEASGHVATFTDPLVECQQCHRRHRQDHLLEAFEAKKGRAAAGME +EITCPDCGTTGKWTEPQMFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKEHFDTWVEACWDWFID +LGIDPANLRKFDVPEEERAHYSDGTIDLEYRFGFAGGDGWGELMGVANRTDYDLTSHANA +SGAKLQYFDQANDVHYTPYVIEPSFGLTRSMMAFLVDAYTEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKLELQEPSQRLAAELRAHWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQSVTIRERDTMSQERVALAQVRAYLAERLTK +>MHAAABBN_00291 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPAEDRAHYSDGTIDLEYDFGFTGGDGWGELMGIANRTDYDLGQHTTH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQSLAAELRGLWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK +>LFPAFLNI_00569 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPYCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001596.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001596.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd5100801eeaad9e46d71f3f3f3222bb83182231 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001596.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02378 +MMDTMTETNPADARPLPIRDASIRLGQALKLAALVEDGAMARDVVQDGLVTVNGAVETRR +GAQLKDGDVVEFHGEAVVIEAGSAD +>MOLHKGIG_00565 +MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL +HDGDVVEFAGEAFVVQAEQA +>NAFOICDF_02262 +MTSSSDVQPLPIRDESIRLGQALKLASLVEDGAMARDVVQDGMVSVNGEVETRRGRQLHD +GDVVEFNGEEIVVEAGQS +>MHAAABBN_00290 +MMDTMTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRR +GAQLHDGDVVEFNGEAFVVQAGQA +>LFPAFLNI_00568 +MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL +HDGDVVEFAGEAFVVQAEQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001597.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001597.fa new file mode 100644 index 0000000000000000000000000000000000000000..07b675675eaa8f6574a96c976be28be60670eb83 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001597.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02379 +MNNDTANTAPSSETAPFTVRWSRPEGERTEDLLILLHGYGANEDDLFGLVPHLPERFTVA +AVRAPMTLQPGGYAWFPLSQDPVTGEIGSDAASVRTAIEDLHAWVGAVREGFRTVSLLGF +SQGMALATSLLRLDPTAYAATVALSGFVVDPTREESGLAGLFDGDDEVARVRPKVFWGRG +QDDPIISEARVEASHAWLNAHVDLMKIVYAGLPHAINQQELGHVKEYLEHMVR +>MOLHKGIG_00564 +MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT +VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL +GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELDEPRLRELFTRDDDVARVRPKVFWG +RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG +>NAFOICDF_02263 +MNDTTPRDPAPFAVRWSRPEGERTEHLLVLLHGYGADEDDLFGLVPQLPEAFTALAVRAP +MDLPQGGAAWFPLTQDPATGEIGSDAGAVRAAVEDLHAWLPGVSGGFRTVSLLGFSQGMA +MATSLLRLDPAAYAATVALSGFVVDPLHVEPELEGLFPADETVDAVTPKVFWGRGQEDPI +ISAQRVEESHGWLTAHTDLTKVVYAGLPHAISPQELGHVREYLTHVVL +>MHAAABBN_00289 +MNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHFTVAAVRAPL +PLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLLGFSQGMAM +ATSLLRLDPEAYACTVALSGFVVDPELTEPRLRELFTRDDDVARVRPKVFWGRGQEDPII +SEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG +>LFPAFLNI_00567 +MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT +VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL +GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELAEPQLRELFTRDDDVARVRPKVFWG +RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001598.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001598.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ad04309ee0c13a61936ad441a132cbed27240fb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001598.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_02380 +MRAESPDGDDFPSESTGGGGRGRRGRLTDDGGASRLLLVSNQQESAPQHPAAAEAEPPAD +VVTRAETAAHPWRRYVAIGDSFTEGIGDPDPDRPGYHRGWADRAAEELARRTPDGEDLAY +ANLAVRGKLLDQIAADQVEPALALRPDLISVCAGGNDILRRADPDDVAVRLDAVVERLSA +NGATVLLFNATDTKDTPVLGRIRGTVAIYNENVRTVALRHDALVADMWSLKELARREMWA +EDRLHFSATGHHTIAAMVLDTLAVPHGLEPLRPEPAAPRTWRQARASDAAWARTHLAPWV +VRRIRGVSSGDGVSAKRPVPAPLFGAEMPHGSDPTEPLDVVAR +>MOLHKGIG_00563 +MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAE +ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPAIALRPDLISVCAGGNDILRGADPDE +IAARLDAVVERLASAGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD +MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWRAARA +SDAAWVRTHLAPWVVRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDIVEP +>NAFOICDF_02264 +METMSPLTNTADSEPPHAEGHASAEPAHPWRRYVAVGDSFTEGIGDPDPERPGYHRGWAD +HLAEELARLTPAGEEFSYASLAVRGKLMDQIRADQIDPAVELAPDLVSICAGGNDILRRA +DPDETALHLDDAVGRLAETGATVLLFNVPDIKETPVLARIRGRVAIYNENIRTVAARHHA +VVADMWSLKDLARPEMWAPDRLHFSPVGHHTIAAMALDTLGVEHELEPLSPKRAAPRTWR +EARVDDARWARTHLVPWVGRRLRGVSSGDGMQPKRPLPAPLFGADMPHGSDYTEHAAD +>MHAAABBN_00288 +MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAE +ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDE +IAVRLDAVVERLASDGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD +MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARA +SDAAWVRTHLAPWVARRIRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTESLNVVEP +>LFPAFLNI_00566 +MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPERPGYHRGWADRLAE +ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDE +IAVRLDAVVERLASDGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD +MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARA +SDAAWVRTHLAPWVVRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDVVEP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001599.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001599.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0a3bf2ea270632f83572f67d054e727cc3df00d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001599.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02381 +MTATVSRPPRAALPEGGRHRLRIGELRTETGGVLPDVELAYETWGELDADGSNAVLVLHA +LTGDSHVAAHAADPTPGWWDALVGPGRAVDTDRWFVVAPNMVGGCHGSTGPSSPAADGRP +WGSRFPFLTLRDAVAAERRLADHLGVGAWQAVIGGSMGGARALEWAATHPERVAGVGVLA +ATARSSADQIAWGQAQTAAIRLDPGFLGGDYYEGAGPAAGLGIARRIAHTTYRTAGELER +RFGRSPQGAEDPFGAVVGVPGGRGRYAVESYLDHQATKLTGRFDANSYLLLTEALLGHDV +GRGRGGVEAALAGYRGRAFVAAVDSDRLYLPAEAQALAAVLPARPPVHTIVSPIGHDGFL +TEYGQVADALRDSLAL +>MOLHKGIG_00562 +MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA +LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP +WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA +ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ +RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLADRFDANSYLVVTEALMGHDV +GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL +TEYGQVADTLKRTLAL +>NAFOICDF_02265 +MTAIDPRILPGHAAHRPHQGPQGEAAPSARSAAPHDARPADRLPAGEFRTLSVGPLELEA +GGRLPGVELAFETWGTLAEDGANAVLVLHALTGDSHVASHRRDESAGWWEELIGPGLAVD +TDRWFVVAPNMLGGCDGSTGPSSPAPDGAPWGGRFPFVTIRDAVAAERRLLDALGVTALQ +AVIGGSMGGARAIEWAVSHPDLVRGVAVLASTASSSAEQIAWAQAQTHAIRLDPEWRGGD +YHPGPGPVTGLGIARRIAHTTYRSAAELQHRFGREPQGAEDPLGTASGERVGRYQVESYL +DHQASKLVGRFDAGSYVALTEALMSHDVGRGRGGVEAALASYPGRAFVAAVDSDRLYFPA +ESERLASLLPGEVPVHTIHSPIGHDGFLTEYGQIADELRRTLEL +>MHAAABBN_00287 +MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELAYETWGTLAADGANAVLVLHA +LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP +WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA +ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ +RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV +GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTITSPIGHDGFL +TEYGQVADTLKRTLAL +>LFPAFLNI_00565 +MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA +LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP +WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA +ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ +RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV +GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL +TEYGQVADTLKRALAL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001601.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001601.fa new file mode 100644 index 0000000000000000000000000000000000000000..1bb95bb856634bc24e6574605c5c6e5a1d399ec9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001601.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02383 +MDHVSYAAGPEGLDATVARIAEALGVERIKGGIHPRFGTQNALFPMAGGQYLEVVEALDH +PASLSAPFGQLVRSRSEQGGGWMSWAVSTTDIGRFERRLGREAVPGNRRFPDGRELSWRQ +IGIKGTIADPQLPFIMRWADGQEDMHPSQAAEAQASIERLSIAGSPDRLAEWLGGEGEDA +HVEDLNVEYVAPSGTPGIVSVTFRTPRGDVTL +>MOLHKGIG_00560 +MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMAGRQYLEVVEALDH +PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ +IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ +VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL +>NAFOICDF_02267 +MNTCRMDHVSYAAGPEGLDATVARIAERLGVERVKGGIHPRFGTQNALFPMTGNQYLEVV +EALDHPASLSAPFGQLVRTRSEQGGGWMSWAVTTNDIGRFERRLGREAVPGNRRFPDGRE +LSWRQIGVKGTLADPQLPFILRWADGQEDMHPSQAAPAQASIARLSIAGSPDRLREWLGG +TEDDEVADVSVDYVAPSGTPGIVSVTFSTPKGEVTL +>MHAAABBN_00285 +MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH +PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ +IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ +VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL +>LFPAFLNI_00563 +MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH +PASLSAPFGQLVRARTEQGGGWMSWAVATPDIGRFERRLGREAVPGNRRFPDGRELSWRQ +IGIKGTLADPQLPYILRWADGQEDMHPSQAAEPQATIEHLNIAGSPERLAEWLGGEDEDG +QVQDVNIEYVAPSGTPGIVSVTFRTPKGEITL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001602.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001602.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ecc747f9852a132955403cf424275676ee7cf7a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001602.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_02384 +MSLPVPPALASPVPTALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDKATQAPLGDQ +TTVLNPTVDDRWAFDLTYQLLGIAFALVPVLLVLHLMHLRGRNPFRTLGLDLRRPGRDLA +WGVGLFAVIGLGTLGVYAAGRALGLTTAIVANAMDESWYQIPVLLLSALRHSLLEEVIVG +AWLVDRIGYLQRLKAAGLDRDPVPAVPAAPARRTGAPSSSWTTPEGLFLPTCVATALLAL +ALLRGAYHLYQGVGPGIGNALMGVVFVLVFLRVRRVMPLVVAHFLLNAVGFVGYPLLARA +GLLG +>MOLHKGIG_00559 +MPATPRTSRTPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQAPLG +EQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRRPGRD +LAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLEEVI +VGAWLVDRLGYLQRLRAAGLARDPAPAVPSSWVSAEGLYLPTRAAVVVLALALLRGAYHL +YQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGYPLLARAGLLG +>NAFOICDF_02268 +MTATARPEHAAGRRGPGAPALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDQATRAP +LGDQTTVLNPTVADRWAFDLTYQLLGIAFSLVPVLLVLHLLWLRGRHPFRVLGLDLRRPG +RDLAWGLGLFTVIGVGTLGVYAAGRALGITTAIVANAMDESWYQVPVLLLSAARHALLEE +VIVGAWLIDRLGYLQRLREAGLGASSSWAGTEGLFLPLRTWPVVLSLALLRGAYHLYQGV +GPGIGNALMGAVFVLVFLRVRRVMPLVLAHFLLDAVGFVGYPLLARAGLLG +>MHAAABBN_00284 +MPATPRTSRTPAGPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQA +PLGEQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRRP +GRDLAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLE +EVIVGAWLVDRLGYLQRLRAAGLAHDPAPAVPSSWVSAEGLYLPTRAAVVVFALALLRGA +YHLYQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGYPLLARAGLLG +>LFPAFLNI_00562 +MPATPRTSRTPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQAPLG +EQTTVLNPALADRWAFDLTYQLLGIGFSLVPVALVLHLMHLRGRDPFRVLGLDLRRPGRD +VAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLEEVI +VGAWLVDRLGYLQRLRAAGLARDPAPAVPSSWVSAEGLYLPTRVAVVVLALALLRGAYHL +YQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHALLDAVGFVGYPLLARAGLLG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001603.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001603.fa new file mode 100644 index 0000000000000000000000000000000000000000..33ba1d3c7433810b1e2025a27947d0fac4b36ee6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001603.fa @@ -0,0 +1,36 @@ +>ACLBLIBL_02385 +MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL +RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG +TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR +AEHVAGIPGRLAPRLGAWPGDDVDARTGADAWADAVARVTRAVTAWTEEPPVPPSLVHGD +LAGHNMRWRAMPAADDAPGEVRWELAGVLDWDLACAWDPALNVAYLSLWHGEDQVERLAV +DAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLRKALPRVARALTALG +>MOLHKGIG_00558 +MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL +RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG +PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR +ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALTDAVTTWTAAPPVPPSLVHGD +LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWGPALNVAYLALWHGEQKVPDLAR +DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG +>NAFOICDF_02269 +MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL +RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG +PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER +AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR +EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV +AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR +KTLPRVGRALAAAAA +>MHAAABBN_00283 +MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL +RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG +PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER +ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALADAVTTWTAAPPVPPSLVHGD +LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWDPALNVAYLALWHGEEKVPDLAR +DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG +>LFPAFLNI_00561 +MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL +RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG +PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER +ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAAVTDAVTAWTAAPPVPPSLVHGD +LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDFACAWDPALNVAYLALWHGEEKVPDLAR +DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001604.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001604.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab784cfc44580b10a70cbf00335fb2071764d737 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001604.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02388 +MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG +TLPVLNREVVEYAVRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD +VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASNSLVDYNRAGVPLIEIVTKPIV +GAGARAPELARAYVTAIRDIVKAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN +VNSTRAVQHAVTHEIQRQAALLAAGGTVTQETRHWHEDTRTTTSGRPKSDADDYRYFPEP +DLVPVHVDAAWVERVRAEMPELPAVRNKRLKAEWGYTDEEFRDVVNAGVLDEIVATVEAG +ASPAAARKWWMGEIARLANVRETAVAELGVTPAHVVEVEELIAAKTINDKIAKQVLGLVA +DGEGTPKEIVEAKGLAVVSDDGALTEAVDAAIAANPDVAEKIRGGKMAAVGALIGPVMKA +TRGQADAGRVREIVLERLGVS +>MOLHKGIG_00557 +MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG +TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD +VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV +GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN +VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP +DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG +ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA +DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA +TRGQADAGRVREIVLERLGVS +>NAFOICDF_02271 +MSTAELMDFQEAMDRFDPVLGFEVHVELNTKSKIFSTGANAFGDEPNTNVTPLDLGLPGT +LPVLNREAVESAIALGLALDAQIAPSCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLDV +ELEDGTVFRVEIERAHLEDDAGKLTHQGGSGRIQGASASLVDYNRAGVPLIEIVTRPIVG +AGDRAPEIARAYVTALRDIVKAIGISDARMEHGNVRCDANVSLMEKGASAFGTRTETKNV +GSTRAVQHAVTHEIQRQAAILAAGGTITQETRHWHEDTRTTTSGRPKSDADDYRYFPEPD +LLPVVVDEAWIERVRAGMPELPAVRNKRLKGEWGFSDEEFRDVVNAGVADQIAQTVEAGA +SPAAARKWWMGEIARLANLREVEAAELGVTPAHVVEIEELIAAKTINDKIAKQVLGLVAD +GEGAPKQIVAAQGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMQAVGALIGPVMKAT +RGQADAGRVREIVLERLGVA +>MHAAABBN_00282 +MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG +TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD +VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV +GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN +VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP +DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG +ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEIEELIAAKTINDKIAKQVLGLVA +DGEGAPKEVVTAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA +TRGQADAGRVREIVLERLGVS +>LFPAFLNI_00560 +MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG +TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD +VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV +GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN +VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP +DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG +ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA +DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA +TRGQADAGRVREIVLERLGVS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001605.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001605.fa new file mode 100644 index 0000000000000000000000000000000000000000..259cae31d97d851d69ff86cb3e219b8b201ad8dc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001605.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02389 +MTQTFDATAELAADQLVRLTALQMAERLRAGTTTSVELVQAHLDRIAEFDGDPRADAAAD +RGVRAYLHVNAEEALAVAAEVDAIRAAGGAEAEALHPLAGVPVAVKDNIVTQGQPTTAAS +RMLDGWMSPYDATVVTRLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDLDRVPGG +SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI +GPAARTVADAAALQQVIGGHDPQDSTSLAEEQADLAAAARGRDLAGLRVGVVTDLPADAF +HPGIRAAFDEHVAALREAGAQIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR +VVPDGGGTIEQVMGATRAAGFGDEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQEDFA +RAFEQVDVLLTPTAPTPAFELGAKTDDPLTMYVNDLATIPANLAGIPGLSLPGGVVEGLP +YGLQLMAPAREDARLYEAGAALERLVEDGRGGPVWAQAPELEKGAQRAATATTAGGRA +>MOLHKGIG_00556 +MTETFDVNATIGADELVRLTALQMAERLRAGTTTSVELVQTHLDRIAAHDGDVRADAAGD +RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS +RMLEGWFSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG +SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI +GPAARTVADAAALQQVIGGHDPQDSTSLADAPADLTAAARGRDLAGLRIGVVTDLPAEAF +HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR +VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA +RAFERVDVLLTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGVPGMSVPGGVVDGLP +YGLQLMAPAREDARLYEAGAALERLVAERRGGPVWAEAPELEKGAQRATTATTAGGRA +>NAFOICDF_02272 +MTQTFDVNASLSADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAVDGDPRSDAASD +AGVRAYLHVNTEEALAVAAEVDAIRAAGGAEAEALHPLAGVPVALKDNIVTVGQPTTAAS +KMLDGWMSPYDATVVERIRAAKLPILGKTNMDEFAMGGSTEYSAFGVTRNPWDGQRVPGG +SGGGSAAAVAGFLAPFALGSDTGGSIREPAAFTGTVGVKPTYGAVSRYGVIAMASSLDQV +GPAARTVADAAALQQVIGGHDAHDSTSLPEEQADLVAAAAGRDLAGLKVGVVTDLDAEGF +HPGVKAAFDADVQALRDAGAEIVEVSCPHFAAALGAYYLIMPSEVSSNLARFDGVRYGHR +VVPDGGGTIEQVMAASRAAGFGGEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA +AAFEQVDVLLTPTAPIPAFRLGEQTKDPLTMYLNDLFTIPANLAGVPGISVPGGLVDGLP +YGLQFMAPAREDARLYEVGAAVEKLVTEREGGPLWARVPEQHPGAARAAQTPAGGTK +>MHAAABBN_00281 +MTETFDVNATLGADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAHDGDVRADADGD +RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS +RMLEGWLSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG +SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI +GPAARTVADAAALQQVIGGHDPQDSTSLADAPADLTAAARGRDLAGLRVGVVTDLPAEAF +HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR +VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA +RAFERVDVLLTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGIPGMSVPGGVVDGLP +YGLQLMAPAREDARLYEAGAALERLVAERRGGPVWAEAPELEKGAQRATTATTAGGRA +>LFPAFLNI_00559 +MTETFDVNATLGADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAHDGDVRADADGD +RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS +RMLEGWLSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG +SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI +GPAARTVADAAALQQVIAGHDPQDSTSLAEAPADLTGAARGRDLAGLRVGVVTDLPADAF +HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR +VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQEDFA +RAFEQVDVILTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGIPGMSVPGGVVDGLP +YGLQLMAPAREDARLYEAGAALERLVAQRRGGPVWAEAPELEKGAQRATTATTAGGRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001606.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001606.fa new file mode 100644 index 0000000000000000000000000000000000000000..f44826668f16f7f31e774afe0050a06af6fa47db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001606.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02390 +MPEITRDQVAHLARLAHIQMSDEELATVSGELEQILGHVSAVQAAAGADVAPTSHPIAMS +NVFREDVPAGMLTQEQAVDQAPDAQDGQFKVPAILDGE +>MOLHKGIG_00555 +MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE +NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE +>NAFOICDF_02273 +MAEITRDQVEHLARLAHIRMTDEELDVMSGELESILESVSQVQAVAGEDVVPTSHPIPLE +NVFREDVPTGMLTQEQALDQAPDAEDGQFKVPAILDGE +>MHAAABBN_00280 +MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILKHVSAVQAAAGDDVTPTSHPIALE +NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE +>LFPAFLNI_00558 +MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE +NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001608.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001608.fa new file mode 100644 index 0000000000000000000000000000000000000000..89a68d27c94b74ef29bdd7de3678b14ead6fea6e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001608.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02393 +MSSPTRVAHVPSQPPGISGLLVVAKAAARAGADVLARRWTGHHPAVPLGREEIGAETKTS +GSDWVTDYDRRAEQAVREVLVAYRPQDEITGEEYGATVPAEPSGLRWSIDPLDGTTNFVR +GLPQFCTSVAVTGPVDEETAALLGVPAGTRRWLAGVVAAPALGRTWFASAGRGAFSTADA +TTAGVDVPDRDAAPVRITGPAPGRSGRLLATGFGYDPARRAMQVRALAALLPAFGDVRRI +GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALIAEEAGVRVRRPASGDGTAHPDWMVAG +DVDEAALAAAQEETA +>MOLHKGIG_00552 +MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR +RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA +VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR +DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV +ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM +TGERA +>NAFOICDF_02278 +MSAAPARPASPAGLLVIAKAAARAGADVLAERWAGHHPAVPLTSDELGADTKSSGSDWVT +DYDRRAEDAVRAVLTGYRPHDEITGEEHGSTAPVEPSGYRWSIDPLDGTTNFIRGLPQFG +TSVAVEGPVDEETAALLGVLPGSRRWLAGVVAAPALGRTWFASAGRGAFSTADATTAGVA +VPDRDAAPVRLTGPVPGRSGRLLATGFGYHPGRRAMQLRALAALLPAFGDVRRIGSAALD +LCMVADGTLDAYAEFGTQEWDWAAGALIADEAGVPVDRPASGDGTGHPDWMTAGDVDAAA +LAAAKEATA +>MHAAABBN_00277 +MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR +RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA +VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR +DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV +ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM +TGERA +>LFPAFLNI_00555 +MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR +RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA +VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR +DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV +ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAV +TGERA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001609.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001609.fa new file mode 100644 index 0000000000000000000000000000000000000000..6e97bef658966a470ccd32b9f7c8203719f1f686 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001609.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02396 +MEPSAETPAAAPRPEAAGATHVGAVRELNEDAWTLVGDPLVLAAVADGMGGHEAGEVASA +AAIEVLRRRGPEVLAPGVAHTPEELGHLVHEADAAVVAAGGGRSGTTLTVLACIDTAANR +WAVANVGDSRIYLRPAGAPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGS +SEPLTVDVAEIPVASGDRLLLCSDGLTGELLDEEIRALIDDADELEDALVKLVEAALWRG +GRDNVTAVLVRIP +>MOLHKGIG_00550 +MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA +AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW +AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR +EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG +RDNITAVLVRIP +>NAFOICDF_02280 +MSEPHAADAAPAEPGAWASVPRPEAVAVTHVGAVRELNEDSWAVVGDPLLLAAVADGMGG +HEAGEVASAAAVAELHRRAPSVLAPGVAHTPQELGALVHEANAAVLAAGGGRAGTTLTVL +ACLDTEVGRWAVANVGDSRIYLRPVGAGVLQQVTVDHSAVQLMVDAGELTPAEARVHPRR +NVITRALGSTQALTVDVMELDVAPGDRFLLCSDGLTGELLDDEILAIMDDAATLDEAAER +LVEAALWRGGRDNITAVLVRIP +>MHAAABBN_00275 +MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA +AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW +AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR +EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG +RDNITAVLVRIP +>LFPAFLNI_00553 +MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA +AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW +AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR +EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG +RDNITAVLVRIP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001610.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001610.fa new file mode 100644 index 0000000000000000000000000000000000000000..b59d3f67c4d400c90d6310572a4919cca54662c8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001610.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02397 +MSRAETPETAPLPIIAPDGSGPAEAPRRKDPHDERRADRHEDRRGEAAADRLEEVDAPPP +GAGWTTAMRTLDAGLVVGPRAYTAREVAQRMGVSTASARKIWRALGYPTSPEGHKAFTEA +DVEAFESVLELVRSGALNEDAAISLARSIGQMTDRMVVWQIEALVEDKIVSEGLTDPEAR +RAAVDLLPEIVTPLERAMQIVYRRQLNRAVKRLTVRVEAGLAASEEGRDGSESDSPLPLA +RAVGFADMVSYTTLSRTMDDRTLARMVQRFETLSAEIISAGGGWLVKTIGDEVMFNAETP +ETGAAIALALAEAIAADDELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADPGTVL +VDAMTAAALSRDERFVLVPQPPRIVRGVGEVRPSLLLNGSAQTLLAD +>MOLHKGIG_00549 +MSRPETPDTAPLPIVPPAEDETARDVEERSAEPAGWTSAMRTLDAGLVVGPRAYTSREVA +QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS +IGQMTDRMVVWQIEALVEDKIASEGLTDPEARRAVVDMLPDMVGPLEKSMRIVYRRQLNR +AVQRLTVRVEAGLAASAEGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL +RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT +WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF +GEVRPSLLLDGSAQTLLAD +>NAFOICDF_02281 +MTRDTHHDAVPETAPLPVQAPAGAADPAVGRRESDALHHGWTSAIRTLDAGLLDRPRSYS +RREAAQRLGISSVSARKIWRALGYPTVKDEEKVFSAEDIDAFEQVLSLVRDGMLNEDTAI +SLARSVGQMTDRMVVWQIEALVEDQIAAEGKTDPEARRAAVEMLPGLVEPLEKVMRIVYR +RQLTNAVQRLTVRVEAGLAASERGRDGSEDDAPLPLARAVGFADMVSYTTLSRTMGERTL +ARTVQRFESKAAEIIAAGGGWLVKTIGDEVLFNAETPEAGATIALALAEAMADDDQLPAA +RVSLAWGRVLSRLGDIYGPTVNLASRLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPR +IVRGFGEVRPSLLMNGAAQPLIAD +>MHAAABBN_00274 +MSRPETPDTAPLPIVPPAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA +QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS +IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR +AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL +RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT +WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF +GEVRPSLLLDGSAQTLLAD +>LFPAFLNI_00552 +MSRPETPDTAPLPIVPSAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA +RRLGVSMGSARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS +IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR +AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL +RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT +WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF +GEVRPSLLLDGSAQTLLAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001611.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001611.fa new file mode 100644 index 0000000000000000000000000000000000000000..35ec3da944279bcc27817d1f899ce9a6f6dafe06 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001611.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02398 +MRLEPGEQVMVRTRTHPRALLRPAAVLVTVAFLLGLAMGVLARPDLPGILTQNRALLETA +AWAVAVLALLPGVLLPVLRWATRRTVVTSRRIVQRTGLGGGADVAMSLVSIADVQRRRRG +SGAGDLHILFQERARQVHWRLRDVPEAARFEEALAHLTRQARVASWPAPAPTGGPR +>MOLHKGIG_00548 +MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGLVAANRAVLEAA +AWVVAALVLLPGTVRPLWRWVFRRTVLTDRRILQGAGIGGSGAAMPLVSIADVQRRRRGS +GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR +>NAFOICDF_02282 +MRLEPGEQVVVRTRSHPRVLVGTAARLTGTAFLLGLAMGLLARPGLPSPLRAAVPWLEAV +VWAAAVVAVLVGVVRPLLRWATRATVLTSERLVQRPGLGAGPEAAMPLVSIADVQRRRRG +ASSGDLHILFQDPLRQVYWRLADVPEAERFEQVLAETTRAARDRARPAMPAWGGVL +>MHAAABBN_00273 +MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA +AWVVAALVLLPGTVRPLWRWVFRRTVVTDRRILQRAGVGGSGAAMPLVSIADVQRRRRGS +GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTRTWPAPVPTGDLR +>LFPAFLNI_00551 +MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA +AWVVAALVLLPGTIRPLWRWVFRRTVLTDRRILQGAGVGGSGAAMPLVSIADVQRRRRGS +GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001612.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001612.fa new file mode 100644 index 0000000000000000000000000000000000000000..915449c2234dce40e217d3162aac452fb506c5ad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001612.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02401 +MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELD +ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIV +DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAF +NIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL +>MOLHKGIG_00546 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD +ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV +DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF +NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL +>NAFOICDF_02284 +MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELD +ALATHRTTAFGMDAKHPAGDGVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVMASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE +DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALV +DDGHLLQLQEMYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAF +NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN +PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL +>MHAAABBN_00271 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD +ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIV +DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF +NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL +>LFPAFLNI_00549 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD +ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV +DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF +NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001614.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001614.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4af868b35f4e665c28aa5cf161d74e98c111b6d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001614.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_02403 +MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRA +DDELNARLLADLEALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV +FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVIEQARAHGA +AGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI +ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPE +RTLNGTAALQAWMQRLSDEAVQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR +PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG +EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLK +AFHTRALRLGGMGLDTLRAALA +>MOLHKGIG_00544 +MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA +DDELNARLLEDLAALELQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV +FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA +AGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI +EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE +RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR +PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG +EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK +AFHTRALRLGGMGLDTLREALA +>NAFOICDF_02286 +MTQTTSAPEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALD +ELNRTTLEELAGLEPADDVDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFD +LMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAGHVAAVRQVEIVVEQARAHGAEG +GFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGIEH +YRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPART +LTGTKALQEWMQRLSDEAVEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPG +RMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAMMNRGTLNLWRRNFAWTSGHGEG +WALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTPEK +GYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAF +HTRALRVGGMGLDTLREALA +>MHAAABBN_00269 +MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA +DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAV +FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA +AGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI +DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE +RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR +PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG +EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK +AFHTRALRLGGMGLDTLREALA +>LFPAFLNI_00547 +MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA +DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV +FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGG +AGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI +DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE +RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR +PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG +EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK +AFHTRALRLGGMGLDTLREALA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001615.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001615.fa new file mode 100644 index 0000000000000000000000000000000000000000..c85da5d6390ab0f324e70b83655da47a1fa0a9f6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001615.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02404 +MRHDDGAAGPGVRPRLVLGSASPGRAEVLTRARVPFRVVVSDVDEAAVGAAAPEADPCEL +AVLLAEAKGRDVAARVAAAGVDGPTLVLGCDSVFEFDGRAHGKPYEPEVAVARWRAQAGR +SGRLHTGQWAGLLLPGEDGAVPDAETSTCVGADVRFAAVDEDTVRAYVATGEPLHCAGAF +TIDGAGAALVESVDGDPNAVIGLSVVVLRAQCEELGLRFADLWEKC +>MOLHKGIG_00543 +MIPHDDGAAGLGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE +LAGLLAEAKGRDVAARVAAAGVDAPTLVLGCDSVFEFDGRAHGKPYEPEVAVERWRAQAS +RQGVLHSGHWLGLVLPESGAGSGMAEEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA +FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGEDFTRLWEPSNAQR +>NAFOICDF_02287 +MSTLPHGGGAPAALVLGSASPGRAQILRRALLPFRTVVSRVDEEAVGAASPGATPAELAR +LLAEAKAEAVAGVVAAEGVDRPTLVLGCDSVFELDGQALGKPWEPETAIARWRAQSGRSG +TLHTGQHVILLTPGTDAAGAPASGATVSAGVAFTDVDEATIRAYVATGEPLQCAGGFTID +GAGAALVESVEGDPNAVIGLSVSTLRRQCSVLGVDLSALWGSSNCDA +>MHAAABBN_00268 +MIPHDDGSAGPGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE +LAGLLAEAKGRDVAARVAAAGVEAPTLVLGCDSVFEFDGRAHGKPYEPEVAVERWRAQAG +RQGVLHSGHWLGLVLPEPGVGSGMAAEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA +FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGQDFTRLWEPSNAQR +>LFPAFLNI_00546 +MIPHDDGAAGPGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE +LAGLLAEAKGRDVAARVAGAGVEAPTLVLGCDSVFEFEGRAHGKPYEPEVAVERWRAQAG +REGVLHSGHWVGLVLPEPGVESGMAAEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA +FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGQDFTRLWEPSNAQR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001616.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001616.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed9186113327cd1e2b75d1bab684a245b6bdd7b4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001616.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02408 +MSRTTTPADGTAAGLEAAAEVPRGRVITASLVGTSIEFYDFYVYATAAVSVFPLIFFPGD +DQTTALLASFAVFGTAFVARPIGSVLFGHFGDIMGRKVTLIGSLLTMGIATFLIGLLPTA +FQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYAAEGKRARAAMWPQLGAPIGFFLA +NGLFLALVIGFGHDSTNPDHDGAFLNWVWRLPFLLSIVMVAVGLYVRVKLEETPVFQRAI +ANDTRVKAPLGEVFKRNWWELILGTFIMYATYVLFYLMTTWILSYAIGKTENGMLGVPYA +EFLVLQLIGILFFAAFVPASGWLADRFGRKPTLLTVSALMVLFGLSFGLWLSAERMGTGA +GVNVPLMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGISYNVSSILGAALTPFL +AAWLVKEYGVAYVGYYLAAASVITMIALALAPETRHTDLDGVTSARERRAASV +>MOLHKGIG_00541 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLSEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNGPLMVAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQKFDVSYVGYYLAAASAITVIALVLSPETRHTDLDTVTSARERRAAR +>NAFOICDF_02290 +MSHTTARSAEAPSVEDVPKSRVILASLVGTSIEFYDFYVYATAAVSVFPLIFFPGDDPTT +ALLASFAVFGTAFVARPIGSILFGHFGDRMGRKVTLIGSLLTMGIATFLIGLLPTAFQIG +LWAPAMLVVLRFCQGLGLGGEWSGAALLATEYADHGKRARAAMWPQLGAPIGFLLANGLF +LILVRAFGHDSTNPQLEGSFLTWVWRVPFLLSIVMVAVGLYVRVKLEETPVFQRALEDDT +RVKAPLGEVFKRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKTQNGMLGVKYADFLV +LQLVGILFFAAFVPVSGWLADRFGRKPTLLVVSGLMVVFGLSFGAWLSPAAMGQGDALNV +PSMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGAALTPFLAGWL +VKEFGVATVGWYLAIASVITMAALALSPETRHADLHEVTSARERRAAAR +>MHAAABBN_00265 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQKFDVAYVGYYLAAASAITVIALALSPETRHTDLDTVTSARERRAAR +>LFPAFLNI_00544 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTSPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQRFDVSYVGYYLAAASAITVIALALSPETRHADLDTVTSARERRAAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001617.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001617.fa new file mode 100644 index 0000000000000000000000000000000000000000..a7ec6c8e9d199a5100870aea4c417bafd1fb24e6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001617.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02409 +MVAAKLGARVTLVERQGVGGAAVLTDVVPSKTLIATADSMRRVGLAEDLGVDLGDAEPRA +DMRQVDRRILDLAGEQSRDIRAALERRGVRVIDGVARVVGPNEVSVRTLQDADAEPEVIT +SDAILVAVGASPRELPTAVPDGERIFNWKQLYAMTELPEHLIVVGSGVTGAEFASAYNRL +GAKVTLVSSRDRVLPGEDADAAELLEKVFQDNGLTVVARSRAEAVERTETGVRVELSGEG +AADTPYVEGSHALVAVGGIPNTAGLGLEDVGVELTESGHVKVDGVSRTTVPSIYAAGDCT +GNLALASVAAMQGRIAVAHLLGDALKPLRPHLLASNIFTSPEIATVGVTQAQVDSGQYQA +DVLRLDFATNPRAKMSGVQEGFVKIFARQGSGTVIGGVVVSPRASELIYALALAVTHKLH +VDDLADTFTVYPSMSGSIAEAARRLHVRI +>MOLHKGIG_00540 +MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGADVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI +>NAFOICDF_02291 +MNVTEENTTFLPSLTIIGGGPGGYEAALVAAKLGARVTVVERAGMGGSAVLTDVVPSKTL +IATADSMRRVMAASGLGVDLGEAQPHADMHAVDRRILELAGQQSSDIHRALEKRGVRVVI +GDAVVTGPHEVTVRRRGIEEGEEPEVITSDAILVAVGASPRELPTARPDSERIFNWKQVY +ALQDLPEHLIVVGSGVTGAEFASAYNQLGAAVTLVSSRDRVLPGEDPDAAELLEDVFAQN +GLDVAGRCRAESVERTETGVRVHLSGEGADGRPYIDGSHCLLAVGGVPNTAGLGLEEVGV +ELTESGHVKVDGVSRTTVPSIYAAGDCTGQLALASVAAMQGRIAVAHLLGDALKPLRPHL +LASNIFTSPEIATVGVTQAQVDSGQYQADVIRLDFATNPRAKMQGVSTGFVKIFARQGSG +TVIGGVVVAPRASDLIYSLALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRV +>MHAAABBN_00264 +MEPVTEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGVGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGAEAHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLSGSGHVLVDGVSRTSVPSIYAAGDCTGTLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI +>LFPAFLNI_00543 +MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGGDVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRAI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001619.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001619.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4751f9ce35dde190a8e3d27006e6749df65afaa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001619.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_02411 +MSGPEHLPPTADDDAVPASEARALALAERWSVEDPDPMHREALRAELDAAAGSGPEAEAA +RASLASRFSGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLARHLWEDVGEDAAAPLAV +VGYDARRGSLGFAQDTAAVLTAAGVQVVLLPDALPTPVLAFAVRHLSADAGVMVTASHNP +PADNGYKVYLGGRMTDEAGRGAQIVSPADVAIAELIDHEAWTADIPLAEDGWTVAGDELL +EAYREAALAVLDEDRHPDRALRIVYTPLHGVGGAVLPGLLDEAGFGPVHVVPEQAEPDPA +FPTVAFPNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPFPGPDGTRVWRMLSG +DAVGTLLGAHLLPALAAAERSVANSVVSSPQLAALAEAQSVAHHVTLTGFKWISRAPRLG +FGYEEALGYCVDPDMVRDKDGITAALVAAELVAGLAARGCTVADALADVDAVTGSMPSGQ +VSVRVADLSVIPRTMAALRAQGPATLAGEPVTVRRDLAEGGAGLPSTDALLFATASGTRV +LVRPSGTEPKLKCYLGARDADPAVAAERLEALRAEVAALVGG +>MOLHKGIG_00538 +MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAALAA +RFAGPLVFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR +RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY +KVYLGGRLTDEAGRGAQIVSPADAEIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA +ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF +PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDADGARTWRMLSGDAVGTL +LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA +LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA +DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG +TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG +>NAFOICDF_02293 +MRALDPRVRELAERWSVEDPEPMHRAVLMDELAAADGDDPAAEAARASLASRFSGPLAFG +TAGLRAEEGPGESRMNRLVVRRTAAGLGRHLWNELGPDQPAPLVAVGYDARRGSADFAAD +TAAVLTAAGAQVVLLPRALPTPVLAFAVRHLHADAGVMVTASHNPPADNGYKVYLGGRMT +DEAGRGAQIVSPADVQIAAQIDHDAWTADIPLAAEGWEVAGEDLLEAYRAAALGVLDPGG +HPGRDLRIVYTPLHGVGGAVLPDLLAEAGFADVHVVPEQAAPDPAFPTVAFPNPEEPGAM +DLALALAAEVGADLVIANDPDADRLALAVPAGDGAAPSWRMLSGDAVGTLLGAHLLPRLA +AQGRSAANSVVSAPQLAALAAAAGVEHHVTLTGFKWISRAPRLGYGYEEALGYCVAPDMV +RDKDGMTAALVAAELAASLKAAGRTLDDARADADAVTGSMPSGQVSVRVQDLRIIADTMA +ALRARPPAALAGDPVTVERDLAAGSADLPATDALLFATDAGTRVLVRPSGTEPKLKCYLG +TQDADPTAAAARLDRLREEVAALVAG +>MHAAABBN_00262 +MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAVLAA +RFAGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR +RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY +KVYLGGRLTDEAGRGAQIVSPADAQIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA +ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF +PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDAHGVRTWRMLSGDAVGTL +LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA +LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA +DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG +TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG +>LFPAFLNI_00541 +MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAVLAA +RFAGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR +RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY +KVYLGGRLTDEAGRGAQIVSPADAEIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA +ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF +PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDADGVRTWRMLSGDAVGTL +LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA +LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA +DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG +TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001620.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001620.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d7dd0249fa2ddb1f83fe832124bec4b24a69ca6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001620.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02412 +MTRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELAGS +DVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRAVA +EAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH +VALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD +>MOLHKGIG_00537 +MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS +DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA +EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH +VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD +>NAFOICDF_02294 +MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE +GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA +VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV +EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD +>MHAAABBN_00261 +MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELADS +DVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRAVA +EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH +VALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD +>LFPAFLNI_00540 +MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS +DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA +EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH +VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001621.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001621.fa new file mode 100644 index 0000000000000000000000000000000000000000..563bd3e180a4b57d4345bd99c2275a85acaa3f9a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001621.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02414 +MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA +LMVPYLVWAVVMSAAALAWFGDDPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFATVL +RRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRRVQP +RIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFGAAV +ERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLALGI +SWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP +>MOLHKGIG_00535 +MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS +LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL +RRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQP +HVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV +ERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL +SWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP +>NAFOICDF_02296 +MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS +LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV +ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR +VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG +AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA +LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA +>MHAAABBN_00259 +MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRSLMVPYLVWAAL +MSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVLRRFLERFPSAV +AWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQPHVRRHRTLIGV +GLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTVERLLRSFARRT +GTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALALSWLAGLALLAT +PLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP +>LFPAFLNI_00538 +MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS +LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL +RRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRRVQP +HVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV +EGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL +SWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001623.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001623.fa new file mode 100644 index 0000000000000000000000000000000000000000..cbbc50dd8fa8afc1a8fe6039de6238eca0cd4c16 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001623.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02419 +MTETGTTDQRAAAQPALDLAVRVRLGHARIAYVMEEAELRGLHVKGYAAEPGVYRGRRSS +SDVDLLVHPSDAAAAVELLASHGWAPVADFSEGSIFEHAATLWHDHLGYVDVHRLFPGLG +TDAARTFDALWAERTTRVIAGRPVPVPGPVHQRLVVIVHAARDSHRGALDVRHIRDTSSP +AEWDALRQEARRLHATAAWHVATGEDADGMDAHDLALFEALQDDESGLDLFRTRWRTAHS +ARERARLVLHTLPVNRPHLQMRLGHAPTRADLWREQRSRATALARWAWTRGVRRGR +>MOLHKGIG_00533 +MGERATRQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDHRRSS +DVDLLVHPADATAVIELLRSHGWEPVATFSEGSIFQHAATLWHDQLGYVDVHRLFPGLGA +SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE +SWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRSAATA +RERAVLVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR +>NAFOICDF_02301 +MTAAPAPLETRVRLAHARITHLMAAAGVRSLHIKGYAMGPGVYAGGRTSSDVDLLVHPAD +LSHALDALTSHGWRRIADFAEGSVFEHAATLWHDQLGYVDVHRRLPGLGRSPVDAFEALW +GERTTTVVAGHAVPVPSLRHQRLVVLVHGARDAGRGRFDVDHLRHTLDAGQWAELRVQAQ +ILGAGAAWSIATGETDVAGVDEREALLLSAVRGDESGIRLLATRWHAARGWRERLHLLVR +TVPVNRAHLQMRLGRPPTTADVLREQASRGAALTRWAAGKAVPRVGR +>MHAAABBN_00254 +MGEHATGQRPAAPPSLDLEVRVRLAHARITHLLERAGIRGLHLKGYATEPGVYPDHRRSS +DVDLLVPPADAAAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFPGLGA +SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE +SWAALREEARRLDAGAAWHVATGEAADGVDTRQLTLFAALHESQSGLELFRTRWRSAATV +RERAALVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR +>LFPAFLNI_00533 +MLAAMGERATGQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDH +RRSSDVDLLVPPADADAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFP +GLGASPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRES +LPAESWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRS +AATVRERAALVARTIPVNRPHLQMRLGRPVTRADLWREQGARLGALAGWAWTKAVRRDR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001625.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001625.fa new file mode 100644 index 0000000000000000000000000000000000000000..619fa8fd9aad91b62094b394c604c86c06fc391f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001625.fa @@ -0,0 +1,110 @@ +>ACLBLIBL_02421 +MPPRPPPVVAPLLPRLRAERAIEAAAASAARPLEARGVELEIGLPDGARAPLLTVLAEAL +AEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGAR +LAVLRRLAHPEEHAQGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALA +DAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDHPVRIEFFGDEVEQMRWFSVADQRSLEDT +TEDGSGHPTELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSP +LLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDIA +GADQSAAGGFLTVAELRAAALEQDQGFWSVTALAPDDELLPDAATLRSTLGVPRTFAGDM +EAMVEHTRTRLAEGWHAVILTDGPGSARRLAELHADAGLTASVADGPVPAEPAPGRVTIA +TAAVGAGFTVPDERLAVITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLALQPGDHVVH +AQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLV +SSYVGGEAPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQS +ELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQ +VAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTH +RLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIR +ETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVARRIAE +LVPEARIAVAHGKMGEARLEQIMVDFWERRFDVLVSTTIIETGLDIANANTLIVEDAHRY +GLSQLHQLRGRVGRGRERAYAYFLYDAQKPLGEVALERLKAVATHNELGAGMQLAMKDLE +IRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDY +VPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPDPVEALVAVARFRNHARAAGIT +EVMLLGQNVKFGPAADLPESRQMRLARMYKGSQVKPALNGVLIPRPKTKPVMGQDLVDVP +LLEWAQQVIDAIFAPEG +>MOLHKGIG_00531 +MSAPETTPVLAPLLPRLRAERALEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEA +LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGA +RLAVLRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL +ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED +TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS +PLLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV +AEADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVPQTFSGD +IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSI +ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGGHVV +HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL +ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ +GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK +QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVIEGLAHGEVDVVIGT +HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI +RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA +ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR +YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL +EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD +YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV +TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV +PLLEWAQQVVDAIFAPEG +>NAFOICDF_02303 +MSPADVTAPVPVLAPLLPVLAREPAFEAAAASAARALPARGQELEIGLPDGARAPLFAHL +ADALAAGHGADAVLLVVTATAREAEDLIGDLAAWADPASVALFPSWETLPHERLSPRSDT +VGARLDVLRRLAHPGEDGRPPLRVVVAPVRSVIQPLVRGLGELAPVHLRVGQERDFDAVV +QDLADAAYARVDMVSRRGEFAVRGGLIDVFPPTADHPVRVEFFGDEVEQMRWFSVADQRS +LQDTSEDGSGHPTELHAPPCRELLVTPSVQERARALMARLPGAADMLERIAEGQAVEGME +SLSPLLADGMTSLVHLLPEGSLTLLVEPERIRSRADDLLATNEEFLAAAWAGAAQGAQAP +VDLGADQSAAGGFLTLAELREAVLEERQGHWSTTALSPDAELLPDASALRSSLGVPTTFG +ADMEAMVRFTRERLADGWSVVLLTDGPGSARRLAELHADAGLTASVLDGPVDPAPAPGRV +RVATAAVGTGFTDPETKLAVVTEQDLFGRHRTAGTRAAGGKLARRRRNAVDPLALQPGDF +VVHSQHGIARFVELQRRPVTGGARKRPGEEESYREYLVLEYAPSKRGAPGDRLFVPTDQL +DLISQYVGGEAPALSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMATRGHSFAPDTP +WQAELEEAFPYIETPDQLTTIEEVKKDMESPVPMDRLVSGDVGFGKTEVAVRAAFKAVQD +GKQVAVLVPTTLLARQHHQTFTDRFAGFPVTVAALSRFQTAKESKEVVEGLAAGEVDVVV +GTHRLLSKEVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLT +GIRETSTLATAPEERHPVLTSVGPYTDQQVIAAIRRELMREGQVFYVHNRVTTIDKVASR +LAQLVPEARIAVAHGKMSESRLEQIMVDFWEKRFDVLVSTTIIETGLDIANANTLIVEDA +HRYGLSQLHQLRGRVGRGRDRAYAYFLYDAQKPLGEVAMERLKAVAQHNELGAGLQLAMK +DLEIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLP +HDYVPGERLRLEMYRSLATAVDDAAVDAVVEEMKDRYGPLPEPVQALVAVARFRNRAREA +GVTEVMLLGQNVKFGPAADLPESRQLRAQRMYKGAQLKPALNALLIPRPKTKPVMGQDLV +DAPLLEWADQVVQAIFAPEPVSAG +>MHAAABBN_00252 +MSAPETTPVLAPLLPRLRAERALEAAAASAARPLESRGVELEIGLPDGARAPLLTVLAEA +LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGTAALFPSWETLPHERLSPRSDTVGA +RLAVLRRLAHPEEHAEGPLRVVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL +ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED +TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS +PLLAEAMTSLPRMLPAGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV +AGADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDDELLPDAATLRATLGVAQTFSGD +IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELTTEAGLTAAVVDGPLPADLAPGRVSI +ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVV +HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL +ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ +GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK +QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGT +HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI +RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA +ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR +YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL +EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD +YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV +TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV +PLLEWAQQVVDAIFAPEG +>LFPAFLNI_00531 +MSAPVLAPLLPRLRAERAIEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEALAEG +HGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGARLAV +LRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALADAA +YSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLEDTTED +GSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSPLLA +EAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDVAGAD +QSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVAQTFSGDIEAM +VAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSIATAP +VGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVVHSQH +GIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLISTY +VGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQGELE +EAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQVAV +LVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTHRLL +SDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIRETS +TLATAPEERHPVLTSVGPYSDQQVIAAIRRELMREGQVFYVHNRVTTIDKVAKRIAELVP +EARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHRYGLS +QLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDLEIRG +AGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDYVPG +ERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGVTEVM +LLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDVPLLE +WAQQVVDAIFAPEG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001626.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001626.fa new file mode 100644 index 0000000000000000000000000000000000000000..9368f402fde2acf8567003fd71fe155633641c63 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001626.fa @@ -0,0 +1,37 @@ +>ACLBLIBL_02422 +MPALWAVALILLLSGTAKLRSGEDVQATFTRLRVPRPFAAPALARAFPWLELLLAAALLQ +PFTQLRPVVGLVAVALFAAFLALVVRAKGDGVSCGCFGEASAAPISRTTVVRNVVFLVLA +VLALAEGIVSLAVHGGGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAA +PAASTPEAPAAVDPADGAEPERHPFPDALVIEDGRYTGLHALASRGAVVALRLSAGCGSC +SRVIARLDEFRASLGPVRLRVLMPQHEAGATPSASTGAIPEDLVVDDPNGAAARGLGLTS +YPMAVLLGTDLLTAGGPVGGADDVLAFLEEIRDIMAAEAPAAPAAPARSPASDTPTPEVR +A +>MOLHKGIG_00530 +MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPALARAFPWLELLLAAALLQ +PFTPLRPVVGLAAVALFAAFLALVVRAQDDGVSCGCFGEASAAPISRTTVVRNVVFLVLA +VLALVEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVTVLLTTAAFLAGRESVPAAPDAA +PATPEAPATPEAPDAADPVGEAEPERRPFPDAVVVADGEYTGLHRLVQDGAVVALRLSTG +CGSCARVIERLDEFKDALGPVRLRVLMPQRAPGADGAIRSGAVDASLVLADPDGAASQAI +GLHSFPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAATDGSTATPEVRA +>NAFOICDF_02304 +MSALWAVALIMLFSGAAKLRSREDVGAVFTRLKVPAPWNDARLARAFPWLELLLALALVQ +PFTVLRPLVGLAAVALFVAFLVLVVRATGDGVSCGCFGEASAAPITGQTVVRNVLFLLLA +VMALFEGVASLAVHGIATEWLPLTAFGEDVTAWTVVVTLLLAAAAVLVGRESVPAAASAV +PVPAAGVPGSAAPAPAEGQGDEPERRPFPVAAVQQGGAFVTLHQLVIPGAVVALRLSVGC +GSCSAVIARLPELVERLGPIRVRVLMPQTVPGGELRHGTIPAELVLEDPAGAAAGGLGLT +GFPSAVLLGADGMTAGGPVFGADEVIAFLEEIGEIVATELPAAAEGSHRP +>MHAAABBN_00251 +MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPGLARAFPWLELLLAAALLQ +PFTLLRPVVGLVAVVLFAAFLALVVRAQDDGVSCGCFGEASAAPISRTTVVRNVVFLALA +VLALAEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAV +PAMPTPEAPAAVDPAAVDPADGDPADAAEPERHPFPDAVVVADGEYTGLHRLVADGAVVA +LRLSTGCGSCARVIERLDEFTDALGPVRLRVLMPQRAPGAEGAIHSGAVDASLVLADPAG +AASQALGLYSFPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAATDGSTATP +EVRA +>LFPAFLNI_00530 +MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPGLARAFPWLELLLAAALLQ +PFTLLRPVVGLVAVALFAAFLALVVRAQDDGVSCGCFGDASAAPISRTTVVRNVVFLALA +VLALAEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAV +PATPTPEAPAVADPADGAEPERHPFPDAVVVADGEYTGLHRLVQDGAVVALRLSTGCGSC +ARVIERLDEFKDALGPVRLRVLLPQYAPGAEGAIRSGAVDASLVLADPAGAASQALGLHS +FPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAAMDGSTATPEFRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001627.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001627.fa new file mode 100644 index 0000000000000000000000000000000000000000..70ad9d137791ef81188e3782a6b07c4013be075d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001627.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02423 +MAFSAQQSIPHPPAAVAAALASEEFHRSVVEQLGGSLVSFRVEGSPEGPMTVTTVRSAPA +DRLPEMARKFIGSSLQVEQVERWEAPAADGSRVGTTTITVPAAKATAEGAQRLTAAGEGS +QYSVDGTVTCKIPLVGSKLAAKAEPMVGKVVNRQARALTSWIGRDGGAAGA +>MOLHKGIG_00529 +MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGALRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG +>NAFOICDF_02305 +MAFSAQQTIPHPPAAVAEALFSEDFHRSVAESLGGGLVSFARQDQADGGVELTIVRSGPT +DRLPDMVRKVVGENLNIEQVERWSAPAADGSRTGTTTIRVPKAKATAEGTLRLAAAPAGT +EYGVNGDLQVKIPLVGSKMAQMAEPMVGKVVARAGREVSAWIDRGGRG +>MHAAABBN_00250 +MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGSLRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVDRQARALSSWLERDGGAARS +>LFPAFLNI_00529 +MAFSAQQPIPHPPSAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRTGTTTITVPSAKATADGSLRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001632.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001632.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb80da26eee7d108e98862f04c8d34ee67b81393 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001632.fa @@ -0,0 +1,31 @@ +>ACLBLIBL_02435 +MKGIILAGGTGSRLHPITHAISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAGQ +FQRLLGDGSRFGISLTYVQQPSPDGLAQAFLLGEEHIGDDHVALVLGDNIFYGPGMGQQL +RRHTEVHGATVFGYRVADPTAYGVVEFDGTGRAVSLEEKPTAPKSHYAVPGLYFYDNDVV +EIARALKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE +SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLDLLENAR +>MOLHKGIG_00516 +MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGIRDILVITTPQDAEQ +FQRLLGDGSQFGVSLTYVQQPSPDGLAQAFVLGEEHIGVDHVALVLGDNIFYGPGMGQQL +RRHTDVEGATVFGYWVKDPTAYGVVEFDTNGKAVSLEEKPAQPKSNFAVPGLYFYDNDVV +EIAKDLKPSPRGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFTDLNDASNFIHAVE +SRQGLKVGSPEEAAWRQGLLTDDQLRERAERLVKSGYGRYLLDLLDSGR +>NAFOICDF_02317 +MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAEQ +FQRLLGDGSQFGVSLSYVQQPSPDGLAQAFILGEEHIGDDRVALVLGDNIFYGPGMGQQL +RRHTEVEGATVFGYWVADPTAYGVVEFDGAGKAVSLEEKPKEPKSNYAVPGLYFYDNDVV +QIAKDLKPSPRGELEITDANRVYLERGMLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE +SRQGLKVGSPEEVAWRQGLLTDDELRQRAEPLVKSGYGRYLLGLLDRADPIGRSSR +>MHAAABBN_00236 +MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAQQ +FQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDEHVALVLGDNIFYGPGMGQQL +RRHAQVDGATVFGYWVVDPSAYGVVEFDDAGKAISLEEKPEEPKSNYAVPGLYFYDNDVV +EIAKSLKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE +SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLELLESGR +>LFPAFLNI_00515 +MNPDRTALNLHHRIGPMKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILA +GISDILVITTPHDAEQFQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDDHVAL +VLGDNIFYGPGMGQQLRRHSEVDGATVFGYWVADPTAYGVVEFDGDGKAVSLEEKPAQPK +SNYAVPGLYFYDNDVVEIAKELKPSARGELEITDVNRTYLERGALNVEVLPRGTAWLDTG +TFKDLNDASNFIRTIESRQGLKVGSPEEVAWRQGLLTDNELRERAEPLVKSGYGRYLLDL +LETGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001634.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001634.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5bc1172cb5fb3ebb4a78a5642be7d6e680a24f6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001634.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02439 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLAQLA +AEYPGLDLSWTVFGENRGRVAALDAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ +RGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRVLHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTSTKARRALHSGSARQIF +IAKHGADALGGDRAPGGLWGAAVRAVATLSTERTIQYSSAVIERAAAVLPAPIARKLIAL +QVEAAAETGRTRPGRARRQF +>MOLHKGIG_00512 +MTETPLAPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEAHVVVDGDVDGSEGMLAQLA +AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHAGGS +GGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRTLHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF +IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPIARKLIAL +QVEAAAETGRTRPGRARRQF +>NAFOICDF_02322 +MSDQTAYEASVIVPSRGGAGRLPRLIGALAAQEEAPPFDVHVVVDGDVDDSASALERLAA +AHPDLPLTWTVFEENRGRVAALNAGADATTGRILIRADDDLEPGVHYIRDHVAAHAEGPG +GAIGLYLNILESTPYQRVYGDAQDVLHREHAYALPADQQWRHWAGNVSVPRAVHEELGGY +DPDYRQYGWEDIDFGYRLHAAGYPVRIRPELATSHHAAAVTTYSKAVRALHGTAARNLFI +QKHGAEVLGGVDAPRGLWGAAVRLVALGATEGSLTRSSALIDAIADRVPITVARKLIALQ +VEGASEAGRAYPERAQRPI +>MHAAABBN_00232 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLGQLA +AERPGLDLSWTVFPENRGRVGALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHSGEP +GGAIGLYLNVLEPTPYQRAYGDTQDVLHREHAYALQADQQWRHWAGNVSVPRALHQQIGG +YDPDYRQYGWEDIDYGYRLHAAGYPVVIRPELETRHHAAAVTTHSKAVRALHGTAARNLF +VGKHGAAPLGTIGAPRGVWGAAVRLVAWGTTEATLTRSSALIDAVADHLPRGLARRLIAL +QVEGAAEAGRAHPHRAQRSI +>LFPAFLNI_00511 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEGMLAPLA +AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ +RGVIGLTANVLPDSAYQRVYGGAQDEAHRRHAYALPAEQQWRHWAGNVSVPRALHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF +IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPVARKLIAL +QVEAAAETGRTRPGRARRQF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001635.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001635.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9fe7213cf4cb37a7c6c6c7c1d0cf264f85554b3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001635.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02440 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAANGFDVVRV +GGPGRLGYLRALRAWDRDRGNDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLAPSRFAADRIRGARVLHNWVPGPTTPPARRARDADEPVTVGFLGRLSEDK +GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTAE +FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGNDHPFVFPQRDAAAL +ADRLQAVRAGDLGAVAHSQRRRWASLFSPEAGRAAVAELLDDLSL +>MOLHKGIG_00511 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRL +GGPGRLGYLRALRAWDRGRGKDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLAPSRFAADRIRGARVLHNWVPAPTTPQAGRARDADEPLTVGFLGRLSEDK +GIVTLLEAAALLRKTDPGAFVFRVAGESRFVADDEAERLATALKAAGEDVQVLGWQDTAE +FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSEHPFVFPQRDAAAL +ADRLQAVRAVDLGAVAHSQQRRWESLFSPEAGRAAVAELLDDLSL +>NAFOICDF_02323 +MTRRIWIAANQGEVGGGEVMLHHLATALHELGRDIAVVAPAAPSATAARLEADGFTVDRV +GGPGRAGYMRALRRWHNGHREDVVWCNGLLPATALAGRPRRIVHLHQWLIRPRDRVLGTL +AMRGALAVIAPSESVAREIPGCRVLHNWVPRPLPLSGAAPARRRPGEGGALRVGYLGRLS +FDKGFHLLMDVAEELHREQPDEWRFFVAGEPRFTTGDDAREIRERLAASRAVTALGWQAP +GDFLPTVDVLVVPSLAPESFGLVAAEAMAAGVPVAVSDSGALPEVAGDDHPLLFECDDHE +ELAAALRRARQIDLAPLVAAQHRRWEALFSPEAGRAGVAALLEELHV +>MHAAABBN_00231 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV +GGPGRLGYMRALRVWDRGRGGDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLVPSRFAADRIHGARVLHNWVPGPTTPQAGRARGTDEPVTVGFLGRLSEGK +GIVTLLEAAALLRRTDPGAFVFRIAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTGE +FLTSVDVLAVPSQWAESFGLVAAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL +ANCLRAVRAVDLGEVAHSQRHRWASLFSPEAGRAAVAELLDDLSL +>LFPAFLNI_00510 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV +GGPGRLGYLRALRAWDRGRDGDDVAWCNGLLPATALAGRPRRIVHLHQVPEKPVLRVFSA +LARPGALAVLVPSRFAANRIRGARVLHNWVPAPTAPQTRPARGADDPVTVGFLGRLSEDK +GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEADRLATALKAAGEDVQVLGWQDSGE +FLATVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL +ANCLRAVRAIDLGAVAHSQRHRWESLFSPEAGRAAVAELLDDLSL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001636.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001636.fa new file mode 100644 index 0000000000000000000000000000000000000000..14ad1baf4812e249b52eefac17da27cfd4c79982 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001636.fa @@ -0,0 +1,70 @@ +>ACLBLIBL_02442 +MITERHLTPYLVFPEDSLLVALQKMTDNRERIVFVVDSHGFLAGSLTDGDFRRWLLANPG +ASLEVAAVEAANRTPATGPVGASPAEVLAALPAGALHLPLLDERGRLAALAINRESELRI +GEHRIGPGRPAFLIAEIGNNHQGSVDLARELVDLAVEAGADAVKFQLRDMDALYRQSGAG +TAGEDLGAQRTLDELAKFSLPAEDMVRVFDHVRDAGVALMCTPWDAPSMRVLAQYPVDGV +KIASADLTNHGLLRDAAAARLPMVLSTGMSREDEIKEAVELVRSSGVPFAVLHAQSTYPA +PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVPLAAVARGASIIEKHFTVDRGLEGNDHK +VSLLPEEFAQMVRQTREIEESIGVAAERVVSTGEAMNRINLAKSLVAARPLAAGETVTED +AVTVKSPGRGLQPNELPRLVGRTLHRDMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR +YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPLPMGFTTHLPDIFSGDFLVDLASD +DDAVWERSIAEVQRTIDITRDLKRWFPKEEAPIMVITMGGFTLDRHIAPAERQAKYDRIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL +>MOLHKGIG_00508 +MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAQPE +ASLDVAAADVAHRDPATAPLGATPAEMREALPAGALHLPLLDERGRLTALAINREAELRI +GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA +TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV +KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIREAAALVRSFGVPFAMLHAQSTYPA +PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK +VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLRVGATITAD +DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR +YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFSEPMPMGFTTHLPDIFSGDFLVDLASD +DDAVWERSIAEVQRTIDITRDLKRWFPHEEEPIMVITMGGFTLDRHIRPEERLPKYERIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL +>NAFOICDF_02326 +MIIERHLTPYLVFPEDSLTVALQKMTDNRERIVFVVDTHGFLQGSLTDGDVRRWLLAHPG +AALDSPAVAAANPSPATGLVGDAPSSVLAALPEGALHLPLLDERGHLTALAINRESELRI +GSHRVGEGRPAFLIAEIGNNHQGSVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA +TAGEDLGAQRTLDELAKFSLSVDDMVKVFDHTRAAGVALMCTPWDAPSMQVLADYPVDGV +KIASADLTNHGLLRDAASRGIPMVLSTGMSREEEIQESAALVRSYGVPFAMLHAQSTYPA +PYKDVNLAYLDRLAEIAQAPVGYSGHERGFHVALAAVVRGASIIEKHFTIDRSLEGNDHK +VSLLPDEFAQMVRQTREIEESIGVAGERVVSTGEAMNRINLAKSLVAARSLTAGDVVAEA +DVTVKSPGRGLQPNQLPQLVGRTLHRDLEEGDFFFAGDLTDSVPTGRQFEFRRPWGLPVR +YHDYAALTKDCTPDFLEFHFSYKDLEIDIDTVFREPMPGGFTTHLPDIFAGDFLVDLASM +DEQVWERSIAEVQRTIDITRDLKRWFPSEEAPIMVITMGGFTLDRHIRPEERQPKYERIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL +>MHAAABBN_00228 +MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAHPE +ASLDVAAADVAHRDPATASLGASPDEMREALPAGALHLPLLDERGRLTALAINREAELRI +GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA +TAGEDLGAQRTLDELAKFSLSAADMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV +KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA +PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK +VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGVTITAD +DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR +YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFREPLPMGFTTHLPDIFSGDFLVDLASD +DDAVWERSIVEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERRPKYERIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL +>LFPAFLNI_00507 +MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLVAHPE +ASLDVAAADVAHRDPVTAPLGASPAEMREALPTGALHLPLLDERGRLTALAINREAELRI +GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA +TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV +KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA +PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK +VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGATITAD +DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR +YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPMPMGFTTHLPDIFSGDFLVDLASD +DDAVWERSIAEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERLPKYERIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001637.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001637.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ef39344efd14476a0bf9b18b97d1494fcef1af6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001637.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02443 +MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEADLHVVVSTDSEEIAEVAR +RYGADVPGLRPAELAQDETPTEPVVEHALAAERAAGVEPEGVMLLQATSPLRLPGTLDRA +VAQFRETGVDSLVGVVPVSPFLWRHAADPADPPVCDFDVAHRKRRQDMDRPDLRFRENGS +LYVTRPWVYDELHNRLGGRIGMFELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLQRVP +DRTQLHGTSTATLGDAL +>MOLHKGIG_00507 +MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL +RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA +VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPIPDFDVTARKRRQDMTRTDLRFRENGS +LYVTRPWVYDRLHNRLGGRIGLLELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLRHRS +DLGAPRTAETPTTGPNRTPGGAQ +>NAFOICDF_02327 +MSILCVIPVRGGSRGLPGKNIRMLGGHPLVAWTIQAALDAEADLHVVVSTDSEEIAEVAR +KYGADVPALRPAELARDDTPTEPVVEHALAAERARGVEPEAVMLLQATSPLRLPGTLDRA +VAAFREPGVDSVVGVVPVSPFLWRHAADPAAAPVADYDVDGRKRRQDMDRADLRFRENGS +LYVTAPWVYDERHNRLGGRIALLELDDLEGVDIDTELDFALAEQQMDQYLAVQKLLQTRP +DLTRTAGGAL +>MHAAABBN_00227 +MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAGEDLHVVVSTDSAEIAEVAL +RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA +VRQFRDTGVDSLVGVVPVSPFLWRHAGDPDGEPIPDFDVTARKRRQDMTRADLRFRENGS +LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP +DLGAPRTAETPTTGPNRTLGGTQ +>LFPAFLNI_00506 +MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL +RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA +VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPTPDFDVTARKRRQDMTRADLRFRENGS +LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP +DLGAPRTAETPTTGPNRTLGGTQ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001639.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001639.fa new file mode 100644 index 0000000000000000000000000000000000000000..510a5835642dbadb8c6270a68fb0f42078d1d7ad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001639.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02445 +MSGTGYTVPARGARGTGRAERLFLVSPAFHGYHRSIARAWAAQGFDVTVHCYDAYATVPM +KLRNKALLELPQKAGVDRTAARVAWDTERAVAALRAARPDRVLVIKGDSLGEAFWSEVVE +AGLPRLLWLYDDLSRHDYSPEFLRAIGPVLSYARSEAEQLAGEGVDAHYLPNGFDPDMAL +PSLPRREELVFVGSRYPNRVELLTTLAEAGVPVRAYGRQWSHHPVDRLRTWEVTRPALPA +ERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYEPGEEV +LVFENPEHLVELGRRVVAEPSWGERIREAGRSRSHAEHTFAHRAALAQEWWT +>MOLHKGIG_00505 +MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG +MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL +EAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA +LPQVPRRDELVFVGSRYPNRVELLARLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP +AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE +VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA +>NAFOICDF_02329 +MSAGTYTIAARGERPVSGRPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYADLG +MKLRNKLALELPQKAGLDRTAARVAWDTDRAVAALRAAAPDRVLVIKGDSLGDAFWDEVT +GRALPRMLWLYDDLSRHDYSMDFLRGIGPVLSYARSEAESLAAQGVDAHYMPNGFDPEMV +LPAVPRTEELVFVGSRYPNRVELLRALASAGVPVRAYGRQWSHHPVDRLRTWELSRPDLP +AERDIPLAEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRPDVAEFYVPGEE +VLVFEDTEHLVELGRRIVAEPAWGDRIRAAGRRRSHAEHTFSHRARMAQEWWA +>MHAAABBN_00225 +MSATGYTVAAPPEARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG +MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL +DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA +LPEVPRRDELVFVGSRYPNRVELLTRLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP +AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE +VLVFEDADHLIELGRRIVADPAWGARIREAGRRRSHVEHTFAHRAAMAQGWWA +>LFPAFLNI_00504 +MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIASAWAAQGFDVAVHCYDAYATLG +MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSAIL +DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA +LPQVPRRDELVFVGSRYPNRVELLSRLTAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP +AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE +VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001640.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001640.fa new file mode 100644 index 0000000000000000000000000000000000000000..83e87d728819e72aac499fa8555599f8f34d6bc7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001640.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02446 +MAAQSTAAAVTVVIPHYGDPAPTLALVDRLLADPGDALAAVVVSDDASPTPYPEAHDPRL +TVVRRERNGGFGANVNTGLSEVDTDLALVLNSDALITGEQIDALVAAAAPFQPAVVSPQV +VNEDGSPQWSGRHFPTVLHQGVEWLTPLARFRHLPLLHEAVGHDVAAARSAAPVAVDWVM +GAVMLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRDRGVASIVVPSVRVEHGMHGSSDPL +RRRGWLVDSRFRYARKFGRPRALKAVLTAATGVNYAVNRVRQARGTDVDAAAVLRDEHAL +IWKGTRR +>MOLHKGIG_00504 +MAAQSTTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL +TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVVAAAPYQPAVVSPQV +VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM +GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL +RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL +VWKGQRR +>NAFOICDF_02330 +MPASRIAPSVTVVIPHYGDPEPTRALVDALLAAPGRSVAGVVVSDDASPEPYPQPAPGRE +GLTVVRREANGGFGANVNTGLAEVRTELALVLNSDAEITGEQIDALVEAARPYQPAVVSP +QVVNEDGSPQWSGRHFPTVTHQTVEWLTPLARFRHLPALHEAVGHDVRAAEADSPVAVDW +VMGAVMLLPMAEVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSVVVPSVRVVHGLHGSSD +PLRRRAWLVDSRFRYARKFGRPRLLRGALTAATGVNWAVNRVRQTRGTDVDANAVFRAER +DLIWKGTRR +>MHAAABBN_00224 +MAAQSPTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL +TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVAAAAPYQPAVVSPQV +VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM +GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL +RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNVLRQARGVDVDARAVLRDEHAL +VWKGKRR +>LFPAFLNI_00503 +MTAQSPTAAVTVVIPHYGDPAPTLALVDRLLSDPGDALAAVVVSDDASPTPYPEAHDPRL +TVVRRERNGGFGANVNTGLAAVTTELALVLNSDADITGAQIDALVAAAAPYQPAVVSPQV +VNEDGSPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAAARSASPVAVDWVM +GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL +RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL +VWKGRRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001641.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001641.fa new file mode 100644 index 0000000000000000000000000000000000000000..96d0b0d98fbab25811d31198919a20f9d65a9866 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001641.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02447 +MPAAPPDPSAAPVREALRIGAGLDAVTVSGLTGAERDELLRSWARCGVETVELTEDADAH +RGPEHPRSWLDWHENLVFLATSRAIESARGTHLMFHAACLAAPDTGAAIVLAAASGTGKT +TATRRLGPHYAYLTDETAMVDPADLSVTPYPKPLSLLEPGGSRPKTQRGPDELGLGLTRA +DAVLARIAVLDRVREAAAPVPARAEPMDVVTALQHLVPQTSSLSLLPRGLVALCTLLDAL +GGVQRLVYAEADDLRPVIDGLLAAAPQPVDPAWEPLDAAELAASEGAAEPGAVRRAAAAD +GILTADGRLVLLAGTTLTVLDGIGPAVWFALESPLTPERIVARLAEDGPVPADAAERVAE +AVAALESAGLLVTTPQGAGPEADALRS +>MOLHKGIG_00503 +MPGAQGEDEAMSETTALRIRTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARADAH +RDADTARPWLQWHEDLVFLATSRTIESARGTHLLFHAACLAAPDTGAAMVLVAASGTGKT +TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP +DARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLDTV +GGAQRLVYAEAEDLRDVVDGLLAAPPTSVTPAWEALTEEELRASVGAAAPGAVSRCAVDD +GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVACLRAEGPVPEDAEARVRK +AMDALVSAGLATAG +>NAFOICDF_02331 +MTDPRRGGRAVRIPAGDGSTTAAGLDETGVRTLLDAWRRCGAEEVAAPAEGAAAYWEATG +WDWFHENLVHSATTAAITAGVGRRLLFHGACLADPGTGSAVALVAASGTGKTTATRRLGP +HYAYLTDETVIVAPDTLEVTPFPKPLSLLGPSGVRPKTQVSPDELGLGDAVPARLARLAV +LDRVRDVDGPVTARAETMGLGDALIAVVPQTSSLARLPRGLRELCRVIDRLGGVQRLVYA +EADGLRPVVDELLAAAPEPLEPAWEPLTPAELAASRETGDAAAGAARREAVDDGIVTDDG +RLILLAGPQLAALEGLGPVVWLMLEEPLTNAQIVERLAAEGPVPDDAADRVADAVTALAE +SGLVRI +>MHAAABBN_00223 +MPGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARADAH +RDADTARPWLQWHEDLVFLATSRTIESARGTHLMFHAACLAAPDTGAAIVLVAASGTGKT +TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP +DARLARIAVLDRVRDPAGPVTPRAEAIELVAALAALVPQTSSLSLLPRGLVTLCRVLDAV +GGAQRLVYAEAEDLRGVVDGLLAAPPTPVTPAWEALTEEELSASVGVATPGAVSRCAVDD +GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDEPRTAADVVARLRAEGPVPEDAEARVRE +AMDALVTAQLATTG +>LFPAFLNI_00502 +MPGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEVVQPPTHTDAH +RGAHTASPWLQWHEDLVFLATSRAIESARGTHLLFHAACLAAPDTGAAMVLVAASGTGKT +TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP +DARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLDTV +GGAQRLVYAEAEDLRDVVDGLLAAPPTPVTPAWEALTEEELRASVGAAVPGAVSRCAVDD +GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVARLRAEGPVPEDAEARVHE +AMDALVTAELARTG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001644.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001644.fa new file mode 100644 index 0000000000000000000000000000000000000000..68f34287a674f25f30d482cc1c761bb3d5457071 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001644.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02450 +MPQSSVRPSAVIVLAAGQGTRMKSTTPKIMHPIGGRSLVGHALAAAHSLAPEHLVAVVRY +ERDRVAEHIESVAEGLGIASLAIADQDEVPGTGRAVELGLAALPKDLEGTVVVTYGDVPL +LTPETLERLVAAHEADGNAVTVLTAALEDATGYGRIVRDGEGLVERIMEHKDALAHAEST +GDSSFVEIREVNSGIYAFDAALLRRTLPAISTDNVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRRLNDRVLRHWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG +TQLHGATQVATGAVVGPDTTLTDTRVGERAVVKRTDATEAVIGADATVGPFTYLRPGTVL +GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGDYTNIGCGNITANYDGEKKHRTVIG +AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTIEGWVPAKRPGTS +SAQAAQAADAQGDAPQG +>MOLHKGIG_00497 +MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLSPEHLVAVVRH +ERARVAEHIETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL +LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEAT +GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG +TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL +GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG +AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS +SAEAARAAGAEGSGAQG +>NAFOICDF_02334 +MPQTAVRPSAVIVLAAGQGTRMKSATPKIMHAIGGRSLVGHALAAAQSLAPEHLVTVVRH +ERDRVAAHIEEAAADLGVTGLAIADQDEVPGTGRAVELGLAALPEDLEGTVVVTYGDVPL +LTPETLQRLVAAHEADGNAVTVLTATLADATGYGRIVRDADGLVERIMEHKDALAHAEAT +GDSSYVEIAEVNSGIYAFDAALLRRTLPQLSTENVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRQLNERVLRRWMKDGVTVVDPSSTWVDVTVELAADVTLKPG +TQLHGSTTVATGAVVGPDSTLVDTRVGERGTVKRTDATEAVIGDDATVGPFTYLRPGTVL +GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVDKHRTVIG +SHVRTGSNTVFIAPVTVGDGAYTGAAATVRQDVPAGALALNAVDQRNVDGWVVSRRAGTA +SAEAAQAAGAVGRDQATEAAQD +>MHAAABBN_00218 +MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH +ERARVADHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL +LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST +GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG +TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL +GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVAKHRTVIG +AHVRTGSNTVFTAPVSVGDGAYTGAGAVVRDDVPAGALALNAVAQRTIEGWVPAKRPGST +SAQAARAAGAEGSGAQG +>LFPAFLNI_00496 +MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH +ERARVAEHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL +LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST +GDDSFVAIREVNSGIYAFDAALLRRTLPEVSTDNVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG +TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL +GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG +AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS +SAEAARAAGAEGSGAQG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001645.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001645.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a2474f1864d2315adc7268d109d909925c1927a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001645.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_02453 +MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVRVGVLDQQDRLDPTHTVRQAVVGDVEDHVWASDPKVRDVLGGLLDGLDLEQTV +EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKDRWRPTDGGLVVVT +HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWILARAERARQAAVVEQKRQQLMKKELAWL +RRGAPARTSKPKFRIEAANAIIADVPEPRDSVSLAKTATARLGKDVLDLEHVGLSLGEKR +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLEPDSGRVKRGKTVVTATLTQDVKE +LDEVAHLRVAEVMAREGSAFQVGDKEMSAGQLLEMLGFGTSRQWTQVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGKVRGLPGGVDQYLELRAAMDAAGASGGPARGAGAARGRNDVVGTCAGMGGPEEDTGP +TEAERRLARKEMARLEKQMTRLRDSRSVLEARMAELGQAQDFDALTAASADLKDLDAQLD +VLEEEWLQAAELTEGD +>MOLHKGIG_00494 +MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV +RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKPRWRPTDGGLVVVT +HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL +RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE +LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGKVRGLPGGVDQYLELRAAMDEAGGPARGAGPVRGRNDVVGTCAGMGGPEEDTGPTEA +ERRLARKEMARLEKQMTRLRDRRSGLEARMAALGQAQDFDALTAASADLKDLDAQLDVLE +EEWLRAAELAEGD +>NAFOICDF_02337 +MAHLLGAENIGISFGTRTVLDGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVHVGVLDQRDVLDPQDTVRRAVVGDVEDHVWASDARIRDVLGGLLAGMDLEQRV +EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLAGHLNARWRPNDGGLVVVT +HDRWFLDAVCTRTWEVHDAAVDPFDGGYAAWILARAERARQAQVTEQKRQQLMKKELAWL +RRGAPARTSKPKFRIEAANAIIADVPEPRDTVSLAKTATARLGKDVIDLEDVTLTLGDRT +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLQPDSGRMKRGKTVVSATLTQDVKE +LDEVADLRVAEVMAREGSAFQVGDREMSPGQLLEMLGFGPTRQWTAVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGRVRDLPGGVDQYLELRVLMDDAGGAAPAPGSSRGRGDAQGTCAGMVVDIPEVSEAER +RQARKDMARLERQMQRLRESRGGIEARMAELGQAQKYDELGAATAELTAVDAELEDLEEQ +WLEAAERDA +>MHAAABBN_00215 +MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV +RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT +HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL +RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE +PDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGKVRGLPGGVDQYLELRAAMADAGGPARGAGVARGRNDVVGTCAGMGGPEEDTGPTEA +ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE +EEWLQAAELAEGD +>LFPAFLNI_00493 +MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKARDVLGGLLDGFDLDQPV +RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT +HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL +RRGAPARTSKPKFRIEAANAIIQDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE +LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGKVRGLPGGVDQYLELRAAMDDAGGPARGAGAARGRNDVVGTCAGMGGPEEDTGPTEA +ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE +EEWLQAAELAEGD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001646.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001646.fa new file mode 100644 index 0000000000000000000000000000000000000000..63094a6cb3f510b9d936279c09ed6975251a6d3c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001646.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02454 +MSEARAGLSGTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD +GRVTVGPCPRQVSLVDSHDVPWDERNLAHRAAVHLRTALGLDEATHGVHLDVAKQVPVAG +GMGGGSADAAAALLACSVLWETGHTRSELAELAAPLGADVPFAVLGGAAVGLGTGAELTP +VAARTPVHLVLVPADAGLSTPVVFGTLDELRRDGHVPEGAAHPEVNQEVVRALTAADPLA +LATVMDNDLQTPAVALFPDLGDVLDLGLDEGALRGMVSGSGPTLLFVVPDEHSALSLATA +VEERTGVRALPVHGPVAGAHVL +>MOLHKGIG_00493 +MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD +GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRHTLGLDPDSHGVHLEVAKQVPVAG +GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGVELTP +VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPPRPEVNEAVLRALTAADPLE +LATAMDNDLQTPAVVLFPELSDVLDLGLDEGALRGMVSGSGPTLLFVAQDEASALRLASA +IEERTGVRALPVHGPVPGAHVL +>NAFOICDF_02338 +MSGLPGPSARHVTVRAPGKVNLSLRVGPPRPDGYHPVASVYLAVSLAETVTAVARPDGDA +RITLAESTRQPSSVDTRDVPWDERNLAHRAALHLRQSLGLAPETHGVHLEVSKQVPVAGG +MGGGSADAAAALLACSVLWDTGLTRSELAELAAPLGADVPFAVTGGAAVGRGTGSELTPV +AARRPVHLVLVPADAGLSTPIVFRTLDELRSLGRAPEGQGEPAVDADVVRALAQADPLAL +ALAMENDLQTPAVTLFPELSDVMDVGLDEGALRAMVSGSGPTLLLLAHSEQDAARLATAV +QERTGVAALAVHGPVPGAHVL +>MHAAABBN_00214 +MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD +GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVPVAG +GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAELTP +VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAADPLE +LATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRLASA +IEERTGVRALPVHGPVPGAHVL +>LFPAFLNI_00492 +MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD +GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVPVAG +GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAELTP +VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAADPLE +LATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRLASA +IEERTGVRALPVHGPVPGAHVL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001647.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001647.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3a19860d7137e50fdb08adbca0992c786ddc0b5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001647.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_02455 +MIDPNTIRRIVQAAGVGPDEHVLEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAERLPHTV +QEFRPASADALAVLHADALRMTAADLDAVRPAAAPGGPTALVANLPYNVAVPVLLHALAE +LPGLRHGLVMVQEEVADRLAAGPGSRVYGVPSAKAAWYAQVDKAGTIGTQVFWPAPRIHS +GLVAFTRREPPTSAVSRAETFAVVDGAFAQRRKTLRAALAGWAGSPQAAEDALVAAGVDP +RTRGEALGIEAFARIAEHGPRRAAGEGSA +>MOLHKGIG_00492 +MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV +LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS +EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG +PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPTGGASRREVFA +VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR +AAEVSA +>NAFOICDF_02339 +MVPPPDAPATAPLLSAADVRRLAAELDLRPTKQWGQNFVIDPNTIRRIVAAADLAPDEHV +LEIGPGLGSLSLGLLDAASAVTAVEIDPVTAARLPATAAEFRPERAADLAVLHADAMTLT +AEGLDSVRPAGAASGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG +PGSRVYGVPSAKAAWYADVRKAGVIGTQVFWPAPRIHSGLVAFTRREPPTQAVDRREVFA +VVDAAFAQRRKTLRAALATWAGSPALAEEALVAAGVDPKARGEALDIAAFARIAEHRPEA +AS +>MHAAABBN_00213 +MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV +LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS +EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG +PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGSTSRREVFA +VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR +AAEEVVA +>LFPAFLNI_00491 +MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV +LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS +EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG +PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGGASRREVFA +VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR +AAEEVVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001648.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001648.fa new file mode 100644 index 0000000000000000000000000000000000000000..9390f7e3394e47ed383d98a94fb7af0ab3243e28 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001648.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_02456 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELG +SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVSM +PLTGLGMALYFLAVAWVIKAVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARAESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFVQGRGGEAFGSL +ALLAMAGFRVLPSMAALMATTNEIRASWPAFERTTAELADAQPVLDAADRPYERLEFARE +IEVRGASYTYPGSDEPVLRDIDLTIPFGTSYAFVGGSGAGKTTLIDLLIGFHHAQDGAVL +VDGVELEANPRGWWDNVAFVPQSVTVVNGSVLHNVVLDLEAAETADRAAVEQVLRDAQLG +EWLDALPEGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT +EVIESLKGRITVLVVAHRLSTVKHCDQIVLMDQGRIIGQGTFRGLQETSPEFQELVRLGD +LSA +>MOLHKGIG_00491 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELG +SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVTVVVGVAM +PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL +ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEES +IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY +VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT +EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGD +LST +>NAFOICDF_02340 +MVTRLLKSRLPEGTQYLVDRPMRIRLGFVVLGSILVALLEMAALASILPLVNLLTTGSPG +APVITELLASVGAVSVAEQTVAFAGVIVVAYLLKAVLVLSFRWWTMGFTNKNLIQTSAKL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTLLTEAVTLLAVGIVVGVTM +PLTALGMGAYFLVVTLIIRHVIRKPASQLGWTLVVTGERANTAALQGLENYKDVKVRGND +SAFMDEYVDARRENAEAIRLKMILTMMPRYVLEVAFVAAIAGLVAVAFASGRGDQAFGSL +ALLAMAGFRLLPSIASVMATSNEIRASWPAFERTVAELKDAQPVLDAADRPYDRLPFERS +LEARNASFTYPGKDEPVLKGIDLSIPFGASYAFVGGSGAGKTTLVDLLIGFHHAQQGGVY +VDGVELQADPRGWWDNVAFVPQSVTVVNGSVLHNVVLDIEAARTADRTEVERVLRDAQMG +DWLDALPDGLDTVVGEGAVGVSGGQRQRLGIARALYRRPRLLVLDEATSALDNVTERKVT +DVIESLKGRITVIVVAHRLSTVKHCDQVVLMDEGRILDQGTFAGLQETSPEFQELVRLGD +LSS +>MHAAABBN_00212 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASIIPLVSLLTSGELG +SPALEGLLARFGAVTVPEQTVAFAVVIVVAFLLKAILVLAFRWWTMGFTNQNLIRTSATL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVAM +PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEAMRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL +ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEEA +IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY +VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT +EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDHGRIIGQGTFAGLQETSPEFRELVRLGD +LST +>LFPAFLNI_00490 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELD +SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVAM +PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL +ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERVTFEEA +IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY +VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT +EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGD +LST diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001650.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001650.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c463de18e657568315bc4c1287c21d0422af3ce --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001650.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02459 +MTPRPTDLPSPSGRIVLAATPIGNLGDASARLRELLAEADVIAAEDTRTARRLCQGLGVT +PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT +CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD +ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAEVHAWAAERHAGEGIRGEIVLVIGPA +SPDAASAGGATEADAVAEVGVLVDSGTRLKEAVATVAAAHGLRSRTLYQAVLAARG +>MOLHKGIG_00487 +MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH +EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT +TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVAEVL +GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS +EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG +>NAFOICDF_02343 +MSLPAASGRIVLAATPLGNLGDATGRLRELLATADVIAAEDTRNTRRLCQGLGITPAGRL +MAHHEHNEAASAAGLLERVRAGETVVMVSDAGMPTVSDPGFRLVEAAVAAGLPVTCAPGA +SAVTTALALSGLPSDRFAFDGFLPRKDGERRRRLEEIRTDPRTVVYFESPQRTASALAVI +AEVLGGARPVCVARELTKLHEEVVRGTADELVAWAVEREAGEGIRGEVAIVVGPAAPDAG +AGADEADVLAEVAALTDSGTRLKEAVAAVAAAHGLRSRELYQAVLDARRG +>MHAAABBN_00207 +MTGRIVLAATPIGNLGDASARLRELMAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHHE +HNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVTT +ALALSGLPTDRFAFDGFVPRKDGDRRRWLTSLLTEARTVVAFESPQRLADALAVVVEVLG +AERPVCVARELTKLHEEVVRGTAADVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEASE +ADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARS +>LFPAFLNI_00487 +MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH +EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT +TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVVEVL +GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS +EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001651.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001651.fa new file mode 100644 index 0000000000000000000000000000000000000000..8dda6564d08821380fca4b39be689beffb8c52c3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001651.fa @@ -0,0 +1,51 @@ +>ACLBLIBL_02461 +MEPVPATALAPRPAAVAVDGAPFGVAALRARLGVSAAPLTRWHWILPLLVTALAGVLRFT +NLAHPDQLIFDETYYPKDAYSLLQSGYERRWEEDVNDAFVRGEAEPLESAAYVVHPPLGK +WLIGLGMLAFGTDNGVGWRFSSAVAGTLSVLLVALVAQHLLRSVSLGAVAGLLLAVEGHH +LVMSRIGLLDIFLSFFVLAAFAALLADRAHGRQLLARRLAHDVARRGHAALATGPWLGWR +PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMAARRDAGVRDWARAGVVKDGLLAF +VAVVGGGLVAYLASWTGWFATEGGYYRMWHRDNPPEGPLAGLVPGPLRSLWHYHVESTTF +HEGLTSPHDYAASPWTWPFMGRPVSYYYRGGEPGQEVCPADAPSACSAAITDIANPLLWW +TGLIAVLVCLWLLIRHRDWRAGALLGAYLAGQVVWFLWPERTMFFFYTVAYEPFLILMIV +LALSLLLRPGRRPGPRWGSALVLAYAAAVVGVSLFFLPVWIGDVIPYDQWRWRMWFNSWI +>MOLHKGIG_00486 +MEPVPATALAPRPAAVAADDGPFGVAALRARLGVSAAPLTRWHWILPLLVTVIAGVLRFT +NLAHPDQLIFDETYYPKDAYSLLESGYERRWGEDVNDAFARGEAEPLEGAAYVVHPPLGK +WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAVAGLLLAVEGHH +LVMSRIGLLDIFLSFFVLAAFAALLADRVHGRRLLAERLAHDVARRGRDALASGPWLGWR +PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVRRWAWAGVEKDGLYAF +VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGVLAGLVPGPLRSLWHYHVESTTF +HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPADAAGACSAAITDIANPFVWW +TGLAAVLVCVWLLVRHRDWRAGALLGAYAAGQLVWSLWPERTMFFFYTIAYEPFLVMMIA +LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI +>NAFOICDF_02344 +MACVPASSLTRRPAHALPAPADDAAAHPFGAAALRARLGVQAAVLTRWHWIVPLAVTVLA +GVIRFTNLAFPDKLIFDETYYPKDAYSLILSGYERRWAPDVDAAFAQGTAQPLDEPAYVV +HPPLGKWLIALGMLAFGPDNGVGWRFSAAVAGTLSVLLVTLVAQRLFRSVSLGALAGLLL +AVEGHHIVMSRIGLLDIFLSFFMIAAFAALLADRDHGRRLLASRLAEQVAAHDAGTRRGD +PLAFGPRLGWRPWRILAGALLGAGCAVKLSGLAFMAVFGILTVLWDMEARRTAGIRHWLR +AGVVRDGLPAFAAVVGAGLAVWLASWTGWFASEGGYYRRWAQDNPPEGPLSALLPGPLRS +LIHYQLEAFTFHEGLTSPHDYGSSPWTWPFMGRPVSYFYEGGKPGENGCPSTAADACSSA +ITDIANPFIWWTGLIAVLVCLAVLVRHRDWRAGALLGAYVAGQVVWFRWPERTMFFFYTV +AYEPFLILMIVLALSLLLRRGHRPGPRWGAVLVAAYLLVAVGVSLFFLPVWIGERIPYPQ +WSWRMWFSTWI +>MHAAABBN_00205 +MEPVPATALAPRPAAVAVDDGPFGVAALRARLGVSAAPLTRWHWILPLLVTVIAGVLRFT +NLAHPDQLIFDETYYPKDAYSLLESGYERRWDEDVNDAFARGEAEPLEGAAYVVHPPLGK +WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAVAGLLLAVEGHH +LVMSRIGLLDIFLSFFVLAAFAALLADRAHGRRLLAERLAHDVARRGRDALASGPWLGWR +PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVRRWAWAGIEKDGLYAF +VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGLLAGLVPGPLRSLWHYHVESTTF +HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPPDAAGACSAAITDIANPFVWW +TGLAAVLVCVWLLVRHRDWRAGALLGAYAAGQLVWFLWPERTMFFFYTIAYEPFLVMMIA +LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI +>LFPAFLNI_00486 +MEPVPATALASRPAAVAVDDGPFGVAALRARLGVSAAPLTRWHWILPLLVTAIGGVLRFT +NLAHPDQLIFDETYYPKDAYSLLESGYERRWDEDVNDAFARGEAEPLEGAAYVVHPPLGK +WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAAAGLLLAVEGHH +LVMSRIGLLDIFLSFFVLAAFAALLADRVHGRRLLAERLAHDVARLGRDALASGPWLGWR +PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVWHWAWAGVEKDGLYAF +VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGLLAGLVPGPLRSLWHYHVESTTF +HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPADAAGACSSAITDIANPFVWW +TGLAAVLVCVWLLVRHRDWRAGALLSAYVAGQLVWFLWPERTMFFFYTIAYEPFFVMMIA +LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001652.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001652.fa new file mode 100644 index 0000000000000000000000000000000000000000..27ba4bdbca0b44d55c75d94299f905540257250d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001652.fa @@ -0,0 +1,55 @@ +>ACLBLIBL_02462 +MPRVFEKVESGVATKAQKAGTGKVYQAARSTAITWSKALEEKKFGSGRGPSPALRARHAL +FDRLVYRKIREALGGEVRTCVSGASALSEELVHFFRGAGVPIVEGYGLTESTAPATVNVP +GAHRVGTVGLPVPGVTVKIAEDGEVLLRGPVMFSGYHGMPEASAESHAEDGFFRTGDIGS +LDEHGYLRITGRKKDVIITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALVTLD +EEELTRWSLDRERSLTPAEAAKDPAVLETIQEAVDRVNEDVSRAESIRRIRILDHAFTED +SGYVTPSQKLKRAQVIEDYAEDVDALYRGR +>MOLHKGIG_00485 +MQNQSPVHESATELIGMPPADSNITDLIVTSCADRPDAPVYAVRNGAGGWVDVHFTAFLT +QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV +TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS +LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPTTTSRTLLFLP +LAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKAQ +KSGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGEV +ISCVSGASALSPELVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVTV +KIAEDGEILIRGPVVFDGYHGMPKASAEAMEDDFFRTGDIGALDEHGFLRITGRKKDVII +TAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDAEAFTQWALDRELTLTPA +EAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIED +HAEDVEALYRR +>NAFOICDF_02345 +MQHASPISESSTDLYGLPAEDTNITDLILSSCAEDPRASVYAVRNGAGAWLDVRFDAFLG +QVRDVAKGLIAHGLQPGQRVALFAPTCYEWAVLDQAVWFAGAVSVPIYETSSAAQVAHIL +GDSQTHAAAVGGDELAATTREAARQAGIDVTVFPMSEAALRVLARDGAAVTDEQLEAART +TATLDDAASVVYTSGTTGRPKGAIITHRNFAAASINVLNFAAGVVDYHPGTNSRTLLFLP +LAHVLAHAVQVICLYARIQMAHSGSTKTLQEDMASFHPTWLLAVPRVFEKLEAGIAAKAE +DGGRGPVYHAAKRTAIEYSEALEAQTHEGGPGPSRALRARHAVFDTLVYGNVRKAFGGEV +LSCVSGASALSPELVHLFRGMGIPIVEGYGLTETTAPATVNIPAAYKVGTVGLPVAGATI +RIADDGEVLVKGPIVFAGYLRQPEATAESMDGDFFRTGDLGTLDEDGFLRITGRKKEVIV +TAGGKNVYPTPLEEIIRQHRLVQHVVVVGDDRPYVGALIVLDPDELKRWSLDRERTLTLE +EAVADEGVLAALQEAVDQANATVSRAESIRRIRVLDHELTEDSGHVTQSQKLKRAQVLAD +YADEIEQLYRGR +>MHAAABBN_00204 +MQNQSPVHESATELVGMPPADSTITDLIVASCADRPDAPVYAVRNGAGGWVDVHFTAFLT +QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV +TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS +LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPETTTSRTLLFL +PLAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKA +QKGGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGE +VISCVSGASALSPDLVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVT +VKIAEDGEILIRGPVVFDGYHGMPKASAEAMEDDFFRTGDIGALDEHGFLRITGRKKDVI +ITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDSEALTQWALDRELSLTP +AEAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIE +DHAEDVEALYRR +>LFPAFLNI_00485 +MQNQSPVHESATELVGMPPADSNITDLIVTSCADRPDAPVYAVRNGAGGWVDVHFTAFLT +QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV +TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS +LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPETTTSRTLLFL +PLAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKA +QKSGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGE +VISCVSGASALSPELVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVT +VKIAEDGEILIRGPVVFDGYHGMPKASAEAMEDGFFRTGDIGALDEHGFLRITGRKKDVI +ITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDSEALTQWALDRELSLTP +AEAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIE +DHAEDVEALYRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001654.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001654.fa new file mode 100644 index 0000000000000000000000000000000000000000..0b29d985c40a694d008c7a615886d6f54019af29 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001654.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02464 +MTETPAESRTPDVDPAYANRATVPGAAFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE +EYGESQPLAGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAVVVGSG +TPEDPQGVPVFAWKNETLEDYWWTASQILTWPGAAEDPERGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGQGDLFVTTTGGKDIIMAEH +MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDAGTDSERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKSQAEYLGVDVAGPYKADHYRY +>MOLHKGIG_00483 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE +EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG +TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH +MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLGGGTEAERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY +>NAFOICDF_02348 +MTETSSARPTPDVDPAFANRSTVPGATFDFAVRDLSLAEAGRHQIRLAEHEMPGLMALRE +EYGESQPLKGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAIVVGSG +TPDAPAGVPVFAWKGESLEEYWWTASQILTWPGAAEDPDRGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ +LAQEGTLLFPAINVNDSVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVEQGDLFVTTTGGKDIIMAED +MLRMKDKAIVGNVGHFDNEIDMAGLGRVDGVVKTEIKPQVHEWTFDTGTEDERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELYDGSTGQGALTGEHYEKQVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY +>MHAAABBN_00201 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE +EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG +TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH +MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPFKADHYRY +>LFPAFLNI_00483 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE +EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG +TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH +MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001656.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001656.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a1d214c05e37556e82825a6cb5b286792b29a06 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001656.fa @@ -0,0 +1,22 @@ +>ACLBLIBL_02466 +MDRLAALEAPGLRHVTARVERIPDRLDERLRALRAGAERDEETLFARAERQGQDGVVITL +FERPLRDAADPEDLDGAVYGVALSRCAEALGVDPQVLDPGWGRA +>MOLHKGIG_00481 +MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPTGRGGRDRRGRGLRHPRP +FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD +EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS +WGRG +>NAFOICDF_02350 +MARMPADPLAPLPPLPPARRDGRGPRPGLRRDVRGRGLRHPLPFGARAGRGRADALMDAV +EKAVDRLAGLQAPGLRRVAARLERIPDRLDERLALQRARAVADEEGLFGRAERDGADGVV +ITLFERPLTESADPADLEEAVYAVALSRCAAALGVDPQVLDPSWGRA +>MHAAABBN_00199 +MARMTAPASSDPLDPLPFRAGDAAGAEPGVEGGPAKAGVSSPAGRGGRDRRGRGLRHPRP +FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD +EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS +WGRG +>LFPAFLNI_00481 +MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPAGRGGRDRRGRGLRHPRP +FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD +EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS +WGRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001657.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001657.fa new file mode 100644 index 0000000000000000000000000000000000000000..933e29c95cb04cba23e45672c589f3a9b2e1e903 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001657.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_02467 +MEHTQRVEDTHRAESAQAAAPRPRGVPSDWFLDPADPLAGADAATLEDQATALLSAHDLE +DEAGTPSATVTALFPGDAGQPVEAAPVADDWAAIPGLVTEPVEGELAWQVDALCAQTDPE +AFFPEKGGSTRDAKRVCEACVVKDQCLEYAMENDERFGIWGGLSERERRRLRRARA +>MOLHKGIG_00480 +MEQTQRVEDAHHADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE +TGTPAATVTALFPGDARPVEAAPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF +PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA +>NAFOICDF_02351 +MQNTQRVEDVARAERAPAASRSRGVPTDWFLDPADPTAGGRATAGLAAESLEDQATAFLA +AHDLDDAGTPAATVTALVPRPAEAPAVDDALVPDAWQPVPGVVMEPAEGELAWQVDALCA +QTDPEAFFPEKGGSTRDAKKVCAACDVRRECLDYAMANDERFGIWGGLSERERRRLRRER +G +>MHAAABBN_00198 +MEQTQRVEDTHRADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE +TGTPAATVTALFPGDARPVEAVPVSQDWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF +PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA +>LFPAFLNI_00480 +MEQTQRVEDTHRADPAQAPAPRPRSVPSDWFLDPADPQADVSGVSLEDQATAFLTAHDLD +GETGTPAATVTALFPGDARPVEAVPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEA +FFPEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001659.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001659.fa new file mode 100644 index 0000000000000000000000000000000000000000..286f805dddabe2abbb90302cc31c06e2c51e4257 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001659.fa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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001660.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001660.fa new file mode 100644 index 0000000000000000000000000000000000000000..0869fed76b10d2d2e2d9f70fa990c1beb046318a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001660.fa @@ -0,0 +1,43 @@ +>ACLBLIBL_02470 +MMAGPAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT +EHLRVLQEVGVAVRPGPEALQHAQDKLVMRAAVERLGLPNPAWAAVRDLDEVLAFGDEHG +WPMILKTPRGGYDGKGVLKLDDADDARASASDGTLGTWLGAGIAPLLAEALVPFTRELSA +QVARTPSGRVAAYPVVDSVQVAGVCDLVVAPARDLDPAVAEAATAAAVRLAEELDVTGML +AVELFETPGVGPGFQINELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGDTAPRGAG +VVMKNLLGGAREDLHAGLADALAAHPQAKVHLYGKAVRPGRKVGHVNVVADHGLTLEQAV +RAAESAAAVLRDGAAPDAVDASPSSPATPHPAGGPPMTATPQNPAQPLQDDAPVVSVVMG +SDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEMVEFGARAHERGIRVIVAGAGGAAH +LPGMLASVTPLPVIGVPVKLKSLDGLDSLLSIVQMPAGVPVATVSVDGARNAGLLAARIL +ASADTEEGERLRAALTEHAAELNAQAQAKGARLRERMAADR +>MOLHKGIG_00477 +MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT +EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG +WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA +QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML +AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG +VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV +RTAESAAALLRDDAPTTGTETEARP +>NAFOICDF_02354 +MIGGGQLARMMAGPAAELGVPFRVLAEAPDASAAQVAPHMVGDHASLEDLRAFAATVDVV +TFDHEHVPTEHLRTLEAAGVAVRPGPDALQYAQDKLLMRGLVERLGLPNPAWAPVSSLEE +VIAFGDEHGWPMILKTARGGYDGKGVLKVDSADDARSGAADGTLGTWLGAGIAPLLAEAM +VPFARELSAQVARRPSGEVAAYPVVASLQTQGVCDVVTAPAPDLAPAVAEAASGAAVRIA +EELDVTGMLAVELFETPGTDAGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDMPL +GGTAPRGDGTVMKNVLGGAHEDLHSGFSEALAAHPEAKVHVYGKGVRPGRKVGHVNVVAE +HGLSLADAERIAESTAAVLRDATAPSAPTPKA +>MHAAABBN_00195 +MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT +EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG +WPMILKTARGGYDGKGVLTLDDADDARASAADGTLAAWLGAGIAPLLAEALVPFSRELSA +QVARTPSGEVAVYPIVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML +AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG +VVMKNVLGGAREDLHAGSVVALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV +RTAESAAALLRDDAPTTGTETEARP +>LFPAFLNI_00477 +MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT +EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG +WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA +QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML +AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG +VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV +RTAESAAALLRDDAPTTGTETEARP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001663.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001663.fa new file mode 100644 index 0000000000000000000000000000000000000000..14a158b19923f6a7d18b9b6183d37d078ba5558f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001663.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02474 +MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD +TVSMAGTVVIGEGEKDEAPMLFNGEEVGDGSGAPVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDLRLPVKQNVALVAKALDKPASQVTVCVLDR +PRHEGLVKEIREAGARVKFILDGDVAAAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT +GGVIQGRLAPTDETEKQKALDAGLDLDAVLSTNDLVTSDHCYFAATGITDGDLLRGVRFV +DGRVVTQSIVMRSWSGTVRTVDAEHDVRKWSKWLEDRGTRTGR +>MOLHKGIG_00473 +MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD +TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR +PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT +GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA +DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR +>NAFOICDF_02358 +MTSASSENTGYENHVPDRNLAMELVRVTEAAAIAASPWVGGGDKNRADGAAVDAMRAFMD +TVAMDGTVVIGEGEKDEAPMLFNGERVGDGKGASVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR +PRHEGLVKEIRAAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT +GGVIQGRLAPTDDAEKQKALDAGLDLDAVLTTDELVTSDHCYFAATGITDGDLLRGVRFA +GGRVHTQSIVMRSKSGTVRTVDAEHHVDKWSQWLKNRG +>MHAAABBN_00191 +MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD +TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR +PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT +GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA +DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR +>LFPAFLNI_00473 +MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD +TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR +PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT +GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA +DGRVHTQSIVMRSSSGTVRTVDADHDVKKWSKWLEDRDAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001664.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001664.fa new file mode 100644 index 0000000000000000000000000000000000000000..16cbc4ff93b18cfb8475a7439f8754ce93342f33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001664.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02475 +MLTVSSTHPTDPTDPNAPAPRPVLTAKQAQRARQPWIGMVLSVVALLALVAVVLILNPEP +PQRPREDRVDVAAAAATVPHDDGVLPALAPEVPESWYANFARLQTMDGVSTWDVGWVVTD +TVFAGMQQAHDVDPTWVTLRVDSVPATETLEIDGLAWDLHADPRAPEKRLVTEVEDTTVV +LTTTGDRAVLEDLARGVAKETR +>MOLHKGIG_00472 +MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE +DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL +QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD +QAVLEDLAHGVAKETR +>NAFOICDF_02359 +MPGMSSPDPAAPPAPRPVLTPKQAQRARAPWIAMVLSTLAVLGIVLVALMVNQPPPAPAQ +ADRVDVAAAASTVPHDDGALPALAPDVPEPWDSTYARVERLQGVDTWDVGWAVNDAVFAG +LKQTSRADPTWLALRVGSAPAVGTVDVDGITWDHYAPQDSKDQHLVAEVRGSTLVLTTSG +DQAVLEDLARAVAKEIR +>MHAAABBN_00190 +MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE +DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL +QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD +QAVLEDLAHGVAKETR +>LFPAFLNI_00472 +MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE +DRVDVAAEAATVPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL +QQAEDVDPTWVSLRVDHVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD +RAVLEDLAHGVAKETR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001667.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001667.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b67e9f5dedc9221fd02c20ede3ba9087c87a5a1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001667.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02478 +MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA +GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV +VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG +>MOLHKGIG_00469 +MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT +GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA +>NAFOICDF_02362 +MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG +GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV +LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA +>MHAAABBN_00187 +MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT +GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA +>LFPAFLNI_00469 +MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT +GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001668.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001668.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ac7bcaea8722b223ed71382b271a336e9f209c1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001668.fa @@ -0,0 +1,49 @@ +>ACLBLIBL_02479 +MVAERVEHGRALTGTTEARPDAAGAAGHAAAARTGAADAVVAPDARETGLRTYVVDTSVL +LSDPRAVLRFAEHEVILPLVVVSELEAKRADPDLGYFARTALRLLDDLRGRHGALDRAVP +ISPEGGTLRVELNHVSTDVLPLGIRGTDNDSRILAVAKAFADEGRDVTVVSKDLPMRVKA +AAMGLSADEYRHELVRDSGWRGTVTLTVEQELLDALYDDGEASLAGVPVDGTDGVGAGVE +ADGTGAGGSGVDRTGAEGPGAAVLPVNTGLVLLAPRGSALARVAEGGRALLVRGDQDVFG +LHGRSAEQRLAIDLLTDPAVGIVSLGGRAGTGKSALALCAGLDAVMERREHRKVVVFRPL +YAVGGQELGYLPGSEGEKMGPWAQAVFDTLGALVSPSVIDEVVDRGMLEVLPLTHIRGRS +LHDAWVIVDEAQSLERNVLLTVLSRMGRNSKVVLTHDVAQRDNLRVGRHDGIAAVVERLK +GHPLFGHVTLTRSERSPIAALVTEMLEDGRG +>MOLHKGIG_00468 +MVAELVEHAQTRQEPSSRPGQARAEAGAAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV +LPLVVVSELEAKRADPDLGYDARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS +VDVLPLGIRGTDNDSRILAVAKALADEGAMVTVVSKDLPMRVKAAAMGLAADEYRHELVR +DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPEEAPAEADRLPVNTG +LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA +GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT +LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN +SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG +RA +>NAFOICDF_02363 +MTLQADGTGRHGRGTGETGAEVREGAASDGRRSYVVDTSVLLSDPRALVRFAEHEVVLPL +VVVSELEGKRQDPDLGHAARHALRLLEDLRVRHGSLEDAVPFTAQGGTLRVELNHVSTDV +LPFGIRGTDNDSRILAVAKALADEGRDVTLVSKDLPMRVKAAAMGLAADEYRHELVRDSG +WRGAVSLRVDEDRLDSLYDDGRMGLHGIPLDEVAGSGVDAVPGEPAPTAVDLPVNTGLSL +TSPRAAGLARVREGGVATLVRGDADVFGLHGRSAAQRLAIDLLTDPSVGIVSLGGRAGTG +KSALALCAGLEAVMERREHRRVVVFRPLYAVGGQDLGYLPGTEGEKMGPWAQAVFDTLSA +IVSPSVIDEVVDRGMLEVLPLTHIRGRSLHDSWVIVDEAQSLERNVLLTVLSRMGRDSKV +VLTHDVAQRDNLRVGRHDGIAAVVETLKGHPLFGHVTLTRSERSPIAALVTELLEEGED +>MHAAABBN_00186 +MVAELVEHAQTRQEPSSRPGQARAEAGAAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV +LPLVVVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS +VDVLPLGIRGTDNDSRILAVAKALADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVR +DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPGEAPAEADRLPVNTG +LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA +GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT +LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN +SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG +RA +>LFPAFLNI_00468 +MVAELVEHAQTRQEPSSRPGQARAEAGPAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV +LPLVVVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS +VDVLPLGIRGTDNDSRILAVAKALADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVR +DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPEEAPAEADRLPVNTG +LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA +GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT +LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN +SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG +RA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001669.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001669.fa new file mode 100644 index 0000000000000000000000000000000000000000..f20a3c8b7f8785bd4b92d69e933ac90d342ff795 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001669.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02480 +MSMHRPTPRLPERGAVPAARPAPSLAERVSGRLVAVIAPTLLLVAALWVVQIALVFFGRL +VIPSLGLIPRSVTGLDGILFSPLLHAGWGHLIGNASALILLGPLAALISGRPLALLAAAW +LGSGVLTWVIGSPGVHIGASGIVYALVAFLVVYGIAVRRVVPVVVSVLVALTHLGSSLIG +LLPAPGVSWTGHLAGAVVGVLLGLWWGRGDRRPRHADI +>MOLHKGIG_00467 +MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG +VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG +LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA +PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR +>NAFOICDF_02364 +MPLPDRRPADDAVPAPRPSLTQAAAQGLVRTVAPTAVLVAAMWVMFLVSIVGGSTLIGGL +GLIPRRAAGLDGILFSPLLHGGWRHLVGNTTALLVLGPVAAAVSRRPLALLAAAWLGSGA +LTWVIGTPGVHVGASGIVYALIAFLLVYGVVARRVLAVVVAVAVAAAHLGSSLLGLLPQP +GVSWTGHLAGAVVGVGLALLWGRADRPARAPLGP +>MHAAABBN_00185 +MSMHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQVVLIFLGRVII +PGVGLIPRRLGGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLG +SGLLTWVIGTPGVHIGASGIVYALIAFLIVYGIAVRRIGAVVVSVLVALTHLGSSLIGLL +PAPGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR +>LFPAFLNI_00467 +MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG +VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG +LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA +PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001670.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001670.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4858c106a52009a6edbf92d587ac06a273b8b69 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001670.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02481 +MQRPEAFYRLYERRLARGLDPERLPRHVGVLVDGNRRWARAFGATTQEGHQAGAERILEF +IDWCDETGIPVVTLYMLSTENLGRPPEELEALLGIILATAERLAEPREGRRPVRVQTVGA +VDMLPEEMARRLRAVEERTRDNDGVHVNVAVGYGGRQEILDAVRELLRDEHGRGRTAAEI +ADAMTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD +FLRALRDYGSRQRRFGA +>MOLHKGIG_00466 +MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF +IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA +VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV +AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD +FLRALRDYGSRQRRFGT +>NAFOICDF_02365 +MRRPEVFYRLYERRLAGELDPERLPHHVGVLVDGNRRWARAFGATTQEGHQAGADRIIDF +IGWCDEVGVPVVTLYMLSTENLARPAAELTPLLEIITTTTQRLAEPREDRAPVRVQPVGA +VDLLPPRMAQQLRDVAERTRDNTGVHVNVAVGYGGRLEIVDAVRELLEEAAAEGRSAADV +AAELTVDAISDRLYTRGQPDPDLVIRTSGEQRLSGFMTWQSAYSEFYFCEAMWPAFRRTD +FLRALRDYGRRQRRFGS +>MHAAABBN_00184 +MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF +IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA +VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV +AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD +FLRALRDYGSRQRRFGT +>LFPAFLNI_00466 +MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF +IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA +VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV +AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD +FLRALRDYGSRQRRFGT diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001671.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001671.fa new file mode 100644 index 0000000000000000000000000000000000000000..4dc9c7650a20d696e8f572bec409493171d0c6d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001671.fa @@ -0,0 +1,26 @@ +>ACLBLIBL_02482 +MDPLTPAREPEAARRLRWRIERIRDPEHPLFKPRLRGWIHAAMAPLTLAAGIVLIVLAPT +ATLRWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLAL +LPPGKAHLLLTLVWAGAVAGVAFRLLWTDAPRWLYTPVYVVLGLAALLYIGDFFAADVAA +GWLIVAGGAAYIVGAVFYALRAPTIHREWFGFHELFHVFTVGGFVCHAVAIYRAVLVVA +>MOLHKGIG_00465 +MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL +RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP +DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL +IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA +>NAFOICDF_02366 +MWEHGGMVTRAPSVENRTGRPLKWRIERIRDPEHPLYKPRLRGWVHAVMAPLVLVAGIVL +IVLAPGATLTWACVVYVVTGLLLFGVSATYHLVQWNETVSRVLKRLDHTNIMLVIAGTYT +PLSLAMLPADKAWTLVTAVWVGAALGVAFRLLWTDAPRWLYTPVYVALGLAAVVYLGDFF +AASVPAAVLICAGGAAYIVGAVFYALKAPTIHREWFGFHELFHVFTVGGFVCHYIAVMMA +VLAA +>MHAAABBN_00183 +MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL +RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP +DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL +IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVT +>LFPAFLNI_00465 +MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL +RWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP +DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL +IVAGGVAYITGAVFYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001672.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001672.fa new file mode 100644 index 0000000000000000000000000000000000000000..cbeb39d28b369d2c37ef708eaa3e6b16c7268ded --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001672.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02483 +MSPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL +RVMVRSVRRVQQRSPEAEAMLVDRHQQHLPEDVRELAPEDEERDAQDRLRHLQEKYPGYL +QEPAPRPQSPDDGRS +>MOLHKGIG_00464 +MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL +RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ +EPAPEPQAPDTGRD +>NAFOICDF_02367 +MSLAPLALSAVSLAASVSPSAPMPAVPEPTLKPGLDKQDISPGIEGFLFTALMVVMAIIV +FRLMVRSVRRVQQRSPEAEAMLVDRHQQHLPEEVREGGERLDGDAHDRIERLRRRYPGYL +QDPTPEPESPDTGREPR +>MHAAABBN_00182 +MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL +RVMVRSVRRVQQRSPEAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ +APAPEPQAPDTGRD +>LFPAFLNI_00464 +MTPLSGLPLVLNALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVF +RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ +EPAPEPQAPDTGRD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001677.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001677.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0b7559e73c40ab4d6536802e7c33d2632e05fd0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001677.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02489 +MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVLVGLGILWWLLSFVSLVLIPVLVAALLA +TLLAPLFEGMRRIGIPGIAASLLCVVLLIVVVVGLVVVAGQQIAQGFSDLGDKLTQAVDG +AIAWLASIGVELPTAGGGLEGLWQTLRDNSGTLLDSAMTFGSTAVNIGAGFFIALFSLIF +FLYDGDRIWRFILVFVPKAHRATVGRAGQTGWRALGNYVRVQIFVAFVDAVGIGLGALIL +GVPLAIPLAVLVFLASFIPMIGATVTGAIAVLFALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSAVLGLAGAVFAVPVLAFVNSFIRALTADPPEQLTD +RSDQALAPGSAADEAVGSHVFEPTKHDDAALASEDDAGTSGDLR +>MOLHKGIG_00458 +MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAELGDQLGQAVDD +AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVSLGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE +RTGHALEPGGAEDETAGSHRYRPSAHDDAALASEADAGTRHGDDA +>NAFOICDF_02373 +MSSTLSTDAKLEKDIPYGLTVAAGWSWRVIAVAAMLWVVWHFAGFASLVIIPVLVAALLA +VLLAPIYRALRRARIPGVLAAVLSIVLLLAAVVLLAWVAGLELVQGFSDLSDQLGASVEH +LVTWVQGMGVPVSFDAAALDNVWSTVKDNSGVLVDGALAFGSTAANVLTGLFIALFTLIF +FLFDGERIWRFLLAFVPHTSRSRVDVAGRTGWNALGSFVRVQIVVAFIDAVGIGLGAWLL +GVPLALPVAVIVFLFSFVPTIGAIASGALACVLALTANGLVNALLMLGVVILVQQIESNL +LQPLIMGRAVSLHPLAVFLGVAAGGVALGLVGAVFAVPLLAFANAFVQALRAKGPGEEIL +PGEKVFRPSDEVIAAARRDAKLDPKLDPTSFDDDSGPDGDVEDGRTGSTRTELKP +>MHAAABBN_00176 +MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAQLGDQLGQAVDD +TIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVTFGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE +RTGHALEPGGAEDEAAGSHRYRPSAHDDAALASEADAGTRHGDDA +>LFPAFLNI_00458 +MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGIAAALLCVLLLVVVVVGLMGLAGQQIVQGVAQLGDQLGQAVDD +AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATLMNSAVSFGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE +RTDHALEPGGAEDEAAGSHRYRPSTHEDAALASEADAGTRHGDGA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001678.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001678.fa new file mode 100644 index 0000000000000000000000000000000000000000..f989d2446cc8f0021e4bb2d71cebd45b56a18816 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001678.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02490 +MSETSAAEAFGAPHATGTQHRLRRAGAEAVAVGLAGALRTYRVHGVDLTEPYGPESIPPA +GNGIQMSPWPNRVAGARWELGGAEQGLDVTEPARGHAIHGLLRNTHFVAEASSEHAVTLR +GEIHPQHGWPFRLTHRVTYELDADGGLTVTQELENHADAPAPVAFGAHPFLRIGDVPVPE +LSLRVPADAWIRTGEDLIPVETLPVEGTDRDFRRGRPVGEDALDVCLTGLAPDADGRHRQ +TLLAGDGRAVTLWSDHAFAYTHVFVTDRLPGRDVAVAVEPLTAPADALNSGEGLHRLAPR +TRWSAQWGLTPHVPPHADEENRS +>MOLHKGIG_00457 +MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLAGALRRYRVAGVDLTEPYGPDVVPPA +ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR +GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGAHPFLRIGDVPTAE +LSLRVPADAWIRTGEDLIPVETLPVDGTDLDFRRGRAVGEAALDVCLTGLTPDADGRHRQ +TLLAADGRAVTLWSDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH +ARWSVQWGLTPHVPDHPHEEDRA +>NAFOICDF_02374 +MTVPPAPDADAVFGAPRASGAQYRIARGGAEAVVAALAGALRTYRLDGVDLTEPYGPDMV +PPAGNGIQMSPWPNRVAGGRWELDGAAQQLDVTEPSRGHASHGLLRNTHFTAESVAEDAV +TLRGEIHPQHGWPFRLTHRVAYALDDAGALTVTMSLENHADAEAPVAFGAHPFLRIGDVP +SAELTLQVPAREWIRTGEDLIPVETLPVDGGPQDFRSGRPVGAQGLDVGLTGLEADADGL +HRARLLAPDGRSVTLWSDPAFTVTHVFVTDRLPGRDVAVAVEPLTAPADALNSGTGLHRL +APGATLTARWGLVPDLAPAAPAAAPKEDAA +>MHAAABBN_00175 +MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLAGALRRYRVGGVDLTEPYGQDVVPPA +ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR +GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGSHPFLRIGDVPTAE +LSLRVPADAWIRTGEDLIPVETLPVDGTELDFRRGRAVGEAALDVCLTGLTPDADGRHRQ +TLLAADGRAVTLWTDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH +ARWSVQWGLTPHVPDHPHEEDRA +>LFPAFLNI_00457 +MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLASALRRYRVGGVDLTEPYGQDVVPPA +ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR +GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGSHPFLRIGDVPTAE +LSLRVPADAWIRTGEDLIPVETLPVDGTDLDFRRGRAVGEAALDVCLTGLTPDADGRHRQ +TLLAADGRAVTLWTDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH +ARWSVQWGLTPHVPDHPHEEDRA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001679.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001679.fa new file mode 100644 index 0000000000000000000000000000000000000000..dee46c001ea835ee7075f10c4448096cbd19ed7c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001679.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02491 +MANPVMNSQNFQQQMQGGGQAQPGWYQGGTQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA +HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL +VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL +YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNMVLTWTGIGNMREGGLGLIIGAIAVLLAAY +SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND +>MOLHKGIG_00456 +MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA +HQQSMEDAFRAPSAGPEQTGRMTYNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL +VLGLVNSFKREPSPVLIMLYALAEGLFLGGISAVFEAAYPGIVVQAVLGTFSVFAVMLAL +YTSGKFRPTPRMTKIVMTAMLGYLVFMLINLVLTWTGIANLRTGGLGLIIGAIAVLLAAY +SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYVEILRIVAILRGND +>NAFOICDF_02375 +MANPVMNSNNFQQQMHAGQQQPGWYQNAAPQAPSGQQQSPYGQSQAYGAQQAAQQAAFQQ +NMEQAFRAPAAGAAETGRMTYNDIVGKTALMLTLVVIGGAIGWTMPALMLIGAIVGLVLG +LVNSFKREPSPVLIMGYALAEGLFLGGISASFEAAYGGIVLQAVLGTVSVFAVMLALYTS +GKFRPTPRMTKIVMAAMIGYMLFMLLNLVLTFTGIANLRLGAMGLIVGAVAVLLAAYSLT +MDFEMGAQGVKNGVPQKYSWTVAFGLTVTLIWLYVEILRILSILRSDD +>MHAAABBN_00174 +MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA +HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL +VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL +YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNLVLTWTGIGNMREGGLGLIIGAIAVLLAAY +SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND +>LFPAFLNI_00456 +MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA +HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL +VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL +YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNLVLTWTGIGNMREGGLGLIIGAIAVLLAAY +SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001682.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001682.fa new file mode 100644 index 0000000000000000000000000000000000000000..279bdd3cc839f92a59b991bfd11a5b9ffe6d5fbf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001682.fa @@ -0,0 +1,27 @@ +>ACLBLIBL_02507 +MAARRRAPLPDPVPARQITGRSLLVVAVLLVAAVLVAPTLRAFLNQQLEIAAAEEEIAAM +QAQREDYEERIRLWDDPGYVTQQARERLQLVMPGETLYSVTGVPEEAPRDPRPEAPAGEP +VNTRLPWAEGLWDSAVRAGPRVSPGPRPDPGSGPARP +>MOLHKGIG_00449 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTASPKADAPTPTPEATTPTPAATGAEVIDL +HSVQERRQAGHHGHLDGHPDADRADTAPAAPASPSAPPRRTAPARPAGRRTRPAPRRAAS +AAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEI +ATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETETETDTEAED +TPAARADEVVNTRLPWAEGLWDSAVRAGLE +>NAFOICDF_02379 +MSARRPRVPRVAVPDTAPERATPAVVEPVVVEPAPVAPAAPEAPAPPAPPGPQVIDLQEA +AQRRRHEATRPSPRPDAERAAAQRVARLREERRRATVREHAAARRRVPLPEPVPARQLTG +RSLVVLAVLIIAAVLVAPTARLMLNQQLEISAAQQDIAEQQRRKAEYEEQIRRWDDPGYV +AQQARQRLELVMPGETLYTVTGLPDESGAVPADSVPQEKVNDRLPWVEGLWDSAVRAATE +>MHAAABBN_00170 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL +QSIQERRQAGHPDVDRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPRGAASAAA +TAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEIATM +QAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATETEDTPAAG +ADEVVNTRLPWAEGLWDSAVRAGLE +>LFPAFLNI_00452 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL +QSVQERRQAGHPGHLDGHPDADRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR +RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA +REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET +EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001687.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001687.fa new file mode 100644 index 0000000000000000000000000000000000000000..803bfe7b0949bd7f3a115cc062837a170894dff4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001687.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02514 +MAAEGTTTAPGVDWDRLRRAALAATEHAYVPYSGFRVGAAALTEDGRLVTGCNIENASYG +LTLCAECALLADLRMGGGGRLAAFVCVDGQGVLTMPCGRCRQLLHEFRAPDMVLLTPAGE +RTMGQVLPDAFGPEDLERAAAR +>MOLHKGIG_00443 +MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY +GLTLCAECALLAELRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG +ERGIDAVLPDAFGPADLERADRP +>NAFOICDF_02385 +MTGTTTPPACAAPVAEADWDRLRAAAADAMERAYAPYSGFRVGAAALTEDGRLVSGCNVE +NAAYGVALCAECALVGQLHMTGGGRLRAFLCVGGDGRLITPCGRCRQLLWEFRAPGLAVL +TAAGVTTVEALLPEAFGPDALEA +>MHAAABBN_00164 +MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVAGCNIENASY +GLTLCAECALLADLRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG +ERGIDAVLPDAFGPADLERADRP +>LFPAFLNI_00446 +MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY +GLTLCAECALLADLRMGGGGRLAAFVCVDGDGVLTMPCGRCRQLLYEFRAPGLVLLTPAG +ERGIDAVLPDAFGPADLERADRP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001690.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001690.fa new file mode 100644 index 0000000000000000000000000000000000000000..711ab8b3df1f43d145be1e2164ae0b741c61eb52 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001690.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02517 +MKLELRGITKRFGTFTANDSVDFVVRSGEVHTLLGENGAGKSTLMNVLFGLYDPTEGEIL +VDDRPVRFAGPGEAMRAGIGMVHQHFMLVPVFTVAENIALGDEHTRAAGVLDLEATRRKI +RAISDEYGFAVDPDAVVEDLPVGVQQRVEIIKALVRDAKVLILDEPTAVLTPQETDELLA +IIDRLRQDGTAIVFISHKLREVKAISEHITVLRRGKVVGTAEPSASAAELAALMVGRQVS +LNRAKTAPTLGEETFKVQDLTVVSPTGQVLVDHVSFAIRQGEILGVAGVQGNGQTELTEA +IMGLHKATGSVTLDGRELVGRSTRQIIRAGVGYVPEDRSTDGLVGSFTVAENMVLNRFDR +EPAGSALQLRPRAVRELAEARVQEFDVRTQGVVSPVSSLSGGNQQKVVMARELVDELRLF +IASQPTRGVDVGSIEFLHERIVRERDNGTPVMIVSTELDEILELSDRIAVMYHGRIVGIV +DGDASRETLGLMMAGQTPESLATETATTEEGPRA +>MOLHKGIG_00440 +MRLELRGISKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL +LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI +REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG +IIRQLREDGTAIVFISHKLREVKAVSDDITVLRRGRVVGTADPSAEAAELAALMVGRSVV +LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA +IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV +APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF +IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV +PGDTSRETLGLMMAGQTPDDAALASGADVAAGTPGTAGEAPAAHPTTEGERP +>NAFOICDF_02388 +MKLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGQIL +LDGEPVAFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRGAGVLDLEATRRKI +REISDAYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLA +IIRQLRADGTAIVFISHKLREVKAISDDITVLRRGRVVGTADPSASAAELASLMVGRDVV +LNRRKTAPQLGEETFRVEHLTVVSPTGQVLVDDVSFGIRQGEVLAVAGVQGNGQTELTEA +IMGLQAKAAGSIRLDGRELLGRSTRQIIHAGVGYVPEDRSTDGLVGSFSVAENMVLNRFD +VAPAGSAVQLRPRAVRELAERRVEEFDVRTQGVDVPVSSLSGGNQQKVVMARELVDGLRL +FIASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVRELADRIAVMYHGRIVDI +VPGDASREHLGLLMAGQTAEDTHQEGARA +>MHAAABBN_00161 +MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL +LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI +REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG +IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV +LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA +IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV +APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF +IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV +PGDTSRETLGLMMAGQTPDDAALASGTDVAADTPGTAGAAPAAHPTTEGERP +>LFPAFLNI_00443 +MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL +LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI +REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG +IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV +LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA +IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV +APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF +IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV +PGDTSRETLGLMMAGQTPDDAALASGADVAADTPGTTGAAPAAHPTTEGERP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001693.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001693.fa new file mode 100644 index 0000000000000000000000000000000000000000..873c707b2b080582769b347443e8c3ac0320b8df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001693.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02520 +MSTDPNLTEAGREDAPGSALSRFHVVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAAGMLVVTGAAHRDAVCGQLPDLDTADLVLEPSPKDSAAAIGLAAAILSLR +DPDTIMGSFAADQVIAPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL +AVPGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG +LMEIAHAWETERRDEVMERVWPELTKTAIDYAVAEPAAAVGDVAVIPGAFTWDDVGDFAA +IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTRRVIALIGIEDVVVVDTEDALLVTT +TDHAQEVKKAVEALKAEGVDEVL +>MOLHKGIG_00437 +MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAAGMLVVTGEAHREAVCTQLPALAETDLVLEPSPKDSAAAIGLAAAILSLR +DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL +RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG +LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA +IARLNPVRDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT +TEHAQEVKKAVEALKAEGVDEVL +>NAFOICDF_02391 +MSIDPTAAQSAPSQPSASALERFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAGGIMVVTGRAHEDAVCRQLPDVGAADLVLEPEPKDSAAAIGLAAAILWLR +DSDTIMGSFAADQVIGPVDVFQDAVRQAVETAATGRIVTIGITPTHAATGFGYIRTGRRL +SVAGAPDAHDVAAFVEKPDQRVAERYVASGRYLWNAGMFVAPVALMLQHLEANEPELHAG +LTEIARAWETPERDAVMARVWPGLKKTAIDYAVAEPAATAGDVAVIPGAFTWDDVGDFAA +IARLNPVKDGSGVTVIGDTPRVYSDSATGVVVTDTSRVIALIGVEDVVVVDTGDALLVTT +TEHAQDVKRTVESLKAQGADDVL +>MHAAABBN_00158 +MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAAGMLVVTGEAHREAVCMQLPALAETDLVLEPSPKDSAAAIGLAATILSLR +DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL +RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG +LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA +IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT +TEHAQEVKKAVEALKAEGVDEVL +>LFPAFLNI_00440 +MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAAGMLVVTGGAHREAVCMQLPDLAETDLVLEPSPKDSAAAIGLAAAILSLR +DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL +RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG +LMQIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA +IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT +TEHAQEVKKAVEALKAEGVDEVL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001697.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001697.fa new file mode 100644 index 0000000000000000000000000000000000000000..417dab97a92c09bc66859c739dcf36bda4ece9ca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001697.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02524 +MSHAATETEAPVAQDQTQAAGGGMGAIESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD +RVLDALHKVKWDHDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLLKDLDLSKPILVEP +IKGLPVEKDLIVDMDPFFQSYREVMPFLVAEGHEPSKERYQSQADRARYDDTTKCILCAA +CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTDA +CPRGIQVTKAIAEVKQAILARQF +>MOLHKGIG_00433 +MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD +RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP +IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA +CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA +CPRGIQVTKAISEVKRAILARQF +>NAFOICDF_02395 +MSHAATETQAPAAPAQQTQGQDGGMGEIESFDITLRVRRFLPESSEESYWDEWRLTMFGT +DRVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSQPITVE +PIKGLPVEKDLIVDMEPFFQSYREVMPFLVAKGHEPSKERYQSQADRAIYDDTTKCILCA +ACTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTE +ACPRGIQVTKAIAEVKQAILARSF +>MHAAABBN_00154 +MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD +RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP +IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA +CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA +CPRGIQVTKAISEVKQAILARQF +>LFPAFLNI_00436 +MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD +RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP +IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA +CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA +CPRGIQVTKAISEVKQAILARQF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001698.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001698.fa new file mode 100644 index 0000000000000000000000000000000000000000..6560e038466e27962550eceaba651f90fffa1a22 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001698.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02525 +MHTPDDAAADADDAAARAALHDRVVRRPLRRLLTLTAVTGALSALGTAGVLALQGAPGYA +RAVLEARSWGRAAVTDADVASFLTPPWGVPAAVLGVLAVAALLMLGVARRVRAVRPVGTV +AVGLGLLSAAFWMVDGGRMVAAGGAGPLVLAAVVAMFLACAVWLLTAHLRATRDAFDG +>MOLHKGIG_00432 +MHPLDDDPHAATDRDPAPDRAALRPLRLFQTVTAVTGALSAAGVAGVLALQSTPGYARAV +LEARSWGASEVTDADVAAFVTPAGAWPVAAAAVVLLAVVLLAGITRRIRAVRPVGSVLVV +LGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAMWLRVAHRRETRDGFDG +>NAFOICDF_02396 +MRSDDVAPASARPSGLDDPAVRGPIRRYQAMTAGTGLVSAAAVAGVLGLQSDPGYAREVL +QSRTWGQYEVSAQQVQDFLTPPGGAVLGAVGVLLTAALLVWGAQRLWGATRWLGTALAGV +GLLSAVFWAVDGGRMAARGASGMAVLVAVGAMAVFCAVWLVTAHSKAVREAFLG +>MHAAABBN_00153 +MMGGMHPLHDDPHETTERDPGPDRAALRPLRLFQTVTAVTGALSAAGVGGVLALQATPGY +ARAVLEARSWGASEVTDADVAAFLTPAGAGPVAAAAVVVLTLVLLAGITRRIRAVRPVGS +VLVVLGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRDAFDV +>LFPAFLNI_00435 +MHPLDDDPHETTDPAPDLASLRPLRLFQTVTAVTGALSAAGVGGVLALQSTPGYARAVLE +ARSWGASEVTDADVAAFLTPAGAWPVAAAAVVVLTLVLLAGITRRIRAVRPVGSVLVVLG +MLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRAAFDV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001701.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001701.fa new file mode 100644 index 0000000000000000000000000000000000000000..92bbfffabbd030183af49ebc6a327f1a7a2d2c1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001701.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02529 +MHTVQQAAGAHAPAGREPVLETENLVKVYGRGESRFDALKGVTLQIQAGESVAIVGKSGS +GKSTLMHLLALLDRPSAGVVAMDGRPVQDVSPAEVARLRNETFGFVFQQFFLNPAQTVLE +NTVLPLKISGVPRAERRERGMAVLERLELADKAGNKATDLSGGQKQRVCIARALVNRPTV +LFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAARCDRRLVMQDGMIVDE +TTTAGAQA +>MOLHKGIG_00428 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAERARRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA +DERVGTERDGARA +>NAFOICDF_02399 +MSTVHTHPPETQASRGEEPVLETENLVKVYGRGASRFDALKGVTLQIHRGESVAVVGKSG +SGKSTLMHLLALLDVPTSGVVAMDGRPVSQLKAAEVAHLRNERFGFVFQQFFLNADQTVL +ENVVLPLKIAGVPRHEREARGREVLERLEIADKAKNRANDLSGGQKQRVCIARALINRPT +VLFADEPTGNLDSATSRSVEEILFGLHRDEGITLVVVTHDDDLAAQCDRRLVMQDGVIVA +AEGAGRAVAAGTGARA +>MHAAABBN_00149 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA +DERVGTERDGARA +>LFPAFLNI_00431 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDDGITLVVVTHDDDLAAKCDRRVELQDGVVID +DERVGTEQDGARA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001702.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001702.fa new file mode 100644 index 0000000000000000000000000000000000000000..88e348bacd32853b3cad741f6460044fdab1b4d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001702.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02530 +MKKNSVQDVLAQDVSATAHLAGASDRHRVLSGMQPSADSLHLGNYLGALTNWVRTQDDFE +AFFFIPDLHAITVPQDPAALAQRTRVAAAQFIAAGIDPERSTLFVQSQVPEHAQLAWVLT +CMTGMGEAMRMTQFKDKSAKQGAEAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQHVE +LTRDLAQRFNHRHGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINVMDDPKR +TAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAMTDVPVAELEGRYVGRMYGHLKVDV +ADAVVERLAPVKARTEELLADPAELDRILAAGAAKARAVATPVLEDVYAKVGFLPPLR +>MOLHKGIG_00427 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLAPVRERALALLDDPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR +>NAFOICDF_02400 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSDRPIPELEAEFEGKMYGHLKV +AVADAVVERLAPVRERALGLLDDPAELDRILAAGAAKAREVATPVLEDVYARVGFLRPLR +>MHAAABBN_00148 +MTMKKNSVQDVLAQDAAATAHLPGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILAAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLAPVRERALELLADPAELDRILASGAEKARAVATPVLEDVYAKVGFLPPLR +>LFPAFLNI_00430 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLVPVRERALALLADPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001703.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001703.fa new file mode 100644 index 0000000000000000000000000000000000000000..07a46cd977d34ce4f2fef64dafc3c3806b2cbd8a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001703.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02531 +MTVLPEKDPVTGKYPEPAEGEPVVHANAGAPKEDGALRVATVNVNGIRASHRKGMREWFA +GRGVDVLTLQEVRAPADITAKLVREVVGEDWDEVHLADAEAAAKGRAGVAIASRFPIEAV +RTGISDADAYFDDAGRWIEADLRLPDGSALTVVSAYVHSGEADTPKQVDKYRFLDEMVRR +LGELSAGPDHALVTGDLNVGHTELDIKNWKGNQKKAGFLPEERAYFDRFFGELGFTDVHR +SLAGQVPGPYTWWSMRGKAFDNDAGWRIDYQMATAALAEKASSAVVDRAPSWGTRFSDHA +PLVVDYRF +>MOLHKGIG_00426 +MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA +GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV +RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR +LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR +ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA +PLVVDYQF +>NAFOICDF_02401 +MTVPQKDPVTGKHPGPAAGEPVVHANAGAPKPEGALRVATVNVNGIRASHRKGMGGWFAG +RGVDVLTLQEVRAPQEIAHALVRDVVGDAWDEVHVADVEAASKGRAGVAVASRFPFEDVR +TGIGGAEDHAADAGRWIEADVRLPDGSLLTVVSAYVHTGGVDTPKQVDKYRLLDEMVRRL +PELAADGRHVLVTGDLNVGHTERDIKNWRGNVKKAGFLPEERAYFDRFFGELGYVDVHRT +LAGDVPGPYTWWSMRGQAFDNDAGWRIDYQMATPELAARATSAVVDRAPSWGTRFSDHAP +LVVDYQF +>MHAAABBN_00147 +MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA +GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV +RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQEDKYRFLDEMVRR +LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR +ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA +PLVVDYQF +>LFPAFLNI_00429 +MTALPEKDPVTGKYPEPAEGEPVVHAHAGAPKADGAVRVATVNVNGIRASHRKGMREWFA +GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV +RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR +LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR +ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA +PLVVDYQF diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001704.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001704.fa new file mode 100644 index 0000000000000000000000000000000000000000..5df3137b674f44f1d55cac8247f86b131da5347a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001704.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02532 +MSQPLTTGSGETRRGPRAGLRVGSVGFAAMIVILIVAIMFAANQNDVIGWLVVAVAAGWL +VFALVVFLQMRRGVQAAGRKVDAAMENARADVAALRGQGAAAAPQAAAHAPAGDPMRDTK +LDHSFKIAQVQVKVVREQLAAGGAMDREMVDRALETIDITAANARDMIKESRGQGGSEGP +VSGTVIG +>MOLHKGIG_00425 +MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL +VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT +KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP +VSGTVIG +>NAFOICDF_02402 +MPQSIPSGSAGTRPARAGLTVGSTGFAVMVAVLLVAIVFAANANDLIGWLVVAIAAGWLV +FAVVVFLQMRKGVREAGRKVDTAMQNARADVAALRAPQQPAPAAAVPAAAGDPMRDTKLE +HSFKICQVQARVITQQLDAEGPLDREMVDRALETITITAQNARDMIKESARDAEGPVSGT +VVS +>MHAAABBN_00146 +MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL +VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT +KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP +VSGTVIG +>LFPAFLNI_00428 +MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL +VFAVVVYLQMRRGVQAAGRKVDTAMQNARADVAALRGRDADAAAPAVAPSAPAADPLRDT +KLDHSFKIAQVQVRVVREQLAAGESMDREMVDRALETIDITASNARDMIKESRAGGAEGP +VIG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001705.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001705.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e39bdc769da4dc379b1b20319a32285701f08a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001705.fa @@ -0,0 +1,49 @@ +>ACLBLIBL_02533 +MGGPVAATARRPANRRAGPVVVRAYPEAVTPRPRSADGDAAPAAFTPEQRRILTALLMPL +FLALMSVSVVNVALPAIESGLHATSADLQWVLAGYTLTFGTVLVASGRAGDLWGRKSLFL +VGIGLYVAGALVSGFAADPLMLNAGRLVTGVGAGVFNPQVVGFIQSNFSGRARGRAYGLF +GTVIGLGVAVGPMLGGLLLGALGPEWGWRSTFLMNAPVGLAAIVMGVLWLPAPTRVHGLP +AAPGPRGIAALDPVGALLLGLGAVCLMVPFIVPGTAGLLVLAAALVTAWWLWEKRVKARA +SATGVQPMVDPALFRRLSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGL +PGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVGVGL +IVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAGA +AAEGAGPPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAVRAA +>MOLHKGIG_00424 +MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ +WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT +GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR +STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP +FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY +LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA +LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA +AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAGESAGPPSAAAYAHAASTAMGMVAVCWA +LTAAVAALDVVRRRRAARAA +>NAFOICDF_02403 +MTLPSPAAAESGAFTADQRRILTVLLIPLFLALMSVSVVNVALPSIEGGLGASSADLQWV +LSGYTLTFGMVLVAAGRAGDLWGRRPLFLAGIALYVLGSLLSGLAPDPLWLNAGRLLTGL +GAGVFNPQTIGFIQSHFTGRARGRAYGLFGMVVGLGVAVGPLLGGLLLGALGPDWGWRST +FLMNVPVGVLAIVMATAWLSPDTRVKGAAGRSGGPRGIAALDPVGALLLGGASLCLMVPF +IAPGTWALLAGAAVLGVGWWLWELRVKRRAAATGVEPMVDPALFRRASFSIGAAESTIFL +SSMPAVFAVTAVFLQQGMGFSPLASGLATLPGAVVQAVASPWAGSKVPSQGARMVFGGGV +VGLASLAILALAFERSAAGAWSPWIVGAALAVMAVSQALILTTTQVLMMEDVAGHEAGAA +GGVAQTAQRMGTALGLSVVMGAFYAALAGAAGPGGAPSAAGFAHAASAAVLMVGACWLVT +TAIAAADLVRRRRTAR +>MHAAABBN_00145 +MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ +WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT +GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR +STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP +FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY +LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA +LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA +AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAAESAGPPSAAAYAHAASTAMGMVAVCWA +LTAVVAALDVVRRRRAVRAA +>LFPAFLNI_00427 +MPLFLALMSVSVVNVALPAIESGLDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKS +LFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQVIGFIQSNFHGRARGRAY +GLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVH +GLPPAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVK +ARAWATGVQPMVDPALFRRPSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGL +VGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVG +VGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAAL +AGAAAESAGSPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAARAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001706.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001706.fa new file mode 100644 index 0000000000000000000000000000000000000000..3469b5d2f5641b30788e48b47f9ccf2e0c9bc5db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001706.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02536 +MSHATPASPSPSQSPADAPDAGPAPVIRARGLRKQYGDFHAVKGIDLDVRPGECFGLLGP +NGAGKSTTMRMLAGTSQRTAGELSILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENI +LIYGRYFGLPYSYLRPKADELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFL +LDEPTTGLDPQARHILWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDGGQIMAAGT +PAALIREHAAREVLEARFGADRNEAAARTVQARAGDGVVHRVEVLPDRVLVYAAHADDLH +AVVQGLVDDGALPAPVTTLTRRASLEDVFLILTGRTLVD +>MOLHKGIG_00422 +MSHTTLHASPGDASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM +LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY +SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ +ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR +EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA +LPAPVTTLTRRASLEDVFLILTGRTLVD +>NAFOICDF_02406 +MTRTTSSPSPAAPAGGGAAPVILARGLRKQYGDFHAVQGIDLDVRPGECFGLLGPNGAGK +STTMRMLAGTSQRTGGELRILGIDPEEDGPAVRARLGVVPQQDNLDEDLTARENILIYGR +YFGLPYSYLRPKAEELLAFAQLTDKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPT +TGLDPQARHTLWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDAGRIMAAGTPASLI +REHASREVLEARFGTDRNATAARLLRESLPGLHRLEVLPDRVLLYTEHADTLQQDLDRLV +AEGHVTAPVTQLTRRASLEDVFLILTGRTLVD +>MHAAABBN_00143 +MSHTTLHASPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM +LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY +SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ +ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR +EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA +LPAPATTLTRRASLEDVFLILTGRTLVD +>LFPAFLNI_00425 +MRLCCRLVSPTTLHAPPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAG +KSTTMRMLAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYG +RYFGLPYSYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEP +TTGLDPQARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAEL +IREHASREVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQ +RLVDEGALPAPATTLTRRASLEDVFLILTGRTLVD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001710.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001710.fa new file mode 100644 index 0000000000000000000000000000000000000000..dc477ce95649fc2382359b8c4b2c182897830311 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001710.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02540 +MTENQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLVETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGAKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYTDEGNLDVVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNTPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNFSNEEAEAMA +GKNADYHRQDLFESIAKGDYPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG +TLTLNRNPENHFAQIESAAFNPGNMVPGVGLSPDRMLLGRSFAYHDAQLYRVGAHVNQLP +VNRPKNEVHNYAFDGQMWYDHTGSRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRKDDDDFGQAGTLVREVFTDAERDAFVETVAGALDGVREDVQARAFQYWKNVDATIGQR +IEDEVNKGQGDDIPGAAGGGEARI +>MOLHKGIG_00419 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG +TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP +VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>NAFOICDF_02409 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYSEEGNYDIVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVG +TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP +VNRPKNAVNNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>MHAAABBN_00140 +MTEYQKKTPHATGSTRQNGAPAISDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYTEEGNYDIVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG +TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP +VNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRADDDDFGQAGTLVREVFSDQERDDFVETVSGALKGVRQDVQARAFEYWKNVDATIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>LFPAFLNI_00422 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG +TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP +VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR +IEDEVKRHEGDGIPGVEAGGEARI diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001711.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001711.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed5441bb4263886cfb880341d49260ef8524a781 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001711.fa @@ -0,0 +1,34 @@ +>ACLBLIBL_02543 +MDTATLSPSPTPASGAEHAHVLTLACTNRMGIVHAVSGALLQVGADITESQQYDSPESGD +FFMRVEFVTPARREEVAAALEPVREEFGMRMGLWDAGHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLELQSLASFYGVPFIHVPVSADPESRDSKAAAEDRLRGLIAEYD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLVQAVRWHAQHRVLADGRRTVVF +S +>MOLHKGIG_00417 +MDTAALSPSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD +FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF +S +>NAFOICDF_02411 +MDSTPAAPSEASARHRIVLTLSCPDRPGIVHAVTGALLEADANITESQQYDSPDTGTFFM +RVAVDAAATREEVEAAVRPVADRFGMHLQVWDADTPLRALVMCSKDGRTLNDLLFQQRTG +SLPVQIPVVVSNHLDLQPLASFYGVPFIHVPLSTDPASRNSKAAAEDRLRELIREYEIDV +VVLARYMQILSDELCRDLEGMAINIHHSFLPSFKGARPYHQAHERGVKIIGATAHYVTAD +LDEGPIIAQSVHPVTHAQTAEDFVERGRDVEGATLVQAVRWHAEHRVLLDGHRTVVFS +>MHAAABBN_00138 +MDTAALSPSPSPASGAEHARVLTLACTNRKGIVHAVTGALLGVEADITESQQYDSPDTGD +FFMRVEFVTPATREDIEQALAPVREEFGMRMGLWDAAQRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLADGRRTVVF +S +>LFPAFLNI_00420 +MDTAALSLSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD +FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF +S diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001712.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001712.fa new file mode 100644 index 0000000000000000000000000000000000000000..a027e3c4a0b4fd5e3f59783ecad24fe1994d9150 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001712.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02544 +MAHIITVAGAGPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGERTNLQ +DNVVLHADKGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKVNAATYLELSAAHREATAER +>MOLHKGIG_00416 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG +>NAFOICDF_02412 +MGHLVTVLGRTPRVDPSAFVARTAVLSGDVELGPRASAFYGVSARGDSAAIRVGEGSNLQ +DNVVLHADAGFPCTLGAGVSVGHAAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +VVLEGTQVPPGSLVAGVPAKVRRGLTEEERASLTVNARTYLDLAAAHRAAEEAEQAGV +>MHAAABBN_00136 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG +>LFPAFLNI_00419 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAEHSSAFYGASARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001714.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001714.fa new file mode 100644 index 0000000000000000000000000000000000000000..44dd3f8de348a04c7068712f106c76cfc642ce40 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001714.fa @@ -0,0 +1,32 @@ +>ACLBLIBL_02546 +MSTAVSAPAPEGRAPEGRGPEGRAPRRRGTGKATALWWILTVVIGVWCLFPLFSIFATSF +KTPADLANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAY +AIARLDFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWIGLIIPYLSLTLPIS +IWTLAAFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFG +ISLTSTETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTN +GAVKG +>MOLHKGIG_00413 +MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD +LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL +DFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA +AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS +TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG +>NAFOICDF_02414 +MSTGNPIPAPQEPVTTRPDGAAERTEAGTAVGDRGVAPTTTRRTRKGSSSWIWWLLAVLI +GVWCLFPLFSIFATSFKTPADLSNGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGIT +VIATLIAVVLATLCAYAIARLDFPGKRIVLTVSLMVSMFPVISLVTPLFNVWRTLGLYDT +WLGLIIPYLSLTLPISIWTLAAFFRQIPWELDQAAQVDGATPLQAFRKVIVPLAAPGVFT +TAIIAFFIAWNDFVFGISLTSTEAARTVPAALAFFTGASQFESPTGAISAAAIVVTIPIV +ILVLLFQRQIVAGLTNGAVKG +>MHAAABBN_00133 +MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD +LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL +DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA +AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS +TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG +>LFPAFLNI_00416 +MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD +LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL +DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA +AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS +TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001715.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001715.fa new file mode 100644 index 0000000000000000000000000000000000000000..990e21d9b2d9acc1b162fe93be1d116e782ca90e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001715.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02548 +MRHDTRARQRRRATLAGAVVAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA +NGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ +AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEVA +RSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDEVTTNLDSEAGRTAARIIS +TIGKEGLGSAGLPTQDENASMLLFQGNNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG +WAVYPRTVEDKDAAPPVGGINLGVGEKSEYQDLAWDAISCITTTEHQSQYFVENGNPPAD +PAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET +DDFIQEVLRGERLL +>MOLHKGIG_00411 +MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA +NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ +AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA +RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS +TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG +WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD +PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET +DDFIQEVLRGERLL +>NAFOICDF_02416 +MGDDGRHIRLASNEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA +GLDMSKPVTWDQLIEVARSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDQV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL +GSVEEGSLPKDLPEDIGWAVYPRTVEDKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQ +QRYAPPSGVSESTPAETDDFIQEVLRGERLL +>MHAAABBN_00131 +MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA +NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ +AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA +RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS +TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG +WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD +PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET +DDFIQEVLRGERLL +>LFPAFLNI_00414 +MRDDGRHIRLASIEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDEIVTVPFWANTQLLWYRKSVAEAA +GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL +GSVEEGSLPEDLPEDIGWAVYPRTVEGKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLDLGAPRPQTPYYNEVSTAIQ +QRYAPPSGVTESTPAETDDFIQEVLRGERLL diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001716.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001716.fa new file mode 100644 index 0000000000000000000000000000000000000000..601cf0ee60df56eee1ac91443b781f7958e6e190 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001716.fa @@ -0,0 +1,81 @@ +>ACLBLIBL_02549 +MPAPSPHSSRPASVDTAVAPALSAALERLGSGLTFVAALPDLEAALDARGAAVVEAPPGT +GKTTVVPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRSAVLDAADRTSAPDALADAA +VGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALL +ADLRQLRPELALVAMSATVDAAALAARWARGMGEEAPLPVVSTPAVLHPLREEHAPFRGR +RLTAEGRVDRAFLDHVAATAARAHAAALDADPTVDALVFVPGVAEVEAVAGRVAARAPDT +EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD +RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGAAPAAPTPALAVVDLAP +VALAFAAWGAPGGRGLTLPKDPPADAMAAAERTLASLGAVDTDGRITPHGAVLAELPLDP +PLGHALLRAAPLTGPRPAAEATAALALDLRASGADLEALVAALRDGRHPESRRWRREADR +LERLARRHAHRAPETREPDGPGPEAATARRHPAGLVAALASPAWIARRAGEAGAYLLASG +TRAALPRNAVVGGLAGQEWLAVAEVARAAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRT +EDTADWRGDRLTGRRVDRMGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRAER +LRRRVHLLHRVLGAPWPDLSDTALPGLDALVDGLAADLAAGRSLAHVDAEALLRGALPWP +EAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGRELVV +LHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRVR +>MOLHKGIG_00410 +MVPMPTPVDPVTVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTV +VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADSHPGADPDARARLADA +AVGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFAL +LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH +RLTAEGRVDRAFLDHVAATAARAHAKALEADPTVDALVFLPGVAEVETVAGRVAALAPDT +EVRVLHGRQEPADQDAALAGRTDPAVPRVVVATAVAESSLTVPGVRLVVDSGLAREPRRD +RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP +VALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLGAVDADGRITPHGAVLAELPLDP +PLGHALLRAAPLTGPRPAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWHREADR +LERLARRHAHHAPETREPDEPGPEAATAPRHSAGLVAALAFPAWIARRAGEEGAYLLASG +TRAALPRDAVGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRSLVERAGAGLRRTE +DTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRDALAADGLARFDPRGRAERL +RRRVHLLHRVLGAPWPDLSDTALPDLDTLVDGLAADLAAGRPLARLDAEALLRGALPWPE +AGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVL +HLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAVAEPTARTNRRAL +>NAFOICDF_02417 +MSTSSASHSTPDLRAALAAASARLGADLAFSASLPALEAALDARAGAVVHAPPGTGKTTA +VPPAVALWLARRAESGGEGGRVLVTQPRRVAVRAAWRRLHGAVADALGPESGPDTGRLPD +AVVGYAVRGDAVGRGASAVEFVTPGLLLRRLLGDPGLEGVGAVVLDEVHERDLDTDVLFA +LLADLRQLRPELALTAMSATLDADALAARWATGMGEDPVPVVRTPSVQHPLTVEHAPFGG +PRTTADGRVDRDFLDHVAATAARAHAEALDADPTVDALVFVPGVAEVEAVAGRVAALAPD +TEVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRR +DRGRGITGLATVQASRAAADQRAGRAARLGPGTAVRCHTAAALGAAPAAPTPALAVADLA +SVVLAFAVWGAPGGDGLVLPEDPPADAMAAAERTLASLDAVDTDGRITPHGTVLAELPLD +PPLGHALLRAAPLTGPRSAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWRREAD +RLERLARRHAHRAPETREPDEPGPAATATARRHPAGLVAALAFPAWIARRAGEEGAYLLA +SGTRAALPRDAVGGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRPLAELAGAGLR +RTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRVALAADGLARFDPSGRA +ERLRRRVHLLHRVLGAPWPDLSDATLPGLDALVDGLAADLAAGRSLTRLDAEALLRGALP +WPEAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREP +VVLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTDRTNRRA +R +>MHAAABBN_00130 +MDPMPTPVDPVAVPSALSTALGRLSAGLTFAAALPELGSALDARGAAVVEAPPGTGKTTV +VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDARARLADA +AVGYAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFAL +LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH +RLTAEGRVDRAFLDHVAATAARAHAEALEADPTVDALVFLPGVAEVEAVAGRVAALAPDT +EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD +RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP +VALAFTAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDP +PLGHALLRAALWTGPRPAAEATAALALDLRAPGADLEALVASVRDGRHPEAGRWRREADR +LERLARRHAHHSLETRAPGEPGPEATAAARRHPAGLVAALAFPAWIARRAGEAGAYLLAS +GTRAALPRDAAGGGLAGQEWLAVAEVARVAGDAAGTGAAIRATAPIDRTLAELAGAGLRR +TEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTE +RLRRRVHLLHRVLGAPWPDLSDAALPGLDALVDGLAADLAAGRSLARLDAEALLRGALPW +PEAGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPV +VLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR +>LFPAFLNI_00413 +MPTPVDPVSVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPP +ALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDAQARLGDAAVG +YAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLAD +LRQLRPELALVAMSATVDAAALAARWARGMGEDAPLPVVSTPAVLHPLREEHTPFRGHRL +TAEGRVDRAFLDHVAATAARAHAEALDADPTVDALVFLPGVAEVEAVAGRVAALAPDTEV +RVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRG +RGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVA +LAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDPPL +GHALLRAAPWTGPRPAAEATAALALDLRAPGADLEALVAAVRDGRHPEAGRWRREADRLE +RLARRHAHHAPGEPGPEAAATVRRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALP +RDAAGGDLTGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRTLAELAGAGLRRTEDTADW +RGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTERLRRRVH +LLHRVLGAPWPDLSDAGLPGLDALVDGLAADLAAGRPLTRLDAEALLRGALPWPEAGRLD +ELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSP +AGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001717.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001717.fa new file mode 100644 index 0000000000000000000000000000000000000000..014a64963d5e317506aa50fe5dd7bf7ad2e37011 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001717.fa @@ -0,0 +1,60 @@ +>ACLBLIBL_02550 +MTTPVQKHLDRLTSAHTGEGDVPDGLGVAMLMVDGHRYVSGSMTSVPLATLASPLFHAQA +LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA +RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA +AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP +GWASTRGGTVLVVVPGHLGLALQSDTTDENALGAAAMAALRTIVEDFELHPSVVTGSPRA +ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVLELGGHLGFSQVDAIARVSRGLPEAL +ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEIRELMAAVEESVEVDL +PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSQHAPHLLPRDAQEAAVAPLLQ +HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL +TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF +TALSQLIRETGALQD +>MOLHKGIG_00406 +MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA +LEDLGAVRVGERVGAVPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA +RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA +AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP +GWASTRGGTVLVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA +ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL +ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL +PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ +HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL +TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF +TALSQLIRETGALQD +>NAFOICDF_02418 +MKSPVQDRLDRLTAAHTPGTAADADATSDAGTGLALSVATVGGDHYSAGELVAVPLAGLA +GPVVHALALEDLGVERVGEAVGTVPRPDLRTRLELEPGTGRPLTPLQDAGTMALAALVKG +RGGRDRAARLLQQLAGLIGRETAPTDAAVRAADRAQHRARAAAWLLRSVGVLEADPDGLL +ADVATLRAAPVTVADLALLAGTLAAHGVHPVSGERVLAEETVRAVLSALDACGMDTVDGA +WALDVGQPGWSSARAGTVIAVVPGHMGIAVQGPADPDDADAPSPAALAALRTLVRDFELH +PSQAAGSPRAAFRTHYRVDQAPSGSVRSAEVLELLSAHGDTAHVLELGGHVGFSQVDALA +HVARNLPAALETIIVDVRSVSSTSHAAAVLAAQWFAYALHHGLDVVVVDRDTAAVDQVMA +TAEASGVTLPDPLHDADDADPGHQDLGPAFRFFDSRSRAVQWAEQRLLARHAPHLLPASE +EEAAMAPLLQHLSSEDARLLESMMDERVYEDGQIIRRAGQPFGGIYVITSGRVELTGQGT +GGRRVRRTVLTPGMTFGEMALGQPGRQPSTVRARGRVTTRVLTAQVMYALQEGFPSLALT +LWEALARDAYTALGQLIRETGALQD +>MHAAABBN_00129 +MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLMVDGHRYVSGSMTPVPLATLASPLFHAQA +LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA +RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA +AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP +GWASTRGGTVFVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA +ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL +ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMAAVEESVEVDL +PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ +HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL +TPGMTFGEMALGQPGRQPSTVRARGPVTTRVLTAQVMVALQEGFPQLALALWEALARDAF +TALGQLIRETGALQD +>LFPAFLNI_00412 +MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA +LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA +RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA +AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSAMDSCGMDTRDSRWAYDVGQP +GWASTRGGTVLVVVPGHLGLALQSNTTDENGLGAAAMTALRTIVEDFELHPSVVTGSPRA +ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL +ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL +PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAALAPLLQ +HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL +TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF +TALGQLIRETGALQD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001718.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001718.fa new file mode 100644 index 0000000000000000000000000000000000000000..5240a5b6848f372dd85c818cfbe96a08049ff525 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001718.fa @@ -0,0 +1,50 @@ +>ACLBLIBL_02551 +MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPSDGLRVGSESRLRIQ +APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL +ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGEDLLGRVPGVGAAASRRAHEAF +EAELSRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR +VVRLVRSPKKAGALDAALWDPGRETVDEDALAGADVVVNLAGEPIAGRFTDEHKEAVHDS +RVRGTRTLVDALARITAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF +LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPIASSGGES +HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPAVIP +VPEAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR +>MOLHKGIG_00405 +MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ +APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL +ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF +EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR +VIRLVRSPKRAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFTDAHKEAVHDS +RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF +LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES +HDGSPWLSWIGADDIAGAFAHAVIDDGVTGPVNAVAPEPVTAREFATVLGRVLHRPAVIP +VPDAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR +>NAFOICDF_02419 +MTETRVFEHRTLLRHPRRTVFDWLAAPGALQRMNPPFASELAAGPSDGLREGSQTRLRIG +APGSLGLFAGAVDGALRAALPAAVSRRIPAALSPRLPWRARHTAYEEGRMFRDEMASGPL +SAWRHTHSVEDAAPGEADTAEGEPGAVVVDRVEYALPGVGTAGRLPVVGRPAADAAHRVF +EAELRRQFEFRGRVMAEDLDFHAGHPGPLVGGPARTVLVTGAGGLVGTQLCALLTGGGHR +VIRLVRSPAQAEAEDAVLWDPAGGTVDTAALRAADVVVNLAGEPLAGRFTEKHRRAVHDS +RVDGTRTLVDAIARLPEAERPTVLVNGSAVGWYGADAGAGPDGRGLTEDLPAGDDFLAGV +VADWEAQARRAEELGLRVVRVRTGIVLSPTGGMLAQLLPLFLAGAGGPVATRGGRSHDGS +PWISWIGVDDIAGVFAHAALAEGVVGAVNGTAPEPVTAKEFARVLGTVLHRPAAVPVPEF +GPRLLLGEQGAAELVRADQKASAELVLDSGYAFRDAALEGALRRLLGR +>MHAAABBN_00128 +MTEITVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ +APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL +ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF +EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR +VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS +RVRGTRTLVDALARIAAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF +LAEVVADWEAEARRAETSGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPVATSGGES +HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAREFATVLGRVLRRPAVIP +VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYEMRDPELEGALRHVLGR +>LFPAFLNI_00411 +MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ +APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL +ASWRHTHLLDDAAPGEADMADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF +EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR +VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS +RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF +LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES +HDGSPWLSWIGADDIAEAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPALIP +VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYQMRDPELEGALRHVLGR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001719.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001719.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd1908359ba128a6f8f14cd14ae2b9cbfe0d7f1c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001719.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02552 +MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEGAEPHAAAIGRLLEALMDR +LEALDPATADREMNPRPVEPHPGVSQPVADALAAYAAGDVAALDALEVAQPGTAFRQRAW +RELRGIAPGSPATYGGLAERCGTPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY +GTAAKRALLAHEAAHAG +>MOLHKGIG_00404 +MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR +LVALDPETADREMNPRPVEPRPGASQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW +RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY +GTAAKQALLAHEAAHAG +>NAFOICDF_02420 +MTHPPAFLPELRWTAATLPGTSLALVAVYSPEDDAVRASGVAVPEGAEPPAAAIGRLLLE +LMDRLEELAPETAAREMDPRPVEPREGLDQTVADALAAYAAGDVDALDGLAVVQPGTAFR +QASWEALRSITPGSPVAYGELATRAGAPKAVRAAGGACAANLAAVVVPCHRVVPASGGVG +SYLYGSAAKAALLAHEAAHAPA +>MHAAABBN_00127 +MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPGDSEPPAAAIGRLLETLMDR +LVALDPETADREMNPRPVEPRPGVSQPVADALAAYTAGDVAALDALDVAQPGTAFRQRAW +RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY +GTAAKQALLAHEAAHAG +>LFPAFLNI_00410 +MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR +LVALDPETADREMNPRPVEPRPGVSQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW +RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY +GTDAKQALLAHEAAHAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001725.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001725.fa new file mode 100644 index 0000000000000000000000000000000000000000..70416d12d804f320e0046f99efda74d54f0faa8f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001725.fa @@ -0,0 +1,46 @@ +>ACLBLIBL_02560 +MTALLSLLAVMIPTLVVWATGGFQRPTIEGALQVGGTLWLALHAVPVTVATVLPTAEGHV +LSGTAWLVPWGLTLIPLLLSWRAGRRLARASYRDQAWQAFAGAVVGYALAGLTVAFLPGT +PELRVSPWAAALLPALLFGIAALAGARREAGTWAHLIGLDLTERIARRSQYERWAGSYAW +SVVRAAVVALLVLAALSALLVAVRLAVEWPAVVTLAQAIDAGPFGGLLLAVLQIGWLPTL +TGWAIAWTAGPGFSVGSDSLYSVFGATPAAAPALPALGALPAAWAPWHPLFLAVPIAAGV +AAGVWLLREGENHLDDWLDARTGHRAVSLALSTLALAVLTGLLAGLLLLVPLALTSGTLG +VGTLTDIGANVWAVCAAVAGWVALGCAAGYLVALALAGRRFIPPAEAAVAAERPRPRRSR +D +>MOLHKGIG_00397 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVTTAMPTAPDHLITGTAWLVPWGLTLLPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV +TVAEAIGGGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLTGLLLLVPLALTSGTLGLGALTDLGSHVWAVSAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD +>NAFOICDF_02431 +MSPRVPSLLRPVPLPLWLQGVVEALVTALTSLALVLVPTLAVWITGGFSSTRIEDVLQTG +GALWLGLHAVPLAVTTVVAQADTPTVTGTVWLVPWALTALPVWLSWRAGRRLARASYREQ +AWQALAGAVAAYAVVALACALLPGEGRITVHPLPSVLLPCLLFTTSAVAGARREAGTWAH +LIGLDLTERIARRSQYERWAGTYAWSVLRGAGVGLAALAGLHALLVTVAVLVRWPRIIEV +QQMVGAGPVGGLMLALLEIGWLPTFTAWAVAWTAGPGFAVGADGHYSVFGTTPAPVPALP +LLEALPAPWAPWHPAFLLVPVLAGAVAGWWLLREGENHLDDWIDSRITARWASLTLSTLA +LALLLGLVSGVAVLVPLALTNGTLGVGSMREIGSNAPLVALAVAGWMALGCALGYLVALA +VVDRPVRGRRRISLPLPGSAPRAVTGRARRLPPRRLPRGVADAEADEPEVAAPAAAREEI +PGRETPAQETPSEEPPAAARPAPRRAGAPRVPRVPRPAPRRARD +>MHAAABBN_00121 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV +TVAQAIGGGPLGGLLVALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPISAGVVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLAGLLLLVPLALTSGTLGLGTLTDIGPHVWAVCAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD +>LFPAFLNI_00403 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTVHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAVLAVLALTGLNALLVAGRLAVEWTAVV +TVAEAIGAGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLTGLLLLVPLALTSGTLGLGTLTDIGSHVWAVCAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGPRDRPSPRRARD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001727.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001727.fa new file mode 100644 index 0000000000000000000000000000000000000000..390dc981724382bde1332e66bb423c5729b1f25c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001727.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02562 +MNHALETLRDEVFARNPGEAEFHQAVSEVFEALDPVMERHPQYVEAGVLHRLCEPERQII +FRVPWIDDNGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ +YKRLTNRFEAGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLKTRGESMDGQQVLISGSG +NVAIYAAEKAASLGATVLTASDSAGYIVDPDGLDLDLLKQIKEVERARISEYVERKGGRA +RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLGNGVKAVAEGANMPCTEAATRLFLHA +KTLFGPGKAANAGGVATSALEMQQNASRDSWNFEYTHDRLEAIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV +>MOLHKGIG_00394 +MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII +FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ +YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG +NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS +RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS +GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV +>NAFOICDF_02434 +MHQVLQTLRDEVFARNPGEAEFHQAVSEVFEALDPVVERHPHYVDAGVLHRLCEPERQII +FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ +YKRLTNRFESGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLRTRGESMDGQKVLISGSG +NVAIYAAEKAAQLGATVLTASDSAGYIVDPDGVDVELLKQIKEVERARISEYAERKGGKV +RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLQNGVKAVAEGANMPSTEAATHLFLDA +GTLFGPGKAANAGGVATSALEMQQNASRDSWDFDYTHDRLERIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV +>MHAAABBN_00118 +MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII +FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ +YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG +NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS +RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS +GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV +>LFPAFLNI_00400 +MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII +FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ +YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG +NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS +RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS +GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001728.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001728.fa new file mode 100644 index 0000000000000000000000000000000000000000..2fcaae7b1608302f995b554517f4ca3c45bed11c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001728.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02564 +MTGPRAVEVRIPLRWADMDAYGHINNIAVVQLLEEARVAAFGVPANTGAGGGEAPPIDLL +EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVEAVKAASVHVGYALHDGVDDTLCAT +ASSVMVFVDGETGRPVRVTPEQRAALQG +>MOLHKGIG_00392 +MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL +EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT +ATSVMVFVDGQTGRPVRISPEQRAALAG +>NAFOICDF_02435 +MTETTTSSAARDGAGRWVEVSVPLRWADMDAYGHINNIAVVQLLEEARVAVFGVPANTGA +GGGGAPPVDLLEGVPEGVRTFVSEHTVKYRAQMPYRPVPLRVRVGVAAVKAVSVEVAYEL +YDGVDGTLCVTARSVMVFVDGASGRPVRLTAEQRAALAG +>MHAAABBN_00116 +MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL +EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT +ATSVMVFVDGQTGRPVRISPEQRAALAG +>LFPAFLNI_00398 +MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL +EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT +ATSVMVFVDGQTGRPVRISPEQRAALAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001733.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001733.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae1b57dad2cf5b4a3b1a5a4d858d297efe7ecf1b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001733.fa @@ -0,0 +1,25 @@ +>ACLBLIBL_02571 +MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV +TLCQVLGASPGDVLDAPEVTVVRLSDAPAISLGGEGIRERLITPRGRRDLQILRADIAPH +GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTLPGREPHSWANPDDRPAI +VLWTLVGHA +>MOLHKGIG_00384 +MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV +TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR +GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV +VLWTLVGHA +>NAFOICDF_01754 +MKSLPLHPTPTTPQVGRRLRALREQARISLADLAQVTGLSKGFLSRVERDLTSPSVASLV +AVCQALGTSPGHVLDAPEVTVVRGGEAPAISLGGQGITESLLSPPGLRPLQVIRAEIAPG +GTGEDELYTVDCEVESVHVVSGRLTLRTVDGAHALAAGDTATFSGQEPHSWQNPDPDSPA +LVLWILAGRT +>MHAAABBN_00108 +MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV +TLCQVLGASPGDVLDAPEVTVVRLADAPAVSLGGEGIRERLITPRGSRDLQILRADIAPR +GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV +VLWTLVGHA +>LFPAFLNI_00390 +MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV +TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR +GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV +VLWTLVGHA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001735.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001735.fa new file mode 100644 index 0000000000000000000000000000000000000000..422fa8a5ea80528f1c9d1e4f774d57b110e5a658 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001735.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02573 +MSPRGRSGSRLTQASLETEGNSFMTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG +VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV +ACGRCRNCRAGRTEVCETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ +AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG +DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM +QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA +PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR +>MOLHKGIG_00382 +MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP +APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPDQ +ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLTVLSDILPTAFHGLV +EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT +ENLQDAVSDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG +IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPVMRYNRQLMMSILWDRMPYLTE +MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR +>NAFOICDF_02445 +MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP +VPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNVACGRCRNCRAGHTEICETANPEQ +ACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM +AAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT +ENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEMQPIAAVNQVLDITRPGGATGIIG +IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE +MVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR +>MHAAABBN_00106 +MTTENRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP +APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEVCETTNPEQ +ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM +EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT +ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDVTRPGGATGIIG +IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE +LVNPRVITLDEAPQAYAEFDQGSVEKFVIDPHGMIAR +>LFPAFLNI_00388 +MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP +APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPEQ +ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPGQEQAMEKILDLAVLSDILPTAFHGLM +EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT +ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG +IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE +MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001736.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001736.fa new file mode 100644 index 0000000000000000000000000000000000000000..746c8d12b1844363559c03cfd9e44ff73eba35e4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001736.fa @@ -0,0 +1,15 @@ +>ACLBLIBL_02574 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLMFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAQSRGIAGEWARPALASVAGMVALVVGLAALGITATLLHAA +>MOLHKGIG_00381 +MRLHHDPGLQPERTVMSWGRTALALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA +>NAFOICDF_02446 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAQADGIAREQARPALASVACMVALVVGLAVLGITATLLHAA +>MHAAABBN_00105 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIARERARPALASVACMVALVVGLAALGITATLLHAA +>LFPAFLNI_00387 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001738.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001738.fa new file mode 100644 index 0000000000000000000000000000000000000000..6added54de3053c6cc863ba193ac9c8112d2b84a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001738.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02576 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSVHRILLRWLARIFGSVFVLALAQRAESDTPYAKDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELTLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGYGA +AAVTYVLGLLFGANVG +>MOLHKGIG_00379 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA +AAVTYVLGLLFGANVG +>NAFOICDF_02448 +MSPAHAATPAALPEPTREQVRRWRRYLADEIAEGQIYRDIAASKDGVERDILIGLAEAEK +RHEEHWRALLGEHAAHPPRPSVHRILLRALARVFGSVFVLALAQRAESDTPYAKDQDATE +HMAADEQIHEEVVRGLASRGREQLAGSFRAAVFGMNDGLVSNLALVMGIGATGVASSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAEHLDLDRNELELVYLARG +MTPEDAKHRALERLGYLSCDCNPQFSARPDGSKGPVDHSESFAEIGSAWGASLSSFCFFA +SGALIPILPYLFGMTGLGALVVAAVLVGIALLFTGGVVGLLSGSSPLWRGLRQLMIGYGA +AAVTYLLGLLVGGSIG +>MHAAABBN_00103 +MSAAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRILLGEHAENPPRPSFRRVLLRWLARIFGSVFVLALAQRAESDTPYEKDQDAPE +GMAADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGAALLFTGGVVGLLSGSSPLARGLRQLAIGYGA +AAVTYVLGLLFGANVG +>LFPAFLNI_00385 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA +AAVTYVLGLLFGANVG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001739.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001739.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ab9bea62b1aa5b9157215152ab9c3c46b58cb8b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001739.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02590 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL +PVFGSVTEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAKFFAL +SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE +LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE +ILQAQA +>MOLHKGIG_00372 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL +PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAEFFAL +SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE +LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE +ILQAQA +>NAFOICDF_02449 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDEDGNAVEL +PVFGSVAEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL +SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE +LKDFGFSTAIGIGGDPVIGTTHIDALEAFEADPETKAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETADLMRE +IMKGL +>MHAAABBN_00088 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL +PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAKFFAL +SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGTGPIGLVSKSGTLTYQMMYE +LRDFGFSTAIGIGGDPIIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE +ILEG +>LFPAFLNI_00379 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL +PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL +SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE +LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE +ILQAQA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001740.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001740.fa new file mode 100644 index 0000000000000000000000000000000000000000..046ad4537cc6f2c31042bb109b4fd626c8265087 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001740.fa @@ -0,0 +1,40 @@ +>ACLBLIBL_02591 +MDLYEYQARDLFEAHGVPVLAGIVAQTPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVAEAGFPEELRADVADVIQKLWVVF +EKEDATLVEVNPLVKTGDGKILALDGKVSLDDNAEFRHEGHAALVDERTEDPLEAKAKAN +DLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD +VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDAATKPLVVRLDGNAVEEGRRIL +QEANHPLVTLAATMDEGADKAAELAHSAN +>MOLHKGIG_00371 +MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF +EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAQFRHEDHAALVDERTEDPLEAKAKAN +GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD +VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL +QEANHPLVTLAATMDEGADKAAELAHSAN +>NAFOICDF_02450 +MDLYEYQARDLFEKHGVPVLQGIVAETPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVNKVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSALTGLDQATADTIVAEAGFPEELRADVAAVIVKLGEVF +KNEDATLVEVNPLVKTGDGTILALDGKVSLDDNAEFRQADHAGLVDKTTEDPLEAKAKAN +DLNYVKLDGQVGIIGNGAGLVMSTLDVVAYAGENHGGVKPANFLDIGGGANAEVMAAGLD +VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDSATKPLVVRLDGNAVEEGRRIL +QEADHPLVTLAATMDEGADKATELAHSAN +>MHAAABBN_00087 +MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF +EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN +GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD +VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL +QEANHPLVTLAATMDEGADKAAELAHSAN +>LFPAFLNI_00378 +MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVHRVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVAEAGFPEELRADVAEVIQKLWEVF +EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN +GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD +VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL +QEANHPLVTLAATMDEGADKAAELAHSAN diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001743.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001743.fa new file mode 100644 index 0000000000000000000000000000000000000000..5c5655ff4bd71b51f5cdf38ee473e79cb8b20db1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001743.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02596 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDAHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNALK +ADRSLESMGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>MOLHKGIG_00365 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>NAFOICDF_02455 +MRTLVLNAGYEPVSVVSDRRALLLVATGKASVLEDGDAPMHSPTRAWGRPLVILLHQYVR +VPHADAAAVSRKGVLRRDGHRCAYCGAHATTVDHVHPRSRGGQNTWENLVACCLRCNSAK +ADRSLDALGWRLRVVPTRPCGVQWRLRELERPAPAWEGWLQFAA +>MHAAABBN_00081 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>LFPAFLNI_00372 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001744.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001744.fa new file mode 100644 index 0000000000000000000000000000000000000000..b042b20ac777034627fe387bccd095eb041a83e7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001744.fa @@ -0,0 +1,23 @@ +>ACLBLIBL_02597 +MGLAGTRLSEEAATPGRFRVRGLAEGVQTDPELLAQLAAAGVTPGRTVTAQAAIDPGYVR +VEGEAADGAPESGALELAVETAAHVWVERLDA +>MOLHKGIG_00364 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGMDR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPDL +LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAAATAAHVWVERLDG +>NAFOICDF_02456 +MTDLIDTTEMYLRTILELEEEGTVPLRARIVERLEHSGPTVSQTVARMERDGLVHVGSDR +RLLLTDEGRERAVAVLRKHRLAERLLSDVIGLDWAYVHDEACRWEHVMSDRVEQRLLEVL +ENPTATPYGTPIPPRPEAQSAGEWSRDLGLAGEPLATAAATPGRFRVGSLSEGVQADPEL +LAELQDAGVLPGGVLEAQPALEAGYVRVQGEGSAEALELSAGTAAHVWVQRL +>MHAAABBN_00080 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGTDR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSREMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPEL +LAQLAGAGVTPGRVVRAQAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG +>LFPAFLNI_00371 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGADR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGARLSEEAATAGRFRVRGLAEGVQTDPEL +LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001746.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001746.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8df1fea963ea88e00739da7b1ad1dacb038c1cc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001746.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02599 +MTDREDATPVEQEQAAPAAEEAVVKAPPARRRAPRRDDLLAAAVDEARAGLAGLAAPEEV +GEHVDVLVDDDRLVTHRFESRLPGYAGWLWYATIARAPRSRLVTVCETGLVAGEGALVAP +PWVPYAERVSEEERERLRAVAEGRVPGAAAPAGQPAPEGDGKG +>MOLHKGIG_00362 +MTTHDDAPRVDHRSPDAEPAEERTAVPPARGRAPRRDELLAADVDTARAGLAGLAAPDEV +GEHVDVLVDDDRLLTHRFACRLPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLVAP +PWVPYAERVNEEERERLKAVAEGRVPGAPAPDAEGDGTPEAAARG +>NAFOICDF_02458 +MTEHSDTPGQTDTSGQTHTPEQAPAVAPAGPAADAAPAASARAPRRRAPKRDELLAAAVD +EARAALTELAEEGQVGPHLGVTVDDDRLMTHRFAAEVPGYTGWVWYSTIARAPRAKKVTV +CETGLEAGEGAVVAPAWVPYADRVSAEERERLAAVAEGRVPDAG +>MHAAABBN_00078 +MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD +EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLV +APPWVPYAERVNEEERERLKAVAEGRVPGAPAPEAEGDGTLGAAALG +>LFPAFLNI_00369 +MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD +EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGALV +APPWVPYAERVNEEERERLKAVAEGRVPGAPAPETAPDDRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001752.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001752.fa new file mode 100644 index 0000000000000000000000000000000000000000..6647d038a8a32a2b934ac0ea39b6e9d0f73789d6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001752.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02607 +MAYQPDRFDEVPEYTDQRGAHRASFAAPAGAAAAGGGARRFSPLLLVAGLVLLAGLFVGV +VLPWLTGDRSEPVAAESSASSPAADPSTSSEPASPTEGAATTEPASPSEDAAAAEASRSQ +AAAQSAAEQSAAEAAAASSRAAEEAAAAEASRSAEAAQAAEASRSAAAAAEASRSAGAAQ +AAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEA +SRSAAAQAAEASRSAAAQAAAAARSTNVTVYNATRTTGLAASYAQRLRSAGFTSVSAQNW +GGYGIQSSTVLYNGSGNQAAAEAVAAELGFPVLQTPNLQVNGVAVVVTG +>MOLHKGIG_00354 +MAYQPDRFDEVPEYTDQRGAHRESFAVAGATATGGGRRLSPLLWVAGLVLLAGLFVGVVL +PWLTGDRSEPVAAESSTTAPAAAPSTSASSVSSSASSASASTASATESATPSEDAVEASR +SAAAAESSRAAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRAAAEAQ +AAEASRSEAAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSA +AASSSRAAAQSAAVRGTHVTVYNATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSST +VLYNGSANKAAAEAVGKELGFPVMQTPNLQVNGIAVVVTS +>NAFOICDF_02466 +MAYPADRFDDVPEYTDQSGAHRESFAAAPAAAGAAGATAAGTEAAAGGGILKWLLAAAAA +VLLVGLFLGLVLPRLNGGDDKPVAGAASSSSSSEPAADASSSSSDAPSSDASSSAGPDSA +APAAPSSDAGAESAAAPSSDAAVESRAAAESSQAAAESSQAAADAQRSRDDAARAASESA +QAAADASSADAAARERAASESAQAAADASRAAEASRSAEASRSAEASRSAEASRSAEASR +SAEASRSAAASRSAAAQESADRAVKSTPVNVYNATRRNGLAASYADRLTGAGYTRVTADN +WPGFRVTSNTVMYNGADKRAAAEAVGRELGMPVQQVPNLQVPGIAVVVVR +>MHAAABBN_00070 +MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL +PWLTGDRSEPVAAESSTTAPAVEPSPSTSTSASSESSSASSASASTASATESATPSEDTA +EASRSAAAAAAESSRVAQEAAAAEAAESSRAAESSRAAAEAAESSRAAAEAQAAEASRSE +AAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAA +AQSAAVRGTHVTVYNATRSQGLAASYAQRLTSAGYTSVDAKNWSGYGIQSSTVLYNGSAN +KAAAEAVGKELGFPVMQTPNLQVNGVAVVVTG +>LFPAFLNI_00361 +MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL +PWLTGDRSEPVAAESSTTAPAVEPSTSASSESSSASSASASTASATESATPSEDTAEASR +SAAAAAAESSRVAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRSAAA +VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSAAVRGTHVTVY +NATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELGFP +VMQTPNLQVNGIAVVVTS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001755.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001755.fa new file mode 100644 index 0000000000000000000000000000000000000000..4bb6fcdacc8a48d3f47c9f41c2a9df7c846b4b9c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001755.fa @@ -0,0 +1,59 @@ +>ACLBLIBL_02610 +MLAPADADGALPAPDVLPEPDVTVPDPVVPVGPPEKRGRRRGRKAREVFVENLPTQALVL +ADRLHSSPYGRRMRSTLQQRREAETHALEARTTLDFALKLGETMFSFGAASLDVETSIIV +VTQAYGILETEVDLTNQSISLNYAPDSSRGESPYTLQRVVRSSSVNFEGLVAVHRLVEEI +ADGRLDRAEAQRRLVEIRHQPKPFPPVFEILFAGVFVACFIPFIGGNWTGSLLGMISTWL +VFWLKIQADRARFPEIFSTMFGAIVATVIALAAFALELPVNPAVVIAGGIMMLLPTARFV +TAVQDAINGFPVTAAGRFLSALLVFTGVMAGIMVAVALGDLAGLEHLDLAEAGTLQHPPL +LLLALVTAAGMSDAVVEQSRWPQILACGLVSGAGYGVFLAAQQLGIGDRLVPAAAATAVG +FLGRLVAQRIAAPALVIVLPSMLFLLPGLMMFRSVYGFTVETGSTLLGLAGLFNAAVIVV +AIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG +>MOLHKGIG_00351 +MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES +AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL +SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL +PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV +ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH +RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG +MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL +PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT +LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAV +AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN +AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG +>NAFOICDF_02469 +MGAEPRRGPAQGTGPLGPDRNPRKDPVRSVDPLAPQDGSPEDGGVPQGARRAGTRPDAAG +SAPAEPAVHVALLPVLRPADARTPAGASDGDAPAGDGVDLAAAPAREPGPEDVLPPVLAP +VAAPTVPVETLPTPEPAPAPEEEPTPAADAPLTAPPLSEPVPTSVLAPAEGDAPTAQEAA +AAVPDVVVPDPLKQHGPEEPRGRRRRRRTREDHRAVFEEVLPTQAIVLVDRLQASPYGKR +MRSTLRQRRDTEAAALEARTTLDFALKLGETMFGFGATSLDVETSIIVVTQAYGIHETEV +DLTNQAISLNYAPDSSRGEVPYTLQRVVRTYSTNFEGLVAVHRLVEEISDGTLERAEAQR +RLVEIRRRPKPYPPAVEILLAGVFVACFIPFIGGTWQGSLLGMVSTWFVFWLHTRTSVFL +PEIYSVMIGAFLATLIALGAYALHVPVNPAIVVAGGIMMLLPTSRFVTAVQDAINGFPVT +AAGRFISAMLVFIGIMAGIMVAVGLTDMLGIARLDLAATQSTAYPTTLLLALVVAATACD +AVVERSGWRTLLASCAVTAAAFAAHTVVAGLGVSAQLLPAAAAAMVGFAGRIVALRVGAP +PIVVVVPAILFLLPGFAVFRGLYEFTVESASTMAGLAGIVNALVIIVGIGAGAVFGDTLA +RPVTERLSPARSTPGPEGHTR +>MHAAABBN_00067 +MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES +AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL +SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL +PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV +ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH +RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG +MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL +PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT +LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGVGFGAYLAAQQVGVSDRLVPAV +AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN +AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRR +>LFPAFLNI_00358 +MEQEGTQEPARFDPRIAEPPAVPTLIPVLRPAGAEDAAAVGDLAIDPEDPGLLDLDPAES +AHPAAAAVAVEPTEPLPPVVRPAAADPEPEPEEPAEPEAETLPEPAADAPLTEPPLSEQV +PTSVLAPADADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENLPTQA +LVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDVETSI +IVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVHRLVE +EIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALGMVST +WLVFWLKVQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLLPTAR +FVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLLGFEQLDLAEAGTLSYP +PLLLLGLVMAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAVAAAA +VGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFNAAVI +VVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001756.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001756.fa new file mode 100644 index 0000000000000000000000000000000000000000..f92aa6bda110cabe6a25da5491da3fd1ecc2d0e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001756.fa @@ -0,0 +1,56 @@ +>ACLBLIBL_02612 +MKSSVQHSTRRRVGALLAGAVLAGGALTSSPAFAAPAEGARAEQAPRPVAAAPLATVDAA +DPNADGYDSFIVTYKETAQNNNGKGRALAWGKAAKAAGVSVKELRETALGSHVVQADRKL +DQSESARFMADLKASGAVEDVEPNAIMTATGLSPADALYSQQWGFTGTNGMRVPGAWDYN +TGSGVTVAVLDTGITSHPDLDRNVVAGYDFISSSAAARDGNGRDSNPRDEGDWYAAGECG +ASQPGNSSWHGTHVAGTVAAVTDTQGVVGVAPNAKIQPVRVLGKCGGSLADIADAIVWAS +GGSVTGVPANANPADVINMSLGGSGTCGTTYQNAINAAVNRGVPVVVAAGNENQPAANAR +PANCSNVITVAASTSQGARSSFSNYGSAVDVTAPGSSIISTINRGLTTPTTAGHASYNGT +SMATPHVAGLTALMLAQQPGITPAQVESTLKSTARSMPVACSAGCGAGLVDATRAVAALG +GGSTTPTPTGVIVNGGFESGATGWTGTPSDFVGNTAGYARSGSNYGVLNGYGRSNTGTVE +QRVTVPASGASLSYWLQVGSDETTTRSQYDTLAVQVVDGSQTTTVKSHSNLEKGTSYAQH +TVDLSAYKGKTVTLRFRGVEDYSNSTVFRIDDVAVTAK +>MOLHKGIG_00349 +MQSSTPRSTRRIGALVAGAVLAGGTLTSSPALAAPSGAAPAAPAASPTVASPLAAAQVED +PNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVVTVDRKLD +QAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRTT +GSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECGT +AGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAAG +GTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVRP +ANCQNTIVVAASTSQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGTS +MATPHVAGLAALLLAAQPSLTPAQVESTLRSTARSMPVTCSAGCGAGLADASAAVSSLGG +AQTEPGPAPVASLIVNGGFESGSTGWTGTPTGFVRTDAAKAASGQAFAQLNGVGRRNTTT +VEQKVTVPASGATLTYALQVDTAETTASRSYDLLDVQVVTGATGTYTVASHSNLDKGGYA +TRTVDLSRFAGTTVTLRFRGTEDSSAATTFRIDEVAVTAR +>NAFOICDF_02471 +MTALTSPSARRRVGSLLAAAVLAGTALTAAPTLAAAERPAEPARTSPAAAAPLADPNADG +YDSFIVTYRETAANSTAQGRAKAWGRAAREAGVSVKELRETALGSRVIATDEKLTQEESA +AFMADLRASGAVEAVEPNVIMTRAALSPADPYYADQWGFTGVNGMRVPGAWDVSTGTGAI +VGVIDTGQTDHADLNANTVPGYDFISDATTARDGGGRDADPRDEGDWYLAGECGQSRASN +SSWHGSHVAGTVAAVANTQGVVGVAPGAKVQHARVLGKCGGTLADIADAIVWSSGGSVPG +VPANPTPVDVINMSLGGQGTCGTTYQNAINAAVGRGVPVVVAAGNENQSAANARPANCQN +TITVAATDVNGNRASYSNYGSAVDVAAPGSGIISTVNAGTTTPTAGAYAQYNGTSMATPH +VAGTVALMLAEDATLTPAEVESSLKTNSRPIPGVCAEGCGAGLVDAAKTLASLRGGTTDP +HPVTPVPGAEKLVNGGFESGLTGWTATGRVAASSTAGLSATGSLHAALNGKGGTSTATLT +QKAVLPAGAAATLSYAVRVDSAETTTARQWDKLTVSVSDGATTTTLRTHSNLDKGRGYLA +QAADLSAYAGKTVTISFSGTEDGSGATTFRIDDVSVKAG +>MHAAABBN_00065 +MQSSTPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGGAPAAPAASPTAASPLAAAQAE +DPNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVITADRKL +DQAESAKFMADLKASGAVEAVEPDALLTATGLSPVDALYSQQWGFTGSHGMRVPGAWDRT +TGSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECG +TAGASDSSWHGSHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGRCGGSLSDIADAVVWAA +GGTVAGVPANPNPADVINMSLGGSGVCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR +PANCRNTIVVAASTPQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGT +SMATPHVAGLAGLLLATKPSLTPANVESTLTSTARSMPVTCSAGCGAGLADAARAVSSLG +GSS +>LFPAFLNI_00356 +MQSSPPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGDAPAAPAATPTAASPLAAAQVE +DPNADGYDSFIVTYKETAATAHAKGRANAWGKAAKEAGVSVKELRETALGSRVIKADRKL +DQAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRT +TGSGVTVAVIDTGITSHPDLDRNVVPGYDFISDGRAARDGGGRDSNPRDEGDWYAAGECG +TAGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAA +GGTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR +PANCRNTIVVAASTSQGARASFSNYGSVVDVTAPGANIISTVNNGATTPTTAGHAAYNGT +SMATPHVAGLAALLLAEQPSLTPAQVESTLTSTARSMPVTCYAGCGAGLADATRAVSSLG +GSS diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001757.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001757.fa new file mode 100644 index 0000000000000000000000000000000000000000..0f49efa826f0f67ba5470b1f6b7c52e26ff5d52f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001757.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02622 +MARNTSGSHTSATDARARARQIQEQQRKKDGRRRTAVIWGSVLAAILVIGLIVAFALNRG +GDEPAAAGPIPAAANEQGGIELTSATTLAEGAGAREVDASTVEVPEQGAAQQPETIPAAE +APAEGEPSEIVLYADFNCVYCADFETSNAAQIEQWLEAGEVTVEYRMVDFRSAPNNQNYS +ARAANAAYCVADQKPEAYNGFVTALFGTYQEHGGKGIDNAALTQLAQDNGADIASCVEDG +TFRSAVEHTTRQAQAAGVGGTPTVFMDGENWAIGGPDQSFQEWAQSKISG +>MOLHKGIG_00347 +MARNTSGSHTSATDARARARQIQEEQRRKDRRRRTGVIWGSVLAAVLVIGLVVAFALTRN +GDDAAAAGPIPAAANEQGGIELTSATGLAEGAGEREVDPSEIEVPKQAASSQPETLPNTE +ARGDGEPTRIVLYADFNCVHCADFESSNAEQIEQWLEQGEVTVEYRMVDFLSAPNNQNYS +ARAANAAYCVADQKPEAYNGFVAALFAAYDEHQGKGLDNAALTQLAQEQGVDISSCVEDG +TFRSAVEHTTRQARVAGVAGTPTVFVDGKNWALDGEDKTFTDWAGAKIAD +>NAFOICDF_02474 +MASRNPAPSEVDARARARQMQVDQQKKARRRRTATIWGAVLAAVLVIGLIVGFVVKGNQG +TEISATGPVPGVVNEEGGVEMTSATALADSGKSERQVDSSSVAVPETATAPEELTTIPAA +GEPADGEPAQIVVYADFNCVHCAEFESQNSEQLQSWLRDGKATVEYRMVNFLSAPNNKNY +SARSANAAYCVAAAKPEAYNEFTTGLFMAWEGHGGKGLSDDELIQRADALGVDIEGCLKD +NTYRPAVEWATNKAKAASVAGTPTVFVNGKNWSTDGGDKSFVDWAKPMVEG +>MHAAABBN_00063 +MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN +GDDAAAAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE +ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS +ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG +TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG +>LFPAFLNI_00354 +MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN +GDDAATAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE +ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS +ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG +TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001758.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001758.fa new file mode 100644 index 0000000000000000000000000000000000000000..45043598d781de28f3442d9f6e5e65940309f62e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001758.fa @@ -0,0 +1,45 @@ +>ACLBLIBL_02623 +MSERIVTVDTVETPSPDDRLTVTGAPSGDASEDPATALLALPWSTALEDWPEDVLAALPR +GISRHVVRFARVGGGVVAVKETTEDLAFREYRLLRRLEGSPAPSVVPVAVVTGRTDGRGE +PLPAALVTRYLHFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVL +FRRDAGGFAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPA +ATPELFVDAYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMML +AAPVEVHAGYHRRRLTRLTGLQVQENQARRLLVDIEAARRAWDPFLDLEGAAHRWVVEVF +DPVVRSVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRVRRDED +AVALHPTTTMLRTVPPADED +>MOLHKGIG_00346 +MDTVETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV +RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV +TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG +FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV +ASYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH +AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV +PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT +TTMLRAVPPADAD +>NAFOICDF_02475 +MDEHEQPRTDPADRLTVTAAPSGDASEDPATSLLALPWERPLEDWPAEVLAALPRGISRH +VVRFARMGAGVVAVKETTEELAFREYRLLRELEDRPSPSVVPVAVVTGRTREDGTALPAA +LVTRHLRFSLPYRAVFSERMERRTLVRLMDALALLLVELHLEGFFWGDVSLSNVLFRRDA +GGFAAHLVDAETGELRERLSTGQREHDLDVARVNIGGELLDLHASGLADPDVDAIATPDL +FVESYRQLWQQLTEPTVFPRGEPWRMDRRFRRLTELGFEVEEYSLRAADAPGMMVAQPTD +VNSGYHRRRLERLTGLHVQENQARRLLVDIEAARRSWDPFMDMDHAAHRWVIEVFDPVVR +SVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLDEAVDSYVETVLRARRDEDALALH +PTTTMLRAVPAPEADPEG +>MHAAABBN_00062 +MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV +RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV +TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG +FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV +ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH +AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV +PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT +TTMLRAVPPADAD +>LFPAFLNI_00353 +MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV +RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV +TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG +FAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV +ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH +AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV +PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT +TTMLRAVPPADAD diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001760.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001760.fa new file mode 100644 index 0000000000000000000000000000000000000000..42c0b5791df0e7d97e289a5a95acad1558971809 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001760.fa @@ -0,0 +1,20 @@ +>ACLBLIBL_02626 +MAFERVDLTTPWLAYWAALLALVIGAALLAAGIWRERRHRRHAAAHGRNTEVDVLDNTRL +QRRVGVVGLVAAVVLAGVGVWTHLAGLDALRQNLTAKYGYTDVERIRQSGTGFIIDLTQP +DGTVLKDEMVLVDPSGEPFIGDDIFIDVIGGA +>MOLHKGIG_00343 +MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADAHGRNTEVDVLDNTRL +QRRVGAVMLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP +DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP +>NAFOICDF_02478 +MTFAPVDLQTPWLLYWAAAVAAVVGVSLALAGRWRERDHRRRQAAAGSHVVMRVLENTRL +QRRVGYGALVLALALAVWGAVAHVQGIDALRGNVRQKYGAEVEDVRQSGSGVTVDLVHPD +GTREEDQYMAVEQDGEPVYGAELVESPPIGG +>MHAAABBN_00059 +MTFAPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL +QRRVGAVMLAVAAVLAGVGVGTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP +DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP +>LFPAFLNI_00350 +MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL +QRRVGAVVLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP +DGTVLRDEMVVVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001761.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001761.fa new file mode 100644 index 0000000000000000000000000000000000000000..d0db1cd875d6bb0b1849f03bfbaaa65bf6202272 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001761.fa @@ -0,0 +1,35 @@ +>ACLBLIBL_02627 +MAWGAAPAPAPAPGEGPALLASAGPEHAEAARERARGALRAGIDAGVDLLDTADIYGAGV +SEETVGALLHELPYEERSALKVQTKCGIVLDEVDADGRPMVRYDSSPEYVRARLEGSLAR +LGELRVDTLVIHRPDVLTPVADTVRAFLDAREEGLVGKLGVSNLGVGRTLEFQRELAAQS +ADGTGLACVQVELGLHHRTLVESVILANHPGAAADADVADLGRVCAAEGIELQAWGSLGQ +GRFSSGDDGAAGVVGEIARELDTSREAVVLAWLLRLPWGVRPVIGSQDPGRIAACADAAA +AAEAMDSAQWHRLWTAARGAPLP +>MOLHKGIG_00342 +MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR +RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA +GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV +GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLMEAVVLANHPDAPADA +DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGAVGEVAAELGGSREAVVLAWLLRL +PWDVRPVIGTQDPERVAACAEAAAAAEAMDSAQWHRLWTAARGAGLP +>NAFOICDF_02479 +MTAQDTAPQTPAASPLILGTMGWGDVERARGALRAGLEAGIGLLDTADIYGAGASEETVG +ALLAELDPAERTRLRVQTKSGIVLHEPGPDGTPAVRYDNSPAYLHERLALSLERLGLDRV +DTLVVHRPDVLTPVSDTVRAFLDAREAGRVDALGVSNMGTRRVLEYQHALREVSADGTGL +ACVQVELGLHHRMLVESVVLANHPAAAPDGGAGDLGEVCAGEGIEIQAWGPLGQGRFTRG +SDGTVPADPAEQAALAAAGGAPAVVARVARELEVSREAVVLAWLLRLPWGVRPVVGTQDP +ARIASCAQAADAAARMDGAQWHRLWTAARGETLP +>MHAAABBN_00058 +MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR +RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHEADPA +GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV +GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA +DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL +PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAVRGAGLP +>LFPAFLNI_00349 +MSTAPTHPPLDLDPTPATPIVLGTMAWGSVPPPPPDADPGAGPEGPAGEAQAEAAVERAR +RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA +GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV +GKLGLSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA +DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL +PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAARGRPLP diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001763.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001763.fa new file mode 100644 index 0000000000000000000000000000000000000000..27e6da70c06fe609f9af6378568fca7a791741ef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001763.fa @@ -0,0 +1,30 @@ +>ACLBLIBL_02629 +MSSSEPAAPAALPRAVGILGAGRAGTGVARAIARIPRLSPGLPEVRALVAGTRRPSAVQR +HLTVYAPAAQAVAAEELAARAEVIVVAVPREDLDDVDPLALAGPGVRAVVDMTNTWGEEL +LPAWLEAGPDDAPGTARIAARWAAAGLEVPVVRALSEVSHHDLDVHGRAAAPRRALAVGT +VPAADASDPGAVVAARDAVAALVTAMGFDAVPYEGLERAAVLEPGGAGFGVAHDARELAA +LLGAGPRG +>MOLHKGIG_00340 +MSSSEAAAPAHALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ +RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDE +PVPAWLDDDAAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE +PADATADPAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL +LADAPTG +>NAFOICDF_02484 +MPHDAAPRPDQPAAFESLPASVGILGAGRAGTALARAIARIRVLHPGTAAPRVVLAATRS +PAAVRRHLAIHAPGAEAAHPGDLATDTELTVVAVPREELDEVDPAWLAGPRTLAVVDMTN +TWGDELVPDWLAAAAAPGLPTMPGSAAIAAHWAEAGLTAPVVRAFSEVSHHELDRDGRAQ +PPLRALGVGADSPGPARAAVAALVTAMGFEPVEYAPLARAAALEPGTRAFTRPLPADELA +RELA +>MHAAABBN_00056 +MSSSEAAAPADALPRVVGVLGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ +RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLTLAGPATRAVVDMTNTWGDE +PVPAWLDDDGAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE +PADATADSAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL +LADAPIG +>LFPAFLNI_00347 +MSSSEAAPADALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQR +HLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDEP +VPDWLDGDGSPGTARIAARWAAAGVRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTEP +ADTAADPAAVAAARDTVVALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAALL +ADAPTG diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001767.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001767.fa new file mode 100644 index 0000000000000000000000000000000000000000..87b4c56d50ee0dea83a12bc460ff982423d567a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Single_Copy_Orthologue_Sequences/OG0001767.fa @@ -0,0 +1,21 @@ +>ACLBLIBL_02680 +MAWWPFRGPSGAPRDDDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITERAA +EYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQTE +AQRLGRRLTRALSSRLRARGEL +>MOLHKGIG_00335 +MSWWPFPRPSASPSPDDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQAA +EYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQGTE +HGRLRRRLTRALTARLRAGEEL +>NAFOICDF_02492 +MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR +SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE +GDLSHHAARLTQVLTARGRAVRELDERQ + +>MHAAABBN_00051 +MSWWPFLRSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA +EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQSTE +HGRLRRRLTRALTARLRAGEEL +>LFPAFLNI_00342 +MSWWPFLHSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA +EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQSTE +HGRLRRRLTRALTARLRAGEEL