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Beyond_Prompt-based_Retrieval

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  1. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Phylogenetic_Hierarchical_Orthogroups/N0.tsv +0 -0
  2. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Phylogenetic_Hierarchical_Orthogroups/N1.tsv +0 -0
  3. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Phylogenetic_Hierarchical_Orthogroups/N2.tsv +0 -0
  4. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Phylogenetic_Hierarchical_Orthogroups/N3.tsv +0 -0
  5. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000007_tree.txt +1 -0
  6. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000025_tree.txt +1 -0
  7. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000026_tree.txt +1 -0
  8. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000027_tree.txt +1 -0
  9. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000041_tree.txt +1 -0
  10. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000046_tree.txt +1 -0
  11. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000067_tree.txt +1 -0
  12. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000080_tree.txt +1 -0
  13. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000081_tree.txt +1 -0
  14. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000091_tree.txt +1 -0
  15. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000094_tree.txt +1 -0
  16. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000110_tree.txt +1 -0
  17. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000118_tree.txt +1 -0
  18. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000119_tree.txt +1 -0
  19. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000145_tree.txt +1 -0
  20. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000148_tree.txt +1 -0
  21. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000157_tree.txt +1 -0
  22. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000159_tree.txt +1 -0
  23. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000163_tree.txt +1 -0
  24. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000166_tree.txt +1 -0
  25. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000185_tree.txt +1 -0
  26. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000206_tree.txt +1 -0
  27. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000215_tree.txt +1 -0
  28. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000227_tree.txt +1 -0
  29. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000240_tree.txt +1 -0
  30. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000255_tree.txt +1 -0
  31. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000265_tree.txt +1 -0
  32. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000272_tree.txt +1 -0
  33. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000306_tree.txt +1 -0
  34. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000308_tree.txt +1 -0
  35. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000310_tree.txt +1 -0
  36. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000325_tree.txt +1 -0
  37. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000328_tree.txt +1 -0
  38. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000332_tree.txt +1 -0
  39. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000336_tree.txt +1 -0
  40. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000338_tree.txt +1 -0
  41. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000342_tree.txt +1 -0
  42. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000356_tree.txt +1 -0
  43. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000368_tree.txt +1 -0
  44. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000372_tree.txt +1 -0
  45. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000379_tree.txt +1 -0
  46. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000384_tree.txt +1 -0
  47. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000410_tree.txt +1 -0
  48. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000431_tree.txt +1 -0
  49. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000433_tree.txt +1 -0
  50. Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000434_tree.txt +1 -0
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Phylogenetic_Hierarchical_Orthogroups/N0.tsv ADDED
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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Phylogenetic_Hierarchical_Orthogroups/N1.tsv ADDED
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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Phylogenetic_Hierarchical_Orthogroups/N2.tsv ADDED
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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Phylogenetic_Hierarchical_Orthogroups/N3.tsv ADDED
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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000007_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((((((GCF_002008305_4_GCF_002008305.4_01033:0.0022954,GCF_002008305_4_GCF_002008305.4_01383:0.145001)n5:0.00377913,GCF_003691675_1_GCF_003691675.1_01111:0.0108997)n4:0.00109931,(GCF_002008305_4_GCF_002008305.4_02076:0,((GCF_023573625_1_GCF_023573625.1_00589:0,GCF_023573625_1_GCF_023573625.1_01886:0)n8:0,(GCF_003691675_1_GCF_003691675.1_02022:0,GCF_003691675_1_GCF_003691675.1_01115:0)n9:0)n7:0)n6:0)n3:0,(GCF_023573625_1_GCF_023573625.1_02204:0,GCF_003691675_1_GCF_003691675.1_01103:0)n10:0)n2:0,(GCF_002008305_4_GCF_002008305.4_01293:0,GCF_023573625_1_GCF_023573625.1_01338:0)n11:0)n1:0,(GCF_003691675_1_GCF_003691675.1_01016:0,(GCF_002008305_4_GCF_002008305.4_00158:0,(GCF_005280335_1_GCF_005280335.1_01213:0,(GCF_023573625_1_GCF_023573625.1_01251:0,GCF_023573625_1_GCF_023573625.1_00591:0)n15:0)n14:0)n13:0)n12:0)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000025_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_1_GCF_020097155.1_00670:0,GCF_023573625_1_GCF_023573625.1_02014:0)n1:0.279611,(GCF_020097155_1_GCF_020097155.1_00617:0.396144,((GCF_023573625_1_GCF_023573625.1_00094:0,GCF_003691675_1_GCF_003691675.1_02112:0)n4:0,(GCF_005280335_1_GCF_005280335.1_00292:0.0261018,GCF_002008305_4_GCF_002008305.4_00099:1.09025e-06)n5:0.00066179)n3:0.34955)n2:0.0388389)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000026_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_023573625_1_GCF_023573625.1_00142:0.00280964,GCF_002008305_4_GCF_002008305.4_00134:9.87312e-07)n1:6.432e-05,(GCF_003691675_1_GCF_003691675.1_02148:0,(GCF_005280335_1_GCF_005280335.1_00251:0.0175198,(GCF_020097155_1_GCF_020097155.1_00186:0.0936942,(GCF_020097155_1_GCF_020097155.1_00187:0.231713,GCF_020097155_1_GCF_020097155.1_02180:0.454447)n5:0.0983268)n4:0.0691732)n3:0.0196287)n2:6.432e-05)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000027_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_003691675_1_GCF_003691675.1_00792:0,GCF_023573625_1_GCF_023573625.1_01022:0)n2:0.020168,GCF_002008305_4_GCF_002008305.4_00161:0)n1:0,(GCF_003691675_1_GCF_003691675.1_00336:0,(GCF_005280335_1_GCF_005280335.1_00724:0,(GCF_003691675_1_GCF_003691675.1_00347:0,GCF_002008305_4_GCF_002008305.4_01073:0)n5:0)n4:0)n3:0)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000041_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_00900:2.39641e-06,((GCF_002008305_4_GCF_002008305.4_01181:2.39641e-06,(GCF_005280335_1_GCF_005280335.1_01707:0.278665,(GCF_020097155_1_GCF_020097155.1_01606:0.460617,GCF_020097155_1_GCF_020097155.1_00314:0.837031)n5:0.0930035)n4:0.0731322)n3:0.025427,GCF_005280335_1_GCF_005280335.1_01708:0.60198)n2:0.0668866)n1:0.017981,GCF_023573625_1_GCF_023573625.1_01131:2.39641e-06)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000046_tree.txt ADDED
@@ -0,0 +1 @@
 
 
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+ ((GCF_020097155_1_GCF_020097155.1_00743:0.707056,(GCF_002008305_4_GCF_002008305.4_01791:0.00349297,GCF_005280335_1_GCF_005280335.1_01085:0.00293503)n2:0.674277)n1:0.0927394,(GCF_020097155_1_GCF_020097155.1_00733:0.238099,(GCF_003691675_1_GCF_003691675.1_01753:0.00664034,(GCF_002008305_4_GCF_002008305.4_02047:0.00280441,GCF_023573625_1_GCF_023573625.1_01981:1.83476e-06)n5:0.0190982)n4:0.0788758)n3:0.00876398)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000067_tree.txt ADDED
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1
+ ((GCF_002008305_4_GCF_002008305.4_00207:0,GCF_023573625_1_GCF_023573625.1_00207:0)n1:0.00188331,(GCF_003691675_1_GCF_003691675.1_02200:0.00194237,(GCF_005280335_1_GCF_005280335.1_00184:0.0441909,(GCF_020097155_1_GCF_020097155.1_00130:0.0118214,GCF_020097155_1_GCF_020097155.1_00132:2.2062)n4:0.245134)n3:0.0364306)n2:0.00188331)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000080_tree.txt ADDED
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+ ((GCF_002008305_4_GCF_002008305.4_00359:0.00218344,GCF_003691675_1_GCF_003691675.1_00075:0.00437356)n1:0.000893405,(((GCF_005280335_1_GCF_005280335.1_02602:0.00604444,GCF_005280335_1_GCF_005280335.1_01252:1.02832)n4:0.00440931,GCF_020097155_1_GCF_020097155.1_02461:0.0461537)n3:0.00641581,GCF_023573625_1_GCF_023573625.1_00366:0.0108177)n2:0.000893405)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000081_tree.txt ADDED
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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000091_tree.txt ADDED
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1
+ ((GCF_003691675_1_GCF_003691675.1_00272:0.00895888,GCF_023573625_1_GCF_023573625.1_00550:0.00985112)n1:0.00103688,((GCF_020097155_1_GCF_020097155.1_02283:0.499474,(GCF_005280335_1_GCF_005280335.1_02399:0.324744,GCF_005280335_1_GCF_005280335.1_02400:0.295269)n4:0.102834)n3:0.129393,GCF_002008305_4_GCF_002008305.4_00547:0.00547575)n2:0.00103688)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000094_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_4_GCF_002008305.4_00610:0.0132419,GCF_003691675_1_GCF_003691675.1_01770:0.00425513)n1:0.0388521,((GCF_023573625_1_GCF_023573625.1_02004:0.114806,(GCF_005280335_1_GCF_005280335.1_00399:0.00293637,GCF_005280335_1_GCF_005280335.1_02642:0.49369)n4:0.0548544)n3:0.01563,GCF_020097155_1_GCF_020097155.1_02202:0.00437363)n2:0.0388521)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000110_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_4_GCF_002008305.4_00965:0.0155366,((GCF_020097155_1_GCF_020097155.1_01871:0.148516,GCF_020097155_1_GCF_020097155.1_00709:1.42047)n3:0.0637393,GCF_005280335_1_GCF_005280335.1_01922:0.0784576)n2:0.0573156)n1:0.00476844,(GCF_023573625_1_GCF_023573625.1_00911:0.00348525,GCF_003691675_1_GCF_003691675.1_00678:0.00302275)n4:0.00476844)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000118_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_4_GCF_002008305.4_01106:5e-07,(GCF_020097155_1_GCF_020097155.1_01679:0.109561,(GCF_005280335_1_GCF_005280335.1_01787:0.0365289,GCF_005280335_1_GCF_005280335.1_01788:0.273458)n3:0.0303842)n2:0.0732109)n1:0,(GCF_023573625_1_GCF_023573625.1_01055:5e-07,GCF_003691675_1_GCF_003691675.1_00825:5e-07)n4:0)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000119_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_1_GCF_005280335.1_01776:0.0240221,(GCF_003691675_1_GCF_003691675.1_00836:0.00231856,(GCF_003691675_1_GCF_003691675.1_00373:1.00686,GCF_020097155_1_GCF_020097155.1_01669:0.0637933)n3:0.0402668)n2:0.00447409)n1:0.0104045,(GCF_002008305_4_GCF_002008305.4_01117:0.00130106,GCF_023573625_1_GCF_023573625.1_01067:0.00099494)n4:0.00113144)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000145_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_1_GCF_020097155.1_00729:0.391735,((GCF_002008305_4_GCF_002008305.4_02051:0.00099388,GCF_023573625_1_GCF_023573625.1_01985:0.0148791)n3:0.00529638,(GCF_002008305_4_GCF_002008305.4_01790:0,GCF_005280335_1_GCF_005280335.1_01086:0)n4:0.899281)n2:0.0999201)n1:0.0937042,GCF_003691675_1_GCF_003691675.1_01757:0.0113706)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000148_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_01527:0.0135481,((GCF_005280335_1_GCF_005280335.1_02335:1.52574,GCF_005280335_1_GCF_005280335.1_00744:0.488337)n3:0.16171,GCF_005280335_1_GCF_005280335.1_01038:0.114376)n2:0.153652)n1:0.00189322,(GCF_023573625_1_GCF_023573625.1_01751:0.0201962,GCF_002008305_4_GCF_002008305.4_01830:0.00865681)n4:0.00189322)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000157_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_1_GCF_020097155.1_00762:0.0362376,((GCF_003691675_1_GCF_003691675.1_01727:0.0165361,GCF_023573625_1_GCF_023573625.1_01955:0.00826094)n3:0.00151844,(GCF_003691675_1_GCF_003691675.1_00095:1.12642,GCF_005280335_1_GCF_005280335.1_00803:0.0364658)n4:0.0110686)n2:0.00122984)n1:0.00883247,GCF_002008305_4_GCF_002008305.4_02018:0.00861506)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000159_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_4_GCF_002008305.4_02070:0.00753475,GCF_023573625_1_GCF_023573625.1_01998:0.00941525)n1:0.092251,((GCF_005280335_1_GCF_005280335.1_00560:0.220773,GCF_005280335_1_GCF_005280335.1_00743:0.205497)n3:0.0200272,(GCF_020097155_1_GCF_020097155.1_00486:0.415061,GCF_003691675_1_GCF_003691675.1_01107:0.858426)n4:0.0706528)n2:0.092251)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000163_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_01805:0,GCF_002008305_4_GCF_002008305.4_02098:0)n1:0.00214829,(GCF_023573625_1_GCF_023573625.1_02038:0.00060442,(GCF_020097155_1_GCF_020097155.1_00595:0.165779,(GCF_005280335_1_GCF_005280335.1_00681:0.0462528,GCF_005280335_1_GCF_005280335.1_01500:2.80146)n4:0.311274)n3:0.0584644)n2:0.00214829)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000166_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_023573625_1_GCF_023573625.1_02113:0.0180894,GCF_002008305_4_GCF_002008305.4_02168:0.0148676)n1:0.00293341,(GCF_003691675_1_GCF_003691675.1_01882:0.00062969,(GCF_005280335_1_GCF_005280335.1_00584:0.168638,(GCF_020097155_1_GCF_020097155.1_00510:0.155425,GCF_020097155_1_GCF_020097155.1_01906:1.52305)n4:0.0443608)n3:0.0885571)n2:0.00293341)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000185_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_023573625_1_GCF_023573625.1_00016:0.00604363,GCF_002008305_4_GCF_002008305.4_00016:0.00656637)n1:0.00537731,(GCF_003691675_1_GCF_003691675.1_02034:0.0173174,(GCF_020097155_1_GCF_020097155.1_00362:0.302655,GCF_005280335_1_GCF_005280335.1_00381:0.272066)n3:0.0804331)n2:0.00537731)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000206_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_02063:0.0249295,GCF_023573625_1_GCF_023573625.1_00045:0.0049915)n1:0.00755675,(GCF_002008305_4_GCF_002008305.4_00050:0.0088175,(GCF_005280335_1_GCF_005280335.1_00353:0.0869967,GCF_020097155_1_GCF_020097155.1_01218:2.13569)n3:0.121476)n2:0.00755675)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000215_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_005280335_1_GCF_005280335.1_00330:0.060159,GCF_020097155_1_GCF_020097155.1_00272:0.119137)n2:0.0266296,GCF_002008305_4_GCF_002008305.4_00065:0.00887067)n1:0.000687665,(GCF_003691675_1_GCF_003691675.1_02078:0.00755811,GCF_023573625_1_GCF_023573625.1_00059:0.00354589)n3:0.000687665)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000227_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_02093:0,GCF_023573625_1_GCF_023573625.1_00074:0)n1:0.00291686,(GCF_002008305_4_GCF_002008305.4_00080:0.00021728,(GCF_005280335_1_GCF_005280335.1_00313:0.0465117,GCF_020097155_1_GCF_020097155.1_00254:0.307176)n3:0.0714858)n2:0.00291686)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000240_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_02108:0.0017603,GCF_002008305_4_GCF_002008305.4_00095:0.0114587)n1:0.00161363,(GCF_023573625_1_GCF_023573625.1_00090:0.0069661,(GCF_005280335_1_GCF_005280335.1_00296:0.17156,GCF_020097155_1_GCF_020097155.1_00241:0.116934)n3:0.119065)n2:0.00161363)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000255_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_02125:0,GCF_023573625_1_GCF_023573625.1_00107:0)n1:0,(GCF_002008305_4_GCF_002008305.4_00112:0,(GCF_005280335_1_GCF_005280335.1_00278:0.060811,GCF_020097155_1_GCF_020097155.1_00219:0.36504)n3:0.066622)n2:0)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000265_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_020097155_1_GCF_020097155.1_00192:0.106184,GCF_005280335_1_GCF_005280335.1_00258:0.0465143)n2:0.0661997,GCF_023573625_1_GCF_023573625.1_00135:0.00148713)n1:0.00205568,(GCF_002008305_4_GCF_002008305.4_00127:2.35628e-07,GCF_003691675_1_GCF_003691675.1_02141:0.0111406)n3:0.00205568)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000272_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_4_GCF_002008305.4_00139:0,GCF_023573625_1_GCF_023573625.1_00147:0)n1:0.00685525,(GCF_020097155_1_GCF_020097155.1_00179:0.39522,(GCF_005280335_1_GCF_005280335.1_00245:0.0186336,GCF_003691675_1_GCF_003691675.1_02153:0.0188404)n3:0.0107855)n2:0.00685525)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000306_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_02201:0.0150212,(GCF_005280335_1_GCF_005280335.1_00183:0.195259,GCF_020097155_1_GCF_020097155.1_00129:0.59497)n2:0.0463758)n1:0.0253261,(GCF_002008305_4_GCF_002008305.4_00208:0.0101545,GCF_023573625_1_GCF_023573625.1_00208:0.0009965)n3:0.0253261)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000308_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_02203:5e-07,GCF_002008305_4_GCF_002008305.4_00210:5e-07)n1:0.00293188,((GCF_005280335_1_GCF_005280335.1_00181:0.109603,GCF_020097155_1_GCF_020097155.1_00127:0.60427)n3:0.118899,GCF_023573625_1_GCF_023573625.1_00210:8.37e-07)n2:0.00293188)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000310_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_005280335_1_GCF_005280335.1_00174:0.0459877,GCF_020097155_1_GCF_020097155.1_00123:0.0733213)n2:0.0192386,GCF_023573625_1_GCF_023573625.1_00212:0.0052428)n1:0.00185385,(GCF_002008305_4_GCF_002008305.4_00212:0.0032272,GCF_003691675_1_GCF_003691675.1_02205:1.50314e-07)n3:0.00185385)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000325_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_005280335_1_GCF_005280335.1_00137:0.232115,GCF_020097155_1_GCF_020097155.1_00102:1.03919)n2:0.20112,GCF_003691675_1_GCF_003691675.1_02247:0.0240396)n1:0.0104249,(GCF_002008305_4_GCF_002008305.4_00234:0.0391921,GCF_023573625_1_GCF_023573625.1_00235:0.00762686)n3:0.0104249)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000328_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_4_GCF_002008305.4_00238:0.00727525,(GCF_005280335_1_GCF_005280335.1_00133:0.0291908,GCF_020097155_1_GCF_020097155.1_00098:0.326244)n2:0.0123398)n1:0.00210037,(GCF_003691675_1_GCF_003691675.1_02251:0,GCF_023573625_1_GCF_023573625.1_00239:0)n3:0.00210037)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000332_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_023573625_1_GCF_023573625.1_00244:0.00536202,(GCF_020097155_1_GCF_020097155.1_00094:0.589522,GCF_005280335_1_GCF_005280335.1_00125:0.116428)n2:0.111399)n1:0.00463574,(GCF_003691675_1_GCF_003691675.1_02256:0.00143411,GCF_002008305_4_GCF_002008305.4_00244:0.00826089)n3:0.00463574)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000336_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_023573625_1_GCF_023573625.1_00251:5.36946e-07,GCF_003691675_1_GCF_003691675.1_02263:0.00401025)n1:0.00283537,(GCF_002008305_4_GCF_002008305.4_00251:0.00346775,(GCF_005280335_1_GCF_005280335.1_00119:0.0798385,GCF_020097155_1_GCF_020097155.1_00087:0.373435)n3:0.0706357)n2:0.00283537)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000338_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_020097155_1_GCF_020097155.1_00081:0.141388,GCF_005280335_1_GCF_005280335.1_00113:0.0378962)n2:0.03238,GCF_002008305_4_GCF_002008305.4_00256:0.00194757)n1:0.000516715,(GCF_003691675_1_GCF_003691675.1_02270:0.00169869,GCF_023573625_1_GCF_023573625.1_00255:0.00359631)n3:0.000516715)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000342_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_4_GCF_002008305.4_00263:0.000202,GCF_003691675_1_GCF_003691675.1_02276:0.002581)n1:0.000502125,((GCF_005280335_1_GCF_005280335.1_00100:0.0644755,GCF_020097155_1_GCF_020097155.1_00071:0.162813)n3:0.0477448,GCF_023573625_1_GCF_023573625.1_00261:0.00458225)n2:0.000502125)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000356_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_020097155_1_GCF_020097155.1_00049:0.132373,GCF_005280335_1_GCF_005280335.1_00069:0.55289)n2:0.145875,GCF_002008305_4_GCF_002008305.4_00284:0.0432016)n1:0.01516,(GCF_003691675_1_GCF_003691675.1_02306:0.00281449,GCF_023573625_1_GCF_023573625.1_00290:0.00277351)n3:0.01516)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000368_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_005280335_1_GCF_005280335.1_00051:0.237306,GCF_020097155_1_GCF_020097155.1_00030:0.536073)n2:0.188856,GCF_023573625_1_GCF_023573625.1_00310:0.0453889)n1:0.00376706,(GCF_002008305_4_GCF_002008305.4_00303:0.0436099,GCF_003691675_1_GCF_003691675.1_00011:0.0446321)n3:0.00376706)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000372_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_005280335_1_GCF_005280335.1_00029:0.159766,GCF_020097155_1_GCF_020097155.1_00025:0.189634)n2:0.168174,GCF_002008305_4_GCF_002008305.4_00308:0.00506146)n1:0.00123752,(GCF_003691675_1_GCF_003691675.1_00023:5e-08,GCF_023573625_1_GCF_023573625.1_00315:0.00430295)n3:0.00123752)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000379_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_020097155_1_GCF_020097155.1_00014:0.217825,GCF_005280335_1_GCF_005280335.1_00018:0.0669788)n2:0.0431822,GCF_002008305_4_GCF_002008305.4_00319:0.00392625)n1:0.00801738,(GCF_003691675_1_GCF_003691675.1_00034:0.002779,GCF_023573625_1_GCF_023573625.1_00326:3.50351e-07)n3:0.00801738)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000384_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_023573625_1_GCF_023573625.1_00331:0.0206578,(GCF_005280335_1_GCF_005280335.1_00013:0.124835,GCF_020097155_1_GCF_020097155.1_00009:0.28506)n2:0.0785386)n1:0.0014341,(GCF_003691675_1_GCF_003691675.1_00039:0.0121211,GCF_002008305_4_GCF_002008305.4_00324:0.00823586)n3:0.0014341)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000410_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_00078:0.021843,GCF_002008305_4_GCF_002008305.4_00362:0.0635)n1:0.00762788,(GCF_023573625_1_GCF_023573625.1_00369:0.0337913,(GCF_005280335_1_GCF_005280335.1_02599:0.192493,GCF_020097155_1_GCF_020097155.1_02458:0.295974)n3:0.139511)n2:0.00762788)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000431_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_4_GCF_002008305.4_00392:0,GCF_003691675_1_GCF_003691675.1_00116:0)n1:0,(GCF_023573625_1_GCF_023573625.1_00398:0,(GCF_020097155_1_GCF_020097155.1_02435:0.224041,GCF_005280335_1_GCF_005280335.1_02564:0.0322585)n3:0.0205535)n2:0)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000433_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_003691675_1_GCF_003691675.1_00118:0,GCF_023573625_1_GCF_023573625.1_00400:0)n1:0,(GCF_002008305_4_GCF_002008305.4_00394:0,(GCF_005280335_1_GCF_005280335.1_02562:0.027214,GCF_020097155_1_GCF_020097155.1_02434:0.029114)n3:0.029143)n2:0)n0;
Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000434_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_020097155_1_GCF_020097155.1_02432:0.0993108,GCF_005280335_1_GCF_005280335.1_02561:0.0654452)n2:0.0297709,GCF_023573625_1_GCF_023573625.1_00402:0.00015823)n1:0.00132263,(GCF_003691675_1_GCF_003691675.1_00120:0.0009349,GCF_002008305_4_GCF_002008305.4_00396:0.0003101)n3:0.00132263)n0;