diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000003_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000003_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..129aa73217a0a728afdcc7844cfe86955453c92c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000003_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00317:0.0567733,(((TT9_LFPAFLNI_01884:0.0154577,TT9_LFPAFLNI_00114:0.00172532)n4:0.00229961,SA211_MHAAABBN_01658:0.0124349)n3:0.00205871,(KBS0714_MOLHKGIG_02280:0.338712,KBS0714_MOLHKGIG_01386:0.00547474)n5:0.000608304)n2:0.030824)n1:0.00702606,(((SA211_MHAAABBN_00319:0,SA211_MHAAABBN_02267:0)n8:0.0104069,SA211_MHAAABBN_00788:0.0015531)n7:0.00699543,(((KBS0714_MOLHKGIG_01068:0.0133446,KD337_16_NAFOICDF_00625:0.0107374)n11:0.00120444,((AS2_ACLBLIBL_01304:0.00500704,(AS2_ACLBLIBL_02631:0.0167597,AS2_ACLBLIBL_02347:0.00125131)n14:0.0132335)n13:0.00549544,((AS2_ACLBLIBL_01281:5e-07,AS2_ACLBLIBL_01312:5e-07)n16:0.00596747,AS2_ACLBLIBL_01317:0.012011)n15:0.00680981)n12:0.0024795)n10:0.00414823,((KD337_16_NAFOICDF_02207:5e-07,(KD337_16_NAFOICDF_01836:5e-07,KD337_16_NAFOICDF_01796:5e-07)n19:0)n18:0.00834597,((AS2_ACLBLIBL_02614:0.037716,SA211_MHAAABBN_01116:0.011639)n21:0.00519576,((SA211_MHAAABBN_01327:5e-07,TT9_LFPAFLNI_01539:5e-07)n23:0,(AS2_ACLBLIBL_02331:5e-07,AS2_ACLBLIBL_00758:4.5e-07)n24:5e-08)n22:0)n20:0.00149001)n17:0.000165557)n9:0.00484671)n6:0.000538523)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000004_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000004_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1f70ec69ec86b83126a8ccc9ca0445b2989b166
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000004_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01829:0.303659,(AS2_ACLBLIBL_00899:0.586123,(((SA211_MHAAABBN_01015:0.0885647,KBS0714_MOLHKGIG_02069:0.00598831)n4:0.118524,AS2_ACLBLIBL_00229:2.54157e-06)n3:0.351008,(AS2_ACLBLIBL_00643:2.54157e-06,(((TT9_LFPAFLNI_01974:2.54157e-06,(SA211_MHAAABBN_01819:2.54157e-06,(KBS0714_MOLHKGIG_02277:2.54157e-06,((KBS0714_MOLHKGIG_01393:2.54157e-06,(SA211_MHAAABBN_02016:2.54157e-06,((SA211_MHAAABBN_01012:0.0329093,(AS2_ACLBLIBL_00228:0,AS2_ACLBLIBL_00895:0)n16:0.261294)n15:0.0941234,(AS2_ACLBLIBL_02100:0.00437312,SA211_MHAAABBN_00355:2.54157e-06)n17:2.54157e-06)n14:9.74e-06)n13:9.74e-06)n12:9.74e-06,(KBS0714_MOLHKGIG_02112:2.54157e-06,SA211_MHAAABBN_01746:2.54157e-06)n18:2.54157e-06)n11:8.766e-06)n10:9.74e-07)n9:9.74e-06)n8:9.74e-06,((TT9_LFPAFLNI_00116:2.54157e-06,SA211_MHAAABBN_01125:2.54157e-06)n20:2.54157e-06,KBS0714_MOLHKGIG_00376:2.54157e-06)n19:2.54157e-06)n7:0.00074121,((TT9_LFPAFLNI_01547:0,(TT9_LFPAFLNI_01880:0,TT9_LFPAFLNI_01549:0)n23:0)n22:0.00038011,AS2_ACLBLIBL_01506:2.54157e-06)n21:2.54157e-06)n6:0.00010439)n5:0.0540488)n2:0.356428)n1:0.303659)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000005_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000005_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72b913e7ecbb0be0a60ebaa8a8f26ba8b0fc061c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000005_tree.txt
@@ -0,0 +1 @@
+(((KD337_16_NAFOICDF_01820:0.0480273,KD337_16_NAFOICDF_00652:0.0381747)n2:0.00967885,AS2_ACLBLIBL_01282:0.0551577)n1:0.0230676,(((KD337_16_NAFOICDF_01832:0.172567,KD337_16_NAFOICDF_01361:0.0470863)n5:0.0189387,KD337_16_NAFOICDF_00641:0.0523848)n4:0.0548108,((SA211_MHAAABBN_01778:0.963278,(KD337_16_NAFOICDF_00227:0.484699,KD337_16_NAFOICDF_00678:1.17641)n8:0.130712)n7:0.895467,(AS2_ACLBLIBL_02274:0.0197706,((KD337_16_NAFOICDF_02206:0.045165,KD337_16_NAFOICDF_00448:0.024019)n11:0.0519192,((KD337_16_NAFOICDF_00645:0,KD337_16_NAFOICDF_00315:0)n13:0.0276021,((KD337_16_NAFOICDF_01890:0.00760725,((KD337_16_NAFOICDF_01835:0.00216597,KD337_16_NAFOICDF_00226:8.503e-05)n17:0.00412963,KD337_16_NAFOICDF_00312:0.00488987)n16:0.00407)n15:0.00215033,(KD337_16_NAFOICDF_00627:0.00079899,((KD337_16_NAFOICDF_02162:0,KD337_16_NAFOICDF_00631:0)n20:0.00285841,(KD337_16_NAFOICDF_00751:0,KD337_16_NAFOICDF_01794:0)n21:0.00010659)n19:0.00068751)n18:0.00179948)n14:0.00719922)n12:0.000678897)n10:7.5433e-05)n9:0.042145)n6:0.176959)n3:0.0230676)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000006_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000006_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70c77760f8750f4887a38b22af14956b818213f0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000006_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01213:0,((TT9_LFPAFLNI_02204:0,KBS0714_MOLHKGIG_00158:0)n2:0,(TT9_LFPAFLNI_01886:0,((SA211_MHAAABBN_01103:0,(TT9_LFPAFLNI_01251:0,((TT9_LFPAFLNI_00591:0,((SA211_MHAAABBN_01016:0,SA211_MHAAABBN_01115:0)n10:0,(KBS0714_MOLHKGIG_02076:0,KBS0714_MOLHKGIG_01293:0)n11:0)n9:0)n8:0,(TT9_LFPAFLNI_00589:0,(SA211_MHAAABBN_01111:0.0108997,(KBS0714_MOLHKGIG_01383:0.145001,KBS0714_MOLHKGIG_01033:0.0022954)n14:0.00377913)n13:0.000989379)n12:0.000109931)n7:0)n6:0)n5:0,(TT9_LFPAFLNI_01338:0,SA211_MHAAABBN_02022:0)n15:0)n4:0)n3:0)n1:0)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000009_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000009_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..494ac1888881dc456e7cc43a964e61201f808a26
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000009_tree.txt
@@ -0,0 +1 @@
+(((KBS0714_MOLHKGIG_02228:0.118103,TT9_LFPAFLNI_01350:3.37906e-07)n2:5.49e-06,SA211_MHAAABBN_02283:3.37906e-07)n1:2.745e-06,((TT9_LFPAFLNI_00607:3.37906e-07,(SA211_MHAAABBN_00344:3.37906e-07,((TT9_LFPAFLNI_01017:3.37906e-07,(KBS0714_MOLHKGIG_01503:0.219835,SA211_MHAAABBN_00091:3.37906e-07)n8:5.49e-06)n7:5.49e-06,((SA211_MHAAABBN_01393:3.37906e-07,TT9_LFPAFLNI_02163:3.37906e-07)n10:3.37906e-07,KBS0714_MOLHKGIG_01400:3.37906e-07)n9:3.37906e-07)n6:4.941e-06)n5:5.49e-07)n4:5.49e-06,((KBS0714_MOLHKGIG_00712:3.37906e-07,TT9_LFPAFLNI_01157:3.37906e-07)n12:3.37906e-07,SA211_MHAAABBN_01014:3.37906e-07)n11:3.37906e-07)n3:2.745e-06)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000013_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000013_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef38ac4c0a9821aecb2898ec3c5caa238a563cbb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000013_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01887:0.0156952,((TT9_LFPAFLNI_01544:0.310013,(SA211_MHAAABBN_01765:0.00214371,((AS2_ACLBLIBL_00706:0.475675,AS2_ACLBLIBL_02496:0.295843)n5:0.36602,(AS2_ACLBLIBL_02276:2.05835e-06,(AS2_ACLBLIBL_02615:2.05835e-06,(AS2_ACLBLIBL_02636:0.0164108,AS2_ACLBLIBL_02495:0.160142)n8:0.0877972)n7:0.0316281)n6:0.0377297)n4:0.00419219)n3:0.0884951)n2:0.0525349,(SA211_MHAAABBN_00341:0.125681,TT9_LFPAFLNI_00898:0.0181851)n9:0.00202057)n1:0.0156952)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000015_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000015_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd3070bcf101333c37daf3e18cd90386eb1e23cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000015_tree.txt
@@ -0,0 +1 @@
+((((KBS0714_MOLHKGIG_01771:0,SA211_MHAAABBN_01478:0)n3:0.00351475,TT9_LFPAFLNI_01700:0.00446625)n2:0.0128569,(AS2_ACLBLIBL_01106:0.0304285,KD337_16_NAFOICDF_01032:0.0938865)n4:0.00598188)n1:0.00535712,(AS2_ACLBLIBL_01897:0.0339341,((KBS0714_MOLHKGIG_00992:0.0125064,KD337_16_NAFOICDF_01844:0.0118856)n7:0.00231212,(SA211_MHAAABBN_00706:0.00465431,TT9_LFPAFLNI_00935:0.00377569)n8:0.00501737)n6:0.00301888)n5:0.00535712)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000016_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000016_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a208a3ceb3e778d938c66130ad05eff305df8d2a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000016_tree.txt
@@ -0,0 +1 @@
+(((AS2_ACLBLIBL_01238:0.00968165,((SA211_MHAAABBN_01361:0.0031751,TT9_LFPAFLNI_01586:0.0018629)n4:0.00153679,KBS0714_MOLHKGIG_01656:0.00653071)n3:0.0164408)n2:0.00724594,KD337_16_NAFOICDF_01149:0.0301557)n1:0.210755,(KD337_16_NAFOICDF_02465:0.0121016,(AS2_ACLBLIBL_02606:0.008174,(KBS0714_MOLHKGIG_00355:0.00086601,(SA211_MHAAABBN_00071:0.00361936,TT9_LFPAFLNI_00362:5.36378e-07)n8:0.00065449)n7:0.00444025)n6:0.0084565)n5:0.210755)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000018_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000018_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4389d4a6346356919dfbd5abbb06b07489beca2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000018_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01886:0.00514618,(((AS2_ACLBLIBL_02616:0,AS2_ACLBLIBL_02497:0)n3:0.0024707,(AS2_ACLBLIBL_02275:0.00604717,AS2_ACLBLIBL_02634:7.3736e-07)n4:0.0115305)n2:0.017677,((SA211_MHAAABBN_00342:0.126053,TT9_LFPAFLNI_01543:0.216031)n6:0.047497,(TT9_LFPAFLNI_00899:0.0680276,SA211_MHAAABBN_01766:0.0447093)n7:0.0049677)n5:0.169111)n1:0.0187902)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000020_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000020_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..823f6d39382a7bf093897241518a39ad31ad3ee0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000020_tree.txt
@@ -0,0 +1 @@
+((KBS0714_MOLHKGIG_00633:0.0137077,((AS2_ACLBLIBL_00405:0.00492553,KD337_16_NAFOICDF_02196:0.00219647)n3:0.0102903,TT9_LFPAFLNI_00598:0.00369116)n2:0.00751134)n1:0.245181,(((KBS0714_MOLHKGIG_01289:0,SA211_MHAAABBN_01008:0)n6:0.00094753,TT9_LFPAFLNI_01247:0.00251147)n5:0.0833185,KD337_16_NAFOICDF_00711:0.075097)n4:0.245181)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000023_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000023_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ccf20f40b0e6f47f68aac18f45e157ce68783e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000023_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02299:0.197298,((AS2_ACLBLIBL_02417:0.0897701,(TT9_LFPAFLNI_00535:0.011344,SA211_MHAAABBN_00256:0.00593104)n3:0.0775176)n2:0.0573558,(AS2_ACLBLIBL_01211:1.04888,(SA211_MHAAABBN_00245:0.0130483,(TT9_LFPAFLNI_00524:0.00675058,KBS0714_MOLHKGIG_00524:0.00442542)n6:0.00956661)n5:0.372936)n4:0.251601)n1:0.197298)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000028_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000028_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3249e7c041e715d607a7b1e6cffa794e6e2dc79
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000028_tree.txt
@@ -0,0 +1 @@
+(((SA211_MHAAABBN_02148:0,(TT9_LFPAFLNI_00142:0.00280964,KBS0714_MOLHKGIG_00134:9.87312e-07)n3:0.00012864)n2:0.0196287,AS2_ACLBLIBL_00251:0.0175198)n1:0.0345866,(KD337_16_NAFOICDF_00186:0.0936942,(KD337_16_NAFOICDF_00187:0.231713,KD337_16_NAFOICDF_02180:0.454447)n5:0.0983268)n4:0.0345866)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000029_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000029_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5d31ba4caa09e1b2198779c63275358486f3f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000029_tree.txt
@@ -0,0 +1 @@
+((TT9_LFPAFLNI_02014:0,KD337_16_NAFOICDF_00670:0)n1:0.139806,(KD337_16_NAFOICDF_00617:0.396144,((AS2_ACLBLIBL_00292:0.0261018,KBS0714_MOLHKGIG_00099:1.47863e-06)n4:0.00066179,(TT9_LFPAFLNI_00094:0,SA211_MHAAABBN_02112:0)n5:0)n3:0.776778)n2:0.139806)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000034_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000034_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69c72a045d8767e7ce45e1436ddd17eb8cb19670
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000034_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00412:0.0302051,((KD337_16_NAFOICDF_00648:0,KD337_16_NAFOICDF_02216:0)n3:0.0117174,KD337_16_NAFOICDF_00325:0.018377)n2:0.00204189)n1:0.00188306,(TT9_LFPAFLNI_01347:0.00511887,(KBS0714_MOLHKGIG_01397:0.00028712,SA211_MHAAABBN_01130:0.0139309)n5:0.00439462)n4:0.00558413)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000035_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000035_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9911e1870dcc6708e92df123589bf90e644ffca5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000035_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00649:6.5333e-07,(KD337_16_NAFOICDF_00326:0.0837726,KD337_16_NAFOICDF_02217:6.5333e-07)n2:0.00373256)n1:0.00287966,(AS2_ACLBLIBL_00413:0.0196547,((KBS0714_MOLHKGIG_01401:0.130959,TT9_LFPAFLNI_01351:0.360286)n5:0.0455866,SA211_MHAAABBN_01131:0.00071144)n4:0.0103328)n3:0.00287966)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000036_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000036_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4b3cd21640001330d2ce97f54d3a36714a9ba07
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000036_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00434:0.00315784,(TT9_LFPAFLNI_02184:0.00430931,(SA211_MHAAABBN_01952:0.004319,((AS2_ACLBLIBL_00493:0.138379,KBS0714_MOLHKGIG_02275:0.72641)n4:0.128501,(AS2_ACLBLIBL_00488:0.0153053,KBS0714_MOLHKGIG_02253:0.0074853)n5:0.0008317)n3:0.00423197)n2:0.000470219)n1:0.00315784)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000037_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000037_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4d7c9070604afd6aae66e1cba1385a19dc0eb1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000037_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00520:0.038105,((TT9_LFPAFLNI_02104:0.00158944,(KBS0714_MOLHKGIG_02160:0,SA211_MHAAABBN_01873:0)n3:0.00916856)n2:0.0363719,((AS2_ACLBLIBL_02580:1.60355,AS2_ACLBLIBL_00589:0.372398)n5:0.399132,AS2_ACLBLIBL_00598:0.0340124)n4:0.00377916)n1:0.0415209)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000039_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000039_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99addd1aaf08ff97dbddb12ca4875589d2d513af
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000039_tree.txt
@@ -0,0 +1 @@
+((TT9_LFPAFLNI_02031:0.764438,((KD337_16_NAFOICDF_00600:0.293335,KD337_16_NAFOICDF_00599:0.300224)n3:0.0333582,KD337_16_NAFOICDF_02101:0.636121)n2:0.0706802)n1:0.0787121,(SA211_MHAAABBN_01802:0.0192402,(KBS0714_MOLHKGIG_02094:0.0395114,AS2_ACLBLIBL_00684:0.0582886)n5:0.00386081)n4:0.0276696)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000040_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000040_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..945a7b3dc7bb7a84433b1b96bbdce0fc8fe6c717
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000040_tree.txt
@@ -0,0 +1 @@
+((SA211_MHAAABBN_01794:0.0105327,KBS0714_MOLHKGIG_02089:0.0152583)n1:0.0312032,(((KD337_16_NAFOICDF_00662:1.81552,TT9_LFPAFLNI_02028:2.19177e-06)n4:0.194314,AS2_ACLBLIBL_00694:2.19177e-06)n3:0.0782589,(AS2_ACLBLIBL_01308:0.00842769,KD337_16_NAFOICDF_02237:0.0376703)n5:0.276615)n2:0.030735)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000043_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000043_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dcc794fd8ef75ec9013b5413c54d714f327945ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000043_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00725:0.00153755,((KBS0714_MOLHKGIG_01072:0,(TT9_LFPAFLNI_01021:0,(SA211_MHAAABBN_00348:0,SA211_MHAAABBN_00335:0)n4:0)n3:0)n2:0.0003895,(SA211_MHAAABBN_00791:0.0041365,KBS0714_MOLHKGIG_00162:0.0188387)n5:0.00209319)n1:0.00153755)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000045_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000045_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d34332d86a12c6b0031ad095eb49dd90232583c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000045_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02256:0.65587,((KBS0714_MOLHKGIG_01015:3.22334e-06,((SA211_MHAAABBN_00729:0.0011255,AS2_ACLBLIBL_01873:0.0035275)n4:0.000524,TT9_LFPAFLNI_00959:0.097084)n3:0.00899222)n2:1.19029,(AS2_ACLBLIBL_00822:1.30473,TT9_LFPAFLNI_00958:3.22334e-06)n5:3.22334e-06)n1:0.65587)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000047_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000047_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a8c44b7c1c8b4244e775c60e8d410680ed1ca31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000047_tree.txt
@@ -0,0 +1 @@
+(TT9_LFPAFLNI_00735:0.264599,((KD337_16_NAFOICDF_00792:0.125211,(AS2_ACLBLIBL_00855:0.0674537,SA211_MHAAABBN_01696:0.200906)n3:0.0645251)n2:0.0847977,(AS2_ACLBLIBL_01010:0.889235,(KD337_16_NAFOICDF_00870:0.787023,KD337_16_NAFOICDF_00943:0.508593)n5:0.0565103)n4:0.0238539)n1:0.00265043)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000048_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000048_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b62afd011eb2e8d15674d48f904c65667f258f0e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000048_tree.txt
@@ -0,0 +1 @@
+(((SA211_MHAAABBN_01753:0.00664034,(KBS0714_MOLHKGIG_02047:0.00280441,TT9_LFPAFLNI_01981:1.9224e-06)n3:0.0190982)n2:0.17528,KD337_16_NAFOICDF_00733:0.238099)n1:0.0463697,((KBS0714_MOLHKGIG_01791:0.00349297,AS2_ACLBLIBL_01085:0.00293503)n5:0.674277,KD337_16_NAFOICDF_00743:0.707056)n4:0.0463697)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000049_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000049_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19709dd5ccbc881fb449bb9b246510333ef80936
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000049_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01023:0.0299424,((SA211_MHAAABBN_01485:0.00726013,((KBS0714_MOLHKGIG_00836:0.444817,KBS0714_MOLHKGIG_00837:0.131953)n4:0.665023,(KBS0714_MOLHKGIG_01778:0.00569369,TT9_LFPAFLNI_01707:0.00439331)n5:0.00159828)n3:0.000177587)n2:0.0602399,AS2_ACLBLIBL_01099:0.0790576)n1:0.00863038)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000050_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000050_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..268efc983d554c2c501d4bb95cdf27972682969f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000050_tree.txt
@@ -0,0 +1 @@
+((KBS0714_MOLHKGIG_00172:1.17994,KD337_16_NAFOICDF_02230:1.20931)n1:0.517935,(KD337_16_NAFOICDF_01399:3.56269e-06,(AS2_ACLBLIBL_01488:0.00633928,((KBS0714_MOLHKGIG_01408:0.00413422,SA211_MHAAABBN_01138:3.56269e-06)n5:0.00013422,TT9_LFPAFLNI_01358:3.56269e-06)n4:0.05862)n3:0.132285)n2:0.517935)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000054_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000054_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bef23d48ef570df79a58a68bbd0caac8b98d2a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000054_tree.txt
@@ -0,0 +1 @@
+((TT9_LFPAFLNI_01517:0.00423125,(KBS0714_MOLHKGIG_01590:0.0089655,SA211_MHAAABBN_01302:0.0020005)n2:0.00446675)n1:0.0900756,(KD337_16_NAFOICDF_01240:0.186076,((KD337_16_NAFOICDF_01828:1.33546,KD337_16_NAFOICDF_00714:1.69504)n5:0.585795,KD337_16_NAFOICDF_00643:0.874345)n4:0.343302)n3:0.0900756)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000056_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000056_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..942ca5c7cc73125e6a5456640cf5fa2c84f97cbb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000056_tree.txt
@@ -0,0 +1 @@
+((((SA211_MHAAABBN_00033:0.00089808,KBS0714_MOLHKGIG_00318:0.00412092)n3:0.00141431,TT9_LFPAFLNI_00325:0.00349074)n2:0.0192356,AS2_ACLBLIBL_00019:0.0517623)n1:0.0212715,(KD337_16_NAFOICDF_00015:0.0556756,KD337_16_NAFOICDF_00687:0.973311)n4:0.0212715)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000057_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000057_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa6a4698ce0fc9dcdc2b0c7132ddaacba0e2523f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000057_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00027:0.233312,(KD337_16_NAFOICDF_00654:1.70175,KD337_16_NAFOICDF_00023:0.169007)n2:0.0187786)n1:0.00733412,((SA211_MHAAABBN_00025:0.00509109,TT9_LFPAFLNI_00317:7.591e-05)n4:0.00785825,KBS0714_MOLHKGIG_00310:0.0061578)n3:0.149015)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000060_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000060_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a15b6f18e0fedaff1a4c8b2ed0a3ba644a97244
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000060_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00046:0.0774871,(((SA211_MHAAABBN_02309:0.00535373,TT9_LFPAFLNI_00293:0.00418227)n3:0.00508912,(KBS0714_MOLHKGIG_01958:2.40111,KBS0714_MOLHKGIG_00287:0.0110356)n4:0.00122618)n2:0.0518398,AS2_ACLBLIBL_00067:0.0580756)n1:0.03715)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000061_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000061_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c7c3a9da9f4783114b1f68ecd29c8946e703f38
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000061_tree.txt
@@ -0,0 +1 @@
+(((SA211_MHAAABBN_02297:0.00368381,(KBS0714_MOLHKGIG_00282:0.00810519,TT9_LFPAFLNI_00281:0.00455281)n3:0.00200369)n2:0.0977394,AS2_ACLBLIBL_00071:0.0693888)n1:0.0507666,(KD337_16_NAFOICDF_00057:0.167643,KD337_16_NAFOICDF_00450:2.04508)n4:0.0507666)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000062_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000062_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5a7a3a89c5ab206bc4a8e4a6d7dc3e6bd06184d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000062_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02346:0.121193,((AS2_ACLBLIBL_00074:0.00234231,(SA211_MHAAABBN_00203:0.0289228,(TT9_LFPAFLNI_00278:0.00560031,SA211_MHAAABBN_02294:1.73025e-06)n4:0.00178397)n3:0.000198219)n2:0.00771069,KBS0714_MOLHKGIG_00279:0.00536081)n1:1.55743)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000064_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000064_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50a0faee01080e35000ea7dd8c38046df2838c3f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000064_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00137:0.220282,(((SA211_MHAAABBN_02135:0,TT9_LFPAFLNI_00127:0)n3:0.0250917,(AS2_ACLBLIBL_00088:0.624841,AS2_ACLBLIBL_00265:0.0533037)n4:0.00592263)n2:0.0203834,KBS0714_MOLHKGIG_00119:0.354892)n1:0.380563)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000066_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000066_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91679b6b249aaad46c1c6e54b59787f5aea27efc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000066_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00079:0.143595,KD337_16_NAFOICDF_00526:0.780972)n1:0.0260305,(AS2_ACLBLIBL_00111:0.144119,((KBS0714_MOLHKGIG_00258:0.00275811,TT9_LFPAFLNI_00257:1.20469e-06)n4:0.0125031,SA211_MHAAABBN_02272:0.00953305)n3:0.0595365)n2:0.0260305)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000068_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000068_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38d9c0e70f3196efc2ef1ecb1ba4ddc481365c46
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000068_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00765:0.0104518,(((TT9_LFPAFLNI_01952:0.00544775,KBS0714_MOLHKGIG_02014:0.00658725)n3:0.00188362,SA211_MHAAABBN_01724:0.00615238)n2:0.0515351,(AS2_ACLBLIBL_00826:0.0606996,AS2_ACLBLIBL_00129:1.37126)n4:0.125)n1:0.0104518)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000069_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000069_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..739dac92e421792839d319f5d10aee65c48a3bde
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000069_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00100:0.0750078,((KBS0714_MOLHKGIG_00236:0.00582243,(SA211_MHAAABBN_00102:0.41198,(SA211_MHAAABBN_02249:0.00185525,TT9_LFPAFLNI_00237:0.00135175)n4:0.00497574)n3:0.00055286)n2:0.0481915,AS2_ACLBLIBL_00135:0.028429)n1:0.0803618)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000074_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000074_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c584d6263157023f158b82c18b21877c83c99027
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000074_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00184:0.0441909,(KD337_16_NAFOICDF_00130:0.0118214,KD337_16_NAFOICDF_00132:2.2062)n2:0.245134)n1:0.0182153,((KBS0714_MOLHKGIG_00207:0,TT9_LFPAFLNI_00207:0)n4:0.00376662,SA211_MHAAABBN_02200:0.00194237)n3:0.00958713)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000075_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000075_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e4ae6c0bbc7ed64370505619f334876e57c3466
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000075_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01744:0.0364455,(((KBS0714_MOLHKGIG_01028:0,SA211_MHAAABBN_00743:0)n3:0,TT9_LFPAFLNI_00972:0)n2:0.015177,(AS2_ACLBLIBL_00185:0.972803,AS2_ACLBLIBL_01852:0.862341)n4:0.984594)n1:0.0364455)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000077_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000077_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..092e81fc48d79667d4ad6138c937c0b9bc15248b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000077_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01743:0.0103629,((AS2_ACLBLIBL_01854:0.619837,AS2_ACLBLIBL_00187:0.489964)n2:0.574448,((KBS0714_MOLHKGIG_01029:0,SA211_MHAAABBN_00744:0)n4:0,TT9_LFPAFLNI_00973:0)n3:0.00769423)n1:0.0103629)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000082_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000082_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..545f2441893c5cb416e415e153b7614014fc0aab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000082_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00326:0.0562451,((SA211_MHAAABBN_02081:0.00378656,KBS0714_MOLHKGIG_00068:0.00132244)n3:0.0184039,TT9_LFPAFLNI_00062:0.0156086)n2:0.0187114)n1:0.0136237,(KD337_16_NAFOICDF_00684:0.716861,KD337_16_NAFOICDF_00266:0.0438693)n4:0.0136237)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000083_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000083_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34679a70f905e676cbb9c6e7c2681ad422a7ad58
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000083_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01735:0.340645,((TT9_LFPAFLNI_00983:0.0105182,(SA211_MHAAABBN_00755:0.0206522,KBS0714_MOLHKGIG_01042:0.0061398)n3:0.0159949)n2:0.142395,(AS2_ACLBLIBL_00331:0.0037765,AS2_ACLBLIBL_00544:0.0090035)n4:0.268078)n1:0.340645)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000088_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000088_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..111d444d480ab97c28003d5d81beaf53030d48b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000088_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02202:0.00218681,((TT9_LFPAFLNI_02004:0.114806,(AS2_ACLBLIBL_00399:0.00293637,AS2_ACLBLIBL_02642:0.49369)n3:0.0548544)n2:0.01563,(SA211_MHAAABBN_01770:0.00425513,KBS0714_MOLHKGIG_00610:0.0132419)n4:0.0777043)n1:0.100236)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000090_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000090_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cda4368ccfa7b84d9b06246d6ae6aaaa42eb8aa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000090_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00384:0.14309,(((KBS0714_MOLHKGIG_02305:0,SA211_MHAAABBN_01998:0)n3:0.00728425,TT9_LFPAFLNI_02246:2.77222e-06)n2:0.076911,(AS2_ACLBLIBL_01948:2.30841,AS2_ACLBLIBL_00432:0.169389)n4:0.018821)n1:0.0530695)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000092_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000092_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16e00d2e9115972341a18517ce61075c41a87f74
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000092_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00427:0.786251,(AS2_ACLBLIBL_00464:1.44313,(TT9_LFPAFLNI_02208:0.193846,((KBS0714_MOLHKGIG_00568:1.44501,KBS0714_MOLHKGIG_00037:1.24672)n4:0.0864029,KBS0714_MOLHKGIG_02274:0.225889)n3:0.0250988)n2:0.539741)n1:0.786251)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000093_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000093_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a7d200069fd39dc9acea075e1f2d81a461383c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000093_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00419:0.054078,(((SA211_MHAAABBN_01960:0.249941,KBS0714_MOLHKGIG_02265:0.0146493)n3:0.00377825,(AS2_ACLBLIBL_00641:0.1453,AS2_ACLBLIBL_00469:0.0122191)n4:0.00135768)n2:0.015481,TT9_LFPAFLNI_02198:0.0527201)n1:0.054078)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000095_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000095_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9df0e283107d24225741334df051ebbabbabb59f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000095_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00486:0.20753,(SA211_MHAAABBN_01107:0.858426,((AS2_ACLBLIBL_00743:0.205497,AS2_ACLBLIBL_00560:0.220773)n3:0.0200272,(KBS0714_MOLHKGIG_02070:0.00753475,TT9_LFPAFLNI_01998:0.00941525)n4:0.184502)n2:0.0706528)n1:0.20753)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000096_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000096_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00ae03426b50dfe12fef5a39c56e3735e309b9be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000096_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00491:0.0672741,(AS2_ACLBLIBL_00566:0.0584983,(SA211_MHAAABBN_01898:0.0137146,(TT9_LFPAFLNI_00166:2.39922,(KBS0714_MOLHKGIG_02184:0.00185681,TT9_LFPAFLNI_02129:0.00420819)n4:0.00901975)n3:0.00100219)n2:0.0629994)n1:0.0920547)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000097_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000097_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..373fcaa4891dc44fa00b8e9be0e775db49d597a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000097_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00505:0.0397588,((TT9_LFPAFLNI_02119:5e-07,(KBS0714_MOLHKGIG_00604:1.63863,(SA211_MHAAABBN_01888:5e-07,KBS0714_MOLHKGIG_02174:5e-07)n4:-0)n3:-0)n2:0.127773,AS2_ACLBLIBL_00578:0.083449)n1:0.0645755)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000098_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000098_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd2f102c74244326ef33afa2671d1162d3b3ef3d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000098_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00510:0.155425,KD337_16_NAFOICDF_01906:1.52305)n1:0.0221804,(AS2_ACLBLIBL_00584:0.168638,(SA211_MHAAABBN_01882:0.00062969,(KBS0714_MOLHKGIG_02168:0.0148676,TT9_LFPAFLNI_02113:0.0180894)n4:0.00586681)n3:0.0885571)n2:0.0221804)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000099_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000099_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..198cd8996d97a79f5d616bcad2f824f83b9b8d4d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000099_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00518:0.327332,(KBS0714_MOLHKGIG_02162:1.57847e-06,(AS2_ACLBLIBL_00595:0.333514,(SA211_MHAAABBN_01875:0.177706,(TT9_LFPAFLNI_02107:0.0652714,SA211_MHAAABBN_01876:0.133206)n4:0.0665854)n3:0.00739838)n2:0.190329)n1:0.427716)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000101_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000101_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5267ca2faf5f7e96a2955fa06966f6f2168cf71c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000101_tree.txt
@@ -0,0 +1 @@
+(((SA211_MHAAABBN_01830:0.0109383,(TT9_LFPAFLNI_02060:0.00899377,KBS0714_MOLHKGIG_02122:0.0118992)n3:0.00210951)n2:0.0136613,(KD337_16_NAFOICDF_00718:0.632372,KD337_16_NAFOICDF_00575:0.0277293)n4:0.00308103)n1:0.0638356,AS2_ACLBLIBL_00658:0.188184)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000103_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000103_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..996cc7bf0aa5efe7bf50887276da7635192b7b6a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000103_tree.txt
@@ -0,0 +1 @@
+(((KBS0714_MOLHKGIG_02093:0.126957,SA211_MHAAABBN_01801:0.246147)n2:0.284873,KD337_16_NAFOICDF_00555:0.907405)n1:0.100808,(SA211_MHAAABBN_01800:0.397647,(AS2_ACLBLIBL_00685:0.0232394,KD337_16_NAFOICDF_00601:0.0451826)n4:0.191462)n3:0.100808)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000105_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000105_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68c9cfb59d746d88742fa60640d18269dd8b23b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000105_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00488:0.0765763,((KBS0714_MOLHKGIG_02072:0.0393932,TT9_LFPAFLNI_02000:0.0240607)n2:0.148161,(AS2_ACLBLIBL_00740:0.178768,(AS2_ACLBLIBL_00736:0.494086,AS2_ACLBLIBL_00741:0.168306)n4:0.0168306)n3:0.00187007)n1:0.613699)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000106_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000106_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50f4cd75dac92c4e6f563cbe49732c98cd821594
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000106_tree.txt
@@ -0,0 +1 @@
+((SA211_MHAAABBN_01527:0.0135481,(KBS0714_MOLHKGIG_01830:0.00865681,TT9_LFPAFLNI_01751:0.0201962)n2:0.00378644)n1:0.076826,(AS2_ACLBLIBL_01038:0.114376,(AS2_ACLBLIBL_00744:0.488337,AS2_ACLBLIBL_02335:1.52574)n4:0.16171)n3:0.076826)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000108_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000108_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cb79e485fcc01103f9b5bb851c1a1fdc45a6617
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000108_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00874:2.30943e-06,((TT9_LFPAFLNI_01841:0.01419,(SA211_MHAAABBN_01617:0.0105851,KBS0714_MOLHKGIG_01921:0.00192786)n3:0.00957146)n2:0.0353308,(AS2_ACLBLIBL_00786:1.41367,AS2_ACLBLIBL_00939:0.0601999)n4:0.00668888)n1:0.925731)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000113_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000113_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb18b49c5e0234b3749cd23748534288ca476273
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000113_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00875:0.100395,(KD337_16_NAFOICDF_00810:0.017556,KD337_16_NAFOICDF_00823:0.142689)n2:0.0158543)n1:0.112217,(SA211_MHAAABBN_01677:0.0042535,(TT9_LFPAFLNI_01909:0,KBS0714_MOLHKGIG_01983:0)n4:0.0011825)n3:0.002525)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000115_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000115_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d38a3f82a705f4e4f3ca58bacd8c734240c2bcf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000115_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00854:0.114096,KD337_16_NAFOICDF_02134:1.3211)n1:0.0298176,(AS2_ACLBLIBL_00920:0.0288417,(SA211_MHAAABBN_01635:0.0029345,(TT9_LFPAFLNI_01858:0,KBS0714_MOLHKGIG_01939:0)n4:0.0069615)n3:0.0581113)n2:0.0298176)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000120_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000120_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f740315b72dedd80ebe3c008c8b42d80e5430133
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000120_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00729:0.195868,((SA211_MHAAABBN_01757:0.0113706,(KBS0714_MOLHKGIG_01790:0,(TT9_LFPAFLNI_01985:0.0148791,KBS0714_MOLHKGIG_02051:0.00099388)n4:0.00476674)n3:0.000529638)n2:0.187408,AS2_ACLBLIBL_01086:0)n1:0.195868)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000123_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000123_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26acebaaaa621c23c88b02dd05806b36ef78dcea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000123_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01126:0.0850984,((SA211_MHAAABBN_01385:0.00250258,(KBS0714_MOLHKGIG_01681:0.00921525,TT9_LFPAFLNI_01610:0.00326075)n3:0.00191685)n2:0.0944815,(AS2_ACLBLIBL_01209:0.173903,AS2_ACLBLIBL_01197:0.103935)n4:0.0115483)n1:0.0664634)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000124_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000124_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6527230f7f381c80312e2faee13d3014abfb678
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000124_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02325:0.0131103,(((TT9_LFPAFLNI_00508:0.021942,KBS0714_MOLHKGIG_00509:0.00744403)n3:0.0181697,SA211_MHAAABBN_00229:0.0416732)n2:0.0028356,(AS2_ACLBLIBL_01218:2.48045,AS2_ACLBLIBL_02441:0.0413839)n4:0.00459821)n1:0.0336927)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000126_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000126_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab7b8abef9f5a55f1d974308d05da8e4326e5cc6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000126_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02336:0.0618205,((TT9_LFPAFLNI_00494:0.0133531,(KBS0714_MOLHKGIG_00495:0.0101662,SA211_MHAAABBN_00216:0.0108968)n3:0.00415844)n2:0.00238419,(AS2_ACLBLIBL_01221:1.79847,AS2_ACLBLIBL_02452:0.0211289)n4:0.00234766)n1:0.0933099)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000128_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000128_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a778d01336e53c814977d34c25fab3df26651ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000128_tree.txt
@@ -0,0 +1 @@
+(((KBS0714_MOLHKGIG_01636:0.024705,TT9_LFPAFLNI_01565:0.018029)n2:0.019837,((KD337_16_NAFOICDF_01210:0.717847,SA211_MHAAABBN_01341:0.00578256)n4:0.00798613,KD337_16_NAFOICDF_01168:0.0112338)n3:0.0012482)n1:0.00922244,AS2_ACLBLIBL_01259:0.0261496)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000129_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000129_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9be4c6403561c83ec07efb69e756b3f2e07678a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000129_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_01273:0.00074256,(KD337_16_NAFOICDF_01182:2.99429e-06,KD337_16_NAFOICDF_00781:2.65218)n2:0.294686)n1:0.00267891,(TT9_LFPAFLNI_01551:0.0129489,(KBS0714_MOLHKGIG_01624:0.00159981,SA211_MHAAABBN_01330:0.00262219)n4:0.00993206)n3:0.0177293)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000131_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000131_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30b9619a63fb9efc3e4c1c563bd7df5158f98e11
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000131_tree.txt
@@ -0,0 +1 @@
+(((AS2_ACLBLIBL_01310:0.0470431,SA211_MHAAABBN_00361:0.0343659)n2:0.0118377,((KD337_16_NAFOICDF_02215:1.31739,KD337_16_NAFOICDF_00689:0.0285913)n4:0.0153969,KD337_16_NAFOICDF_02211:0.0302448)n3:0.00336053)n1:0.0024746,KBS0714_MOLHKGIG_00620:0.0201246)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000132_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000132_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef5c0c1b8e11aa71b92bffbdb01a512426d2aa7e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000132_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00456:0.0719097,(((TT9_LFPAFLNI_01512:0.00705462,SA211_MHAAABBN_01296:0.0107404)n3:0.004935,(KBS0714_MOLHKGIG_02251:0.0624845,KBS0714_MOLHKGIG_01585:0.0049464)n4:0.0005496)n2:0.00599,AS2_ACLBLIBL_01337:0.012057)n1:0.743811)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000133_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000133_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eca4ce80a130e904fa58f886cc07d0f85c582fc8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000133_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00458:0.0836396,(SA211_MHAAABBN_01295:0.00279783,(TT9_LFPAFLNI_01511:0,(KBS0714_MOLHKGIG_02249:0.0427568,(KBS0714_MOLHKGIG_01584:0,AS2_ACLBLIBL_01338:0)n4:0)n3:0)n2:0.00174217)n1:1.4706)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000134_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000134_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc98a66706dd333dc11995cb3ac05337da051482
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000134_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01234:0.00370966,(TT9_LFPAFLNI_01509:0.00712669,(KBS0714_MOLHKGIG_01582:0.00093419,(AS2_ACLBLIBL_01340:5.1719e-07,(SA211_MHAAABBN_01293:0.206233,SA211_MHAAABBN_01292:0.028122)n4:0.00312467)n3:0.269752)n2:0.00312781)n1:0.00370966)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000136_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000136_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5008a611124b8ada0b0bf565797befb8e664ffb7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000136_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01248:0.058148,((TT9_LFPAFLNI_01496:0.0124412,(KBS0714_MOLHKGIG_01569:8.964e-05,SA211_MHAAABBN_01279:0.00352636)n3:0.00429334)n2:0.0943537,(AS2_ACLBLIBL_02577:0.281976,AS2_ACLBLIBL_01355:0.0874038)n4:0.00971153)n1:0.0438714)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000138_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000138_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2d23b111adeb9674f5989289387d040ba86ea6c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000138_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_01267:0.0898296,KD337_16_NAFOICDF_01296:1.82395)n1:0.020907,(AS2_ACLBLIBL_01376:0.0397266,((KBS0714_MOLHKGIG_01549:0.00145993,TT9_LFPAFLNI_01476:0.00242707)n4:0.00446074,SA211_MHAAABBN_01259:0.00168778)n3:0.0434067)n2:0.020907)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000139_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000139_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dcd1f80de5aa8862c3c95f2d63004bd6f5badb7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000139_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00286:3.33824,KD337_16_NAFOICDF_01277:0.101605)n1:0.0185478,(AS2_ACLBLIBL_01386:0.128368,(KBS0714_MOLHKGIG_01539:0.0217871,(TT9_LFPAFLNI_01466:0.0161868,SA211_MHAAABBN_01249:0.0424702)n4:0.0092894)n3:0.0515244)n2:0.0185478)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000140_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000140_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d65f9b9e8c26d4d503cf79260ba75db6f913d18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000140_tree.txt
@@ -0,0 +1 @@
+(((SA211_MHAAABBN_01182:0.0783039,(TT9_LFPAFLNI_01400:0.0126206,KBS0714_MOLHKGIG_01450:0.0209564)n3:0.0438566)n2:0.0175669,AS2_ACLBLIBL_01449:0.0893554)n1:0.0339901,(KD337_16_NAFOICDF_01775:2.07476,KD337_16_NAFOICDF_01353:0.118945)n4:0.0339901)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000142_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000142_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5525454c9835378bdbe633dcb8a180a7136b58b7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000142_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_01501:0.616067,((TT9_LFPAFLNI_00111:4.24095e-06,(KD337_16_NAFOICDF_00694:0.309231,KD337_16_NAFOICDF_00347:0.207293)n4:1.03222)n3:0.347121,KD337_16_NAFOICDF_00288:0.496316)n2:0.0551463)n1:0.325028,SA211_MHAAABBN_02019:1.27543)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000144_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000144_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8da1c03d5a4b25b086b0f9715d66d664885e9c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000144_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_01415:2.21555,KD337_16_NAFOICDF_01447:0.0115707)n1:0.120247,((KBS0714_MOLHKGIG_01341:0.009796,(SA211_MHAAABBN_01061:0,TT9_LFPAFLNI_01296:0)n4:0.003374)n3:0.0441125,AS2_ACLBLIBL_01551:0.0524475)n2:0.120247)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000146_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000146_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6bcc0257ee9fd13ed5c551acb4cc48e9b3b7e8a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000146_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_01600:0.0519711,(KD337_16_NAFOICDF_02080:1.39602,KD337_16_NAFOICDF_01496:0.0787985)n2:0.00875539)n1:0.0120889,(KBS0714_MOLHKGIG_01285:0.00195938,(SA211_MHAAABBN_01004:0,TT9_LFPAFLNI_01243:0)n4:0.00594563)n3:0.0153359)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000147_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000147_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6460b274fab6bd2b76e58d49794d422c49ca5a6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000147_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01510:0.036005,(((KBS0714_MOLHKGIG_01272:0,SA211_MHAAABBN_00991:0)n3:0,(TT9_LFPAFLNI_01882:3.04938,TT9_LFPAFLNI_01230:0)n4:0)n2:0.0455615,AS2_ACLBLIBL_01615:0.0321735)n1:0.0123965)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000152_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000152_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c67e16a7de3a0d87097564486e87ad19a449bea1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000152_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01843:0.0721513,(((SA211_MHAAABBN_00707:0.0156684,KBS0714_MOLHKGIG_00993:0.0122966)n3:0.00293419,TT9_LFPAFLNI_00936:0.0146753)n2:0.0126844,(AS2_ACLBLIBL_01817:1.43444,AS2_ACLBLIBL_01896:0.0256521)n4:0.00285023)n1:0.0412507)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000153_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000153_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4703bc496e61eee8f3738fcd02a22ecf751070ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000153_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01711:0.0567583,(AS2_ACLBLIBL_01822:0.0847533,((SA211_MHAAABBN_00784:0,TT9_LFPAFLNI_01012:0)n3:0.00147494,(KBS0714_MOLHKGIG_00838:1.45797,KBS0714_MOLHKGIG_01065:0.00620375)n4:0.000689306)n2:0.0846834)n1:0.0948587)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000156_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000156_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b60172614c461a6415daf491859f3f7c424a84a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000156_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01946:0.143848,((TT9_LFPAFLNI_00842:0.00736487,(AS2_ACLBLIBL_02050:1.36524,AS2_ACLBLIBL_02052:0.00527682)n3:0.000586313)n2:0.262658,(KBS0714_MOLHKGIG_00886:0,SA211_MHAAABBN_00608:0)n4:0.385195)n1:0.143848)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000160_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000160_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..112d068d2592c60206c3672e2e8a6e75290bf3ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000160_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_02098:0.365229,KD337_16_NAFOICDF_00342:2.50642)n1:0.124246,(AS2_ACLBLIBL_02222:0.178768,(SA211_MHAAABBN_00462:0.0170646,(KBS0714_MOLHKGIG_00731:0.00550922,TT9_LFPAFLNI_00695:0.00286778)n4:0.00998886)n3:0.154712)n2:0.124246)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000161_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000161_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cce4279dfe46fefa0b33714baf6ce782cc2a8a6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000161_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02443:0.441404,((TT9_LFPAFLNI_00662:0.0142763,(SA211_MHAAABBN_00429:0.00176296,KBS0714_MOLHKGIG_00692:0.00083404)n3:0.0165046)n2:0.278019,(AS2_ACLBLIBL_02263:0.114302,AS2_ACLBLIBL_02262:0.217547)n4:0.0241719)n1:0.613258)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000162_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000162_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48b318ed124881cd12e83a406db48a3736c43982
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000162_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02170:0.0499441,(((TT9_LFPAFLNI_00620:0.00460756,SA211_MHAAABBN_00387:0.00714744)n3:0.0232114,(KBS0714_MOLHKGIG_00841:2.72111,KBS0714_MOLHKGIG_00650:0.0268802)n4:0.00298669)n2:0.0482096,AS2_ACLBLIBL_02313:0.0815279)n1:0.166145)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000164_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000164_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9a1a37c8e2f461e8d2bc809e84b940c1d878921
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000164_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01190:0.917143,(KBS0714_MOLHKGIG_00611:0.138852,(AS2_ACLBLIBL_02344:0.186836,(SA211_MHAAABBN_01771:0.2065,(TT9_LFPAFLNI_02008:0,SA211_MHAAABBN_00327:0)n4:0.0992486)n3:0.0110276)n2:0.0324626)n1:0.057854)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000165_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000165_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d6bce750f949193752d45ed99bd63c4c5786d0f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000165_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02283:0.249737,((AS2_ACLBLIBL_02399:0.324744,AS2_ACLBLIBL_02400:0.295269)n2:0.102834,((TT9_LFPAFLNI_00550:0.00985112,SA211_MHAAABBN_00272:0.00895888)n4:0.00207375,KBS0714_MOLHKGIG_00547:0.00547575)n3:0.129393)n1:0.249737)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000169_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000169_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4923aad55330282bf079040a1fa0bc91419f1153
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000169_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02410:0.695983,((SA211_MHAAABBN_00139:0.0808988,(TT9_LFPAFLNI_00421:0.00305769,KBS0714_MOLHKGIG_00418:3.28998e-06)n3:0.125543)n2:1.11298,(AS2_ACLBLIBL_02541:0.0640491,AS2_ACLBLIBL_02542:0.962954)n4:0.106995)n1:0.139046)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000171_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000171_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c39cc4bb60695583f25d60394d451e4d6b8bb775
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000171_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_02569:0.0298479,(KD337_16_NAFOICDF_02444:0.157277,KD337_16_NAFOICDF_01756:0.110968)n2:0.0123298)n1:0.00163472,(TT9_LFPAFLNI_00392:0.00424781,(KBS0714_MOLHKGIG_00386:3.29291e-07,SA211_MHAAABBN_00110:0.00382219)n4:0.00306019)n3:0.00628444)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000174_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000174_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6e62b114b53d7fe2c2752ccd5dfe7d9a2c3c59a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000174_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00005:0.0770464,(AS2_ACLBLIBL_00004:0.0948421,(KBS0714_MOLHKGIG_00331:0.0114766,(TT9_LFPAFLNI_00338:0.00573612,SA211_MHAAABBN_00047:0.00630288)n3:0.00121638)n2:0.0320009)n1:0.0770464)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000176_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000176_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cb4a1218ccba1bf0701b05689dc6d892316cfd8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000176_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00007:0.0421752,(((KBS0714_MOLHKGIG_00326:1.66969e-07,TT9_LFPAFLNI_00333:0.00328113)n3:8.013e-05,SA211_MHAAABBN_00042:0)n2:0.0339272,AS2_ACLBLIBL_00009:0.0454107)n1:0.0421752)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000177_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000177_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee31651ac73e41031f240ee7d8c7f6c1cb54a0e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000177_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01180:0.384831,((TT9_LFPAFLNI_00383:0,KBS0714_MOLHKGIG_00377:0)n2:0.0012205,(AS2_ACLBLIBL_00011:1.3444,AS2_ACLBLIBL_02586:0.00423315)n3:0.00047035)n1:0.462107)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000178_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000178_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23193e2748b1d391dc710855a33a88b6c4fd227d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000178_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00008:0.05766,(AS2_ACLBLIBL_00012:0.022531,(TT9_LFPAFLNI_00332:0.00554275,(KBS0714_MOLHKGIG_00325:0.00187475,SA211_MHAAABBN_00040:0.00386125)n3:0.00492825)n2:0.0296332)n1:0.05766)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000180_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000180_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe7f26560187f1be45ccee4d083d713b917d05a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000180_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00010:0.0513269,(AS2_ACLBLIBL_00014:0.0302272,(TT9_LFPAFLNI_00330:1.57375e-07,(SA211_MHAAABBN_00038:0,KBS0714_MOLHKGIG_00323:0)n3:0.00341036)n2:0.021188)n1:0.0513269)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000181_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000181_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30fb413301d801ef0a9c2db73dd60542324a4813
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000181_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00011:0.300041,(AS2_ACLBLIBL_00015:0.126411,((KBS0714_MOLHKGIG_00322:0,SA211_MHAAABBN_00037:0)n3:0,TT9_LFPAFLNI_00329:0)n2:0.0883725)n1:0.300041)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000183_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000183_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c66a74230bcb159a231ef4b5e35dc77386af9709
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000183_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00013:0.0895922,(AS2_ACLBLIBL_00017:0.0404035,(TT9_LFPAFLNI_00327:0.001789,(KBS0714_MOLHKGIG_00320:0,SA211_MHAAABBN_00035:0)n3:0.000795)n2:0.033456)n1:0.0895922)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000184_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000184_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6afc72c34e7f139d87226c372ab7673cc22650c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000184_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000186_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000186_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c66f3fa15ce6dd24963d8ac09eedda66302f4b3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000186_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000187_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000187_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..453adcc44430f6dae0d582588d45dca57f89d38e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000187_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000188_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000188_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78252e60a89c1fa45529295d55c3182af618d526
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000188_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00019:0.0734043,(AS2_ACLBLIBL_00023:0.0420385,(KBS0714_MOLHKGIG_00314:0.0125535,(TT9_LFPAFLNI_00321:0,SA211_MHAAABBN_00029:0)n3:0.00657653)n2:0.0256357)n1:0.0734043)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000189_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000189_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23efd039a173eeca4aa17412a9524de73168aaaa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000189_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00020:0.142969,((SA211_MHAAABBN_00028:0.00279158,(KBS0714_MOLHKGIG_00313:0.016032,TT9_LFPAFLNI_00320:0.00991297)n3:0.00355341)n2:0.111215,AS2_ACLBLIBL_00024:0.177797)n1:0.142969)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000190_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000190_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4fadfc4f285d6c2e464b24e7d9949cfbd9ad0305
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000190_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00022:0.149273,(AS2_ACLBLIBL_00026:0.0731005,(TT9_LFPAFLNI_00318:0.00463789,(SA211_MHAAABBN_00026:0.00757323,KBS0714_MOLHKGIG_00311:0.0111478)n3:0.00474161)n2:0.0716028)n1:0.149273)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000191_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000191_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6252fa2afb43954af099f36c61af6c30358f7604
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000191_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00025:0.0948172,(AS2_ACLBLIBL_00029:0.159766,(KBS0714_MOLHKGIG_00308:0.00506146,(TT9_LFPAFLNI_00315:0.00430295,SA211_MHAAABBN_00023:5e-08)n3:0.00247504)n2:0.168174)n1:0.0948172)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000193_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000193_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c3f8eb7f2ec5de1d104b32709dda193b9b3c6d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000193_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00027:0.2058,(AS2_ACLBLIBL_00031:0.047884,((SA211_MHAAABBN_00021:0.00421262,TT9_LFPAFLNI_00313:0.00048638)n3:0.00421882,KBS0714_MOLHKGIG_00306:0.010653)n2:0.0303082)n1:0.2058)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000195_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000195_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa2097db78c93ee5842eceb2b056130e07fbbf22
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000195_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00030:0.268036,((TT9_LFPAFLNI_00310:0.045389,(KBS0714_MOLHKGIG_00303:0.0435995,SA211_MHAAABBN_00011:0.0446425)n3:0.00753413)n2:0.188856,AS2_ACLBLIBL_00051:0.237306)n1:0.268036)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000196_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000196_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e49a9dc10629b372a582a01771173e182d3905b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000196_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00031:0.144112,(AS2_ACLBLIBL_00053:0.15923,(KBS0714_MOLHKGIG_00301:0.0172749,(TT9_LFPAFLNI_00308:0.00913737,SA211_MHAAABBN_00009:0.00826163)n3:0.00981913)n2:0.0703851)n1:0.144112)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000201_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000201_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de22e854afa95f1dc9e0634e73386ac442fb9003
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000201_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00039:0.0975049,(AS2_ACLBLIBL_00060:0.0203972,(KBS0714_MOLHKGIG_00294:2.44609e-07,(TT9_LFPAFLNI_00301:0.0052005,SA211_MHAAABBN_00002:0.0003625)n3:0.0078115)n2:0.0173465)n1:0.0975049)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000204_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000204_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e2b0191673f0b66430a1f9f565e5cde607f42a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000204_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00042:0.0550846,(AS2_ACLBLIBL_00063:0.0247269,(TT9_LFPAFLNI_00298:0.0104384,(KBS0714_MOLHKGIG_00291:0.00032912,SA211_MHAAABBN_02314:0.00308387)n3:0.00766363)n2:0.0682341)n1:0.0550846)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000205_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000205_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..deb51311913b02cffc3824d05d13f004cc4fd62c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000205_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00044:0.209007,(AS2_ACLBLIBL_00065:0.152219,((TT9_LFPAFLNI_00295:0,SA211_MHAAABBN_02311:0)n3:0.0125852,KBS0714_MOLHKGIG_00289:0.0144987)n2:0.102469)n1:0.209007)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000207_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000207_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86071cee7cacd14536014a179a44343576df79a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000207_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00049:0.0661865,(AS2_ACLBLIBL_00069:0.55289,(KBS0714_MOLHKGIG_00284:0.0432016,(TT9_LFPAFLNI_00290:0.00277351,SA211_MHAAABBN_02306:0.00281449)n3:0.0303199)n2:0.145875)n1:0.0661865)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000208_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000208_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d41034874f14a892c57a0ea7387b61f805f0fbd3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000208_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00056:0.0657936,(AS2_ACLBLIBL_00070:0.0427068,(KBS0714_MOLHKGIG_00283:0.0127327,(SA211_MHAAABBN_02298:0.00494125,TT9_LFPAFLNI_00282:0.00824575)n3:0.0538892)n2:0.0625322)n1:0.0657936)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000212_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000212_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58e4670c6fbbfef56862b228bd8f95256127e8ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000212_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00061:0.0607551,(((KBS0714_MOLHKGIG_00277:0.0060403,SA211_MHAAABBN_02292:0.0010207)n3:0.00322846,TT9_LFPAFLNI_00276:0.00058695)n2:0.0364983,AS2_ACLBLIBL_00076:0.0441028)n1:0.0607551)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000214_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000214_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..354aecac831b94ae19529accfea55abc9ff09cec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000214_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00064:0.0484605,((KBS0714_MOLHKGIG_00270:0.0089415,(TT9_LFPAFLNI_00268:0,SA211_MHAAABBN_02285:0)n3:0.0038495)n2:0.0199855,AS2_ACLBLIBL_00087:0.037145)n1:0.0484605)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000216_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000216_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..769ed0d7b3f55bb1a53c0a11fef5fbbdb13a84fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000216_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00135:0.269143,((SA211_MHAAABBN_02133:0,TT9_LFPAFLNI_00125:0)n2:0.0130685,(AS2_ACLBLIBL_00090:0.596531,AS2_ACLBLIBL_00267:0.0139324)n3:0.00154805)n1:0.891348)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000217_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000217_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05512998e39a9f0558c2b047dc5c2e38c416dc9e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000217_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00066:0.138728,(AS2_ACLBLIBL_00095:0.018418,((TT9_LFPAFLNI_00266:0,SA211_MHAAABBN_02281:0)n3:0.00191217,KBS0714_MOLHKGIG_00268:0.00065183)n2:0.0268919)n1:0.138728)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000218_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000218_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07c100c19622f0a870fc9c552de1a170904b1394
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000218_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00067:0.165323,(((SA211_MHAAABBN_02280:0,TT9_LFPAFLNI_00265:0)n3:0,KBS0714_MOLHKGIG_00267:0)n2:0.042428,AS2_ACLBLIBL_00096:0.070796)n1:0.165323)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000219_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000219_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e9a96c6a146b4fe96acf9de604fa2d2b2b43db6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000219_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00068:0.041795,(AS2_ACLBLIBL_00097:0.043914,(SA211_MHAAABBN_02279:0.00552067,(KBS0714_MOLHKGIG_00266:0.0202227,TT9_LFPAFLNI_00264:0.0060323)n3:0.00518333)n2:0.0676559)n1:0.041795)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000220_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000220_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cb3c62b9d9c59bb5643c6d8095a1e6a139edda8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000220_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00069:0.0445065,(AS2_ACLBLIBL_00098:0.066229,(KBS0714_MOLHKGIG_00265:0,(SA211_MHAAABBN_02278:0,TT9_LFPAFLNI_00263:0)n3:0)n2:0.007051)n1:0.0445065)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000221_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000221_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92d648e3c8e8d00cdaf13d206a55c5bb64104ee8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000221_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00070:0.247996,((TT9_LFPAFLNI_00262:0.0188155,(SA211_MHAAABBN_02277:0,KBS0714_MOLHKGIG_00264:0)n3:0.0101615)n2:0.337909,AS2_ACLBLIBL_00099:8.46146e-07)n1:0.247996)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000223_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000223_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..beb3739a25899c6353a51024641da19c56715010
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000223_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00075:0.387597,(AS2_ACLBLIBL_00105:0.257119,(TT9_LFPAFLNI_00260:0.018594,(SA211_MHAAABBN_02275:0.00474012,KBS0714_MOLHKGIG_00262:0.00613788)n3:0.0201375)n2:0.29261)n1:0.387597)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000224_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000224_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..428c7b97a278aae53166cba04c834304dbaff75a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000224_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000229_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000229_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd950c21adb2c7e0ec6b3c923f77c0f6a12d4126
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000229_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000230_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000230_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6dc9f42ddf2b9bd6fe0552d0111a7dce33f30d86
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000230_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00090:0.0506466,(AS2_ACLBLIBL_00122:0.0462358,(SA211_MHAAABBN_02260:0.00112284,(KBS0714_MOLHKGIG_00248:0.0135395,TT9_LFPAFLNI_00248:0.00052145)n3:0.00156916)n2:0.0238348)n1:0.0506466)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000232_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000232_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39111ece996893c1220222abb7f2e682d0a14d7f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000232_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00094:0.294761,(AS2_ACLBLIBL_00125:0.116428,((SA211_MHAAABBN_02256:0.002943,KBS0714_MOLHKGIG_00244:0.006752)n3:0.00927148,TT9_LFPAFLNI_00244:0.00473793)n2:0.112023)n1:0.294761)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000233_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000233_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a5d16362bdf627c42ba6774d1a4a5d2d6e6107e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000233_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00095:0.390665,(AS2_ACLBLIBL_00128:0.15731,((SA211_MHAAABBN_02254:0.0164058,TT9_LFPAFLNI_00242:0.00908116)n3:0.0115275,KBS0714_MOLHKGIG_00241:0.0120704)n2:0.0789046)n1:0.390665)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000234_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000234_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bce6a1cb5a27060154fc1df07be4b2cf19b25ea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000234_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00096:0.289405,(AS2_ACLBLIBL_00131:0.230069,(KBS0714_MOLHKGIG_00240:0.0383175,(SA211_MHAAABBN_02253:0.0253818,TT9_LFPAFLNI_00241:0.00516825)n3:0.021751)n2:0.181465)n1:0.289405)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000235_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000235_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f5505c7122197737e753e2c3e63307c4c13a774
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000235_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00097:0.241137,(AS2_ACLBLIBL_00132:0.0503878,((SA211_MHAAABBN_02252:0,TT9_LFPAFLNI_00240:0)n3:0.00267921,KBS0714_MOLHKGIG_00239:0.00539179)n2:0.0559528)n1:0.241137)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000237_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000237_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88a657bc27dec64b8ca163182a16335763032954
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000237_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00099:0.395781,((TT9_LFPAFLNI_00238:0.00910662,(SA211_MHAAABBN_02250:0.0105264,KBS0714_MOLHKGIG_00237:0.0167926)n3:0.00407788)n2:0.0627709,AS2_ACLBLIBL_00134:0.0704626)n1:0.395781)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000238_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000238_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6a94b287adfa16a5221820c20eaa8e75bfff303
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000238_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00101:0.0981587,((KBS0714_MOLHKGIG_00235:0.010068,(SA211_MHAAABBN_02248:0.00348491,TT9_LFPAFLNI_00236:0.00496609)n3:0.0184167)n2:0.0722038,AS2_ACLBLIBL_00136:0.0640627)n1:0.0981587)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000241_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000241_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..086cf2e07fcb3965152dd8ff8b8bf4a9a3c60545
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000241_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_01265:0.0181057,AS2_ACLBLIBL_00143:1.30571)n1:0.0262444,(SA211_MHAAABBN_01336:0.0080386,(TT9_LFPAFLNI_01560:0.00564948,KBS0714_MOLHKGIG_01631:0.00622352)n3:0.0135084)n2:0.0262444)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000242_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000242_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46dd2033b98ba4a8182c6764d3e9fff1076c80d1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000242_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00105:0.047207,(AS2_ACLBLIBL_00147:0.099015,(TT9_LFPAFLNI_00233:0.00759775,(SA211_MHAAABBN_02245:0.007762,KBS0714_MOLHKGIG_00232:0.001516)n3:0.0153688)n2:0.130152)n1:0.047207)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000244_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000244_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a03d1735ecb6bebfe1e9006f7a3f7461ce35984
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000244_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00107:0.0545693,(AS2_ACLBLIBL_00150:0.0388973,(TT9_LFPAFLNI_00232:0.00374306,(KBS0714_MOLHKGIG_00231:0,SA211_MHAAABBN_02244:0)n3:0.00306094)n2:0.0298963)n1:0.0545693)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000247_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000247_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a529198b3af40ba87e9fe63b51c66f25c44269e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000247_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00112:0.186842,(AS2_ACLBLIBL_00154:0.226913,(TT9_LFPAFLNI_00227:0.0519559,(KBS0714_MOLHKGIG_00226:0.050669,SA211_MHAAABBN_02239:0.056377)n3:0.0157836)n2:0.157034)n1:0.186842)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000249_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000249_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9ca7a96ae69398a70e865e84ebc32faed7afd5d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000249_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00114:0.252698,(AS2_ACLBLIBL_00156:0.156775,(KBS0714_MOLHKGIG_00224:0.011117,(SA211_MHAAABBN_02237:0.0083275,TT9_LFPAFLNI_00225:0.0326005)n3:0.0198225)n2:0.189554)n1:0.252698)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000250_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000250_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee13d566a73cb33989a08aab8b4b8214a182e8c6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000250_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00116:0.0536942,(AS2_ACLBLIBL_00158:0.0091505,(TT9_LFPAFLNI_00223:0.00027925,(KBS0714_MOLHKGIG_00222:5e-07,SA211_MHAAABBN_02235:5e-07)n3:0.00281325)n2:0.0199933)n1:0.0536942)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000251_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000251_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5608471da60ae3d6efde6b76dac5c69ee5d73f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000251_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00118:0.0608092,(AS2_ACLBLIBL_00160:0.241906,(SA211_MHAAABBN_02233:0.151954,(KBS0714_MOLHKGIG_00220:0.0475816,TT9_LFPAFLNI_00221:0.0136934)n3:0.0154439)n2:0.128961)n1:0.0608092)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000252_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000252_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57959bef52d985ffc94b58140505de5ea7256217
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000252_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00119:0.423364,(((KBS0714_MOLHKGIG_00215:1.27052e-06,TT9_LFPAFLNI_00215:0.0325369)n3:0.00834588,SA211_MHAAABBN_02208:1.27052e-06)n2:0.170898,AS2_ACLBLIBL_00166:0.228703)n1:0.423364)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000253_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000253_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3f87370b6d702c3acf30a51129d1eea22561069
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000253_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00120:0.122058,(AS2_ACLBLIBL_00169:0.261873,(KBS0714_MOLHKGIG_00214:0.025921,(SA211_MHAAABBN_02207:0.0295485,TT9_LFPAFLNI_00214:0.0258265)n3:0.0055545)n2:0.265166)n1:0.122058)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000256_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000256_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ded5f3e2120852549d41afbdd915d2f6579a3847
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000256_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00123:0.0366607,((TT9_LFPAFLNI_00212:0.00489422,(KBS0714_MOLHKGIG_00212:0.00294793,SA211_MHAAABBN_02205:1.50314e-07)n3:0.0037077)n2:0.0195872,AS2_ACLBLIBL_00174:0.0459877)n1:0.0366607)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000259_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000259_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe2d9c52cf18295da524cbbf487411ba956b60ae
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000259_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00128:0.384466,((KBS0714_MOLHKGIG_00209:0.01807,(SA211_MHAAABBN_02202:0.00308325,TT9_LFPAFLNI_00209:0.00757775)n3:0.0116335)n2:0.123908,AS2_ACLBLIBL_00182:0.168882)n1:0.384466)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000260_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000260_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61b6c97256d178fd34dbe5a67dd9c9b781f65773
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000260_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00129:0.297485,(((TT9_LFPAFLNI_00208:0.0009965,KBS0714_MOLHKGIG_00208:0.0101545)n3:0.0506523,SA211_MHAAABBN_02201:0.0150212)n2:0.0463758,AS2_ACLBLIBL_00183:0.195259)n1:0.297485)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000261_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000261_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1c4b4c1f1d1d51b69ff4437b1372ed8a7ec277c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000261_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00143:0.005721,((TT9_LFPAFLNI_00205:0.00201322,(SA211_MHAAABBN_02198:0.00249862,KBS0714_MOLHKGIG_00203:1.38e-06)n3:0.00425141)n2:0.0109469,AS2_ACLBLIBL_00188:0.266162)n1:0.005721)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000262_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000262_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..526e4a1fc65d025f585d6e961cbc4cd9f52aa922
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000262_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00144:0.0107077,((AS2_ACLBLIBL_00190:0.231385,SA211_MHAAABBN_02197:0.0139604)n2:0.00943712,(KBS0714_MOLHKGIG_00202:0.00337213,TT9_LFPAFLNI_00204:0.00538387)n3:0.00942662)n1:0.0107077)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000266_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000266_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d822326a4684e79d8ae139761f7ed8509be7da64
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000266_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00152:0.00172033,((TT9_LFPAFLNI_00195:0.256679,(SA211_MHAAABBN_02191:0,KBS0714_MOLHKGIG_00195:0)n3:0.0197561)n2:0.013849,AS2_ACLBLIBL_00204:0.535484)n1:0.00172033)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000269_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000269_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24ea97e2fcc5d3840fc47d3b706c79e1e4525154
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000269_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00155:0.058552,(KBS0714_MOLHKGIG_00192:0.007467,((SA211_MHAAABBN_02188:0.00071021,AS2_ACLBLIBL_00208:0.0350218)n3:0.00377146,TT9_LFPAFLNI_00192:0.00076437)n2:0.00478935)n1:0.058552)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000271_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000271_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..435a2f2649f32e57007303f895f6471574629ef7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000271_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00159:0.0084405,(AS2_ACLBLIBL_00214:0.007411,(SA211_MHAAABBN_02183:0.00117051,(KBS0714_MOLHKGIG_00187:0,TT9_LFPAFLNI_00184:0)n3:0.00082849)n2:0.000845)n1:0.0084405)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000273_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000273_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56163105f6ac5d6b45426ecc198a72594145408b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000273_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00161:0.0539193,(AS2_ACLBLIBL_00216:0.0198214,((SA211_MHAAABBN_02181:0.00996683,TT9_LFPAFLNI_00182:0.00797417)n3:0.00943126,KBS0714_MOLHKGIG_00185:0.0118123)n2:0.00480471)n1:0.0539193)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000275_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000275_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e29d15f7eda0edd93c4650716dddbea363581b59
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000275_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00163:0.224418,(((KBS0714_MOLHKGIG_00183:0.00737417,TT9_LFPAFLNI_00180:0.00165483)n3:0.00301062,SA211_MHAAABBN_02179:0.00386036)n2:0.00228314,AS2_ACLBLIBL_00218:0.00670995)n1:0.224418)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000279_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000279_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e3df7ede527a8948c51e9cb0640814fa0b61c19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000279_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00168:0.00824587,(AS2_ACLBLIBL_00222:0.0140792,((KBS0714_MOLHKGIG_00179:4.3367e-08,SA211_MHAAABBN_02175:0.00350675)n3:0.0011735,TT9_LFPAFLNI_00176:0.0023115)n2:0.005831)n1:0.00824587)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000281_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000281_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06144e321d0597bdb2325db1d5205ef63ae25e45
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000281_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00170:0.0568365,(AS2_ACLBLIBL_00231:0.028986,(SA211_MHAAABBN_02166:0,(KBS0714_MOLHKGIG_00152:0,TT9_LFPAFLNI_00160:0)n3:0)n2:0.026646)n1:0.0568365)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000282_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000282_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a19c175b17c32661022fc24b746d62e687f711
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000282_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00171:0.0360377,(AS2_ACLBLIBL_00232:0.0335217,(TT9_LFPAFLNI_00159:0.00447651,(KBS0714_MOLHKGIG_00151:0.00485136,SA211_MHAAABBN_02165:0.00883564)n3:0.00414749)n2:0.0193162)n1:0.0360377)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000283_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000283_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..857839dfc61a547bf2557ce5a6c25ba3927be2c1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000283_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00172:0.21225,(((KBS0714_MOLHKGIG_00150:0,TT9_LFPAFLNI_00158:0)n3:0,SA211_MHAAABBN_02164:0)n2:0.0889695,AS2_ACLBLIBL_00233:0.0831285)n1:0.21225)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000284_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000284_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a45832e5cb10b2401f5c164cb6afc7e4c614b3e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000284_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00819:0.166438,(AS2_ACLBLIBL_00234:0.0907178,((SA211_MHAAABBN_02163:0.00098251,TT9_LFPAFLNI_00157:0.00029049)n3:0.00224511,KBS0714_MOLHKGIG_00149:0.00119554)n2:0.0635741)n1:0.166438)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000288_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000288_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afa066d778d408b1d3ac4a759b8b25087291794b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000288_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00174:0.0915702,(AS2_ACLBLIBL_00240:0.0257976,(KBS0714_MOLHKGIG_00144:0.00180838,(SA211_MHAAABBN_02158:0.00174638,TT9_LFPAFLNI_00152:0.00404563)n3:0.00443363)n2:0.0423821)n1:0.0915702)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000290_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000290_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0ba4b949d19e2c1fc84a362e68d4c894ce28752
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000290_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00176:0.117915,(AS2_ACLBLIBL_00242:0.0481546,((KBS0714_MOLHKGIG_00142:3.5312e-07,SA211_MHAAABBN_02156:0.0198869)n3:0.00034687,TT9_LFPAFLNI_00150:3.5312e-07)n2:0.0495954)n1:0.117915)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000292_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000292_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..515a54932b5cd9ccc12f5e411b6408c311ff1ace
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000292_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00178:0.0376153,(AS2_ACLBLIBL_00244:0.0276185,(SA211_MHAAABBN_02154:0.00744,(TT9_LFPAFLNI_00148:0,KBS0714_MOLHKGIG_00140:0)n3:0.023539)n2:0.0241115)n1:0.0376153)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000294_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000294_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ae1341d66ee213349e29fc2e34427a8efb39c32
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000294_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00180:0.0714061,((KBS0714_MOLHKGIG_00138:0.00377384,(TT9_LFPAFLNI_00146:0.00481782,SA211_MHAAABBN_02152:0.00464418)n3:0.00485221)n2:0.104455,AS2_ACLBLIBL_00246:0.131797)n1:0.0714061)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000296_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000296_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8e333691ff3022cff3a69792ec92fea7a83e1a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000296_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00182:0.167584,(AS2_ACLBLIBL_00248:0.119881,(KBS0714_MOLHKGIG_00136:0.0076375,(TT9_LFPAFLNI_00144:5.67653e-07,SA211_MHAAABBN_02150:0.00949525)n3:0.0131265)n2:0.0834665)n1:0.167584)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000297_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000297_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a298cc16ab166383194bfcaf91c2a020f65d6db2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000297_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00185:0.0893213,((SA211_MHAAABBN_02149:0,KBS0714_MOLHKGIG_00135:0)n2:0.0030125,(AS2_ACLBLIBL_00250:0.00656507,TT9_LFPAFLNI_00143:0.00021693)n3:0.0015835)n1:0.0893213)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000299_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000299_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f768d5694ba6dd442b60e849facea96b61e4070d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000299_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00651:1.00577,(AS2_ACLBLIBL_00254:0.226576,(TT9_LFPAFLNI_00139:0.0254462,(KBS0714_MOLHKGIG_00131:2.32596e-06,SA211_MHAAABBN_02145:0.00666087)n3:0.00346935)n2:0.0524041)n1:1.00577)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000301_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000301_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..643bb71c5457c28d8421a97398b5ceecd19a7df7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000301_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00193:0.104091,((KBS0714_MOLHKGIG_00126:0.00729887,(TT9_LFPAFLNI_00134:3.93911e-07,SA211_MHAAABBN_02140:0.00283038)n3:0.0159786)n2:0.0533061,AS2_ACLBLIBL_00259:0.10669)n1:0.104091)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000302_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000302_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c6377597926adb763b58a26229a74728f4c0f90
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000302_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00194:0.0237013,(((SA211_MHAAABBN_02139:0.00534978,TT9_LFPAFLNI_00133:0.00306022)n3:0.0400653,KBS0714_MOLHKGIG_00125:0.0350232)n2:0.483112,AS2_ACLBLIBL_00260:0.160599)n1:0.0237013)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000303_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000303_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a99fde62722010dab1eab8ccce9f693fc3a24b17
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000303_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00195:0.3927,((AS2_ACLBLIBL_00261:0.25696,KBS0714_MOLHKGIG_00124:0.118793)n2:0.0183959,(TT9_LFPAFLNI_00132:0.0267875,SA211_MHAAABBN_02138:0.0092775)n3:0.167934)n1:0.3927)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000305_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000305_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc8497b0d08852488c411f4e50a511c6d4ca38ce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000305_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00197:0.0413381,((KBS0714_MOLHKGIG_00122:0.0432875,AS2_ACLBLIBL_00263:0.0519605)n2:0.00256775,(SA211_MHAAABBN_02136:0.0127045,TT9_LFPAFLNI_00130:0.0074875)n3:0.0393867)n1:0.0413381)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000307_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000307_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86c462c63b0106d4bfecdeabd13e417ff53e09e1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000307_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00203:0.192359,(AS2_ACLBLIBL_00271:0.121443,(SA211_MHAAABBN_02129:0.0175316,(KBS0714_MOLHKGIG_00116:0.0147018,TT9_LFPAFLNI_00121:0.0211802)n3:0.0137249)n2:0.0958642)n1:0.192359)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000309_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000309_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a3e5280affc4c560593c7b47f025848cfc32d84
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000309_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000311_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000311_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..698951a592561e46fd31fe3ee138e65257fa2939
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000311_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00220:0.300935,(AS2_ACLBLIBL_00279:0.0749548,((SA211_MHAAABBN_02124:0.00334266,KBS0714_MOLHKGIG_00111:7.88572e-07)n3:0.00080698,TT9_LFPAFLNI_00106:0.00254069)n2:0.105215)n1:0.300935)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000316_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000316_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c96ad20d88817592216ee6df98b871e1f92391d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000316_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00225:0.0944171,(((TT9_LFPAFLNI_00101:0.00321775,KBS0714_MOLHKGIG_00106:0.00564125)n3:0.00608925,SA211_MHAAABBN_02119:0.00419425)n2:0.0821338,AS2_ACLBLIBL_00284:0.0728518)n1:0.0944171)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000317_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000317_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84303ad51e4b48db7bfd3724cd4a22c6063b192c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000317_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00232:0.338139,((KBS0714_MOLHKGIG_00104:0.0312685,(SA211_MHAAABBN_02117:0.0183057,TT9_LFPAFLNI_00099:0.0292682)n3:0.0072205)n2:0.0995865,AS2_ACLBLIBL_00286:0.255642)n1:0.338139)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000318_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000318_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff3dd55219163ac0f0918e667a219047569ee904
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000318_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00233:0.0920817,(AS2_ACLBLIBL_00287:0.0485156,((SA211_MHAAABBN_02116:0.00291238,TT9_LFPAFLNI_00098:0.0160256)n3:0.00253513,KBS0714_MOLHKGIG_00103:0.0115364)n2:0.0895951)n1:0.0920817)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000320_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000320_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1edf19a561d1551d7bacdd87925ca016bf7ea50
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000320_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00235:0.248849,((KBS0714_MOLHKGIG_00101:0,SA211_MHAAABBN_02114:0)n2:0.0337498,(AS2_ACLBLIBL_00289:0.105492,TT9_LFPAFLNI_00096:0.0609512)n3:0.0701897)n1:0.248849)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000322_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000322_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4a9c21ea75f295df2a50b0ac65176c985f1dbc8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000322_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00238:0.0859011,(((KBS0714_MOLHKGIG_00098:0,TT9_LFPAFLNI_00093:0)n3:0.00069725,SA211_MHAAABBN_02111:0.0162697)n2:0.170815,AS2_ACLBLIBL_00293:0.171404)n1:0.0859011)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000324_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000324_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..422e24e52b6e1b3d054c127ba154ade706257328
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000324_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00240:0.0511757,((KBS0714_MOLHKGIG_00096:0.00605025,(TT9_LFPAFLNI_00091:0.00398725,SA211_MHAAABBN_02109:0.00083575)n3:0.00690025)n2:0.0669068,AS2_ACLBLIBL_00295:0.100721)n1:0.0511757)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000326_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000326_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1968abfcf8c8b689be3c6eb9e1dfd07d1aa69ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000326_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00242:0.23404,(AS2_ACLBLIBL_00297:0.210753,(SA211_MHAAABBN_02107:0.0166687,(KBS0714_MOLHKGIG_00094:0.002366,TT9_LFPAFLNI_00089:0.007203)n3:0.00983425)n2:0.260768)n1:0.23404)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000327_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000327_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af6b842f2e8c78f43a8bcafb668f8f0e1865f7c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000327_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00243:0.103811,(AS2_ACLBLIBL_00298:0.0461525,(SA211_MHAAABBN_02106:0.00896211,(KBS0714_MOLHKGIG_00093:0.00071485,TT9_LFPAFLNI_00088:9.15e-06)n3:0.00818489)n2:0.0323149)n1:0.103811)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000335_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000335_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd34e6a42565949471834e40621ff497cf290d4a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000335_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00251:0.243345,(AS2_ACLBLIBL_00307:0.120451,(KBS0714_MOLHKGIG_00084:0.0132625,(TT9_LFPAFLNI_00079:0,SA211_MHAAABBN_02097:0)n3:0.0202975)n2:0.053005)n1:0.243345)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000337_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000337_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..292a92cfc800c31dd4dcec8ab982df6d88a493f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000337_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00253:0.221913,(AS2_ACLBLIBL_00312:0.221575,((KBS0714_MOLHKGIG_00081:0.00015175,TT9_LFPAFLNI_00075:0.00077325)n3:0.00752275,SA211_MHAAABBN_02094:0.00827975)n2:0.168609)n1:0.221913)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000341_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000341_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fff07bc5c8da806b0dd60176dd455c1b7e4dafd1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000341_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00257:0.107629,(AS2_ACLBLIBL_00316:0.0298874,((SA211_MHAAABBN_02090:0.0105849,TT9_LFPAFLNI_00071:0.00990812)n3:0.00463163,KBS0714_MOLHKGIG_00077:0.00353188)n2:0.0182241)n1:0.107629)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000343_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000343_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34e4c8b84b73913226773953ad1735a17c643192
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000343_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00260:0.0636932,(AS2_ACLBLIBL_00319:0.0172576,(TT9_LFPAFLNI_00068:0.00274287,(SA211_MHAAABBN_02087:0.00083888,KBS0714_MOLHKGIG_00074:0.00028412)n3:0.00081462)n2:0.0357841)n1:0.0636932)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000344_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000344_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1332e420bdb3edad37836f39629c2259fe89b6b3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000344_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00262:0.0101298,(AS2_ACLBLIBL_00320:0.0315933,((KBS0714_MOLHKGIG_00072:0,SA211_MHAAABBN_02085:0)n3:0.00103644,TT9_LFPAFLNI_00066:0.00461356)n2:0.0332578)n1:0.0101298)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000345_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000345_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e85a17cfbc7a3a5c29c542bfb9abf1b2cd2f70db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000345_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000347_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000347_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d1e5d350bcf5cf4dd458300de6879460606d716
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000347_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000348_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000348_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3de5ef6e11e6b3cd73315ebd32116dff53b8a384
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000348_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00267:0.0761272,((TT9_LFPAFLNI_00061:0.00241945,(SA211_MHAAABBN_02080:0,KBS0714_MOLHKGIG_00067:0)n3:0.00401155)n2:0.0450878,AS2_ACLBLIBL_00327:0.148028)n1:0.0761272)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000351_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000351_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52d74f20308cbb04ec382c8d1d4044e42174a4f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000351_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00274:0.0472863,(AS2_ACLBLIBL_00333:0.19579,(KBS0714_MOLHKGIG_00062:0.003993,(SA211_MHAAABBN_02075:0.007586,TT9_LFPAFLNI_00057:0.004013)n3:0.0047435)n2:0.25125)n1:0.0472863)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000353_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000353_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e4699d53d755ef2badc04a6fa0674d22f7efba8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000353_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00276:0.135546,(AS2_ACLBLIBL_00335:0.097742,(SA211_MHAAABBN_02073:0.0182548,(TT9_LFPAFLNI_00055:0.00375275,KBS0714_MOLHKGIG_00060:0.00401725)n3:0.00892275)n2:0.139053)n1:0.135546)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000355_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000355_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fb1f44dd58a817901810696ac5353937fa4def0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000355_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00278:0.18872,(AS2_ACLBLIBL_00338:0.134075,(SA211_MHAAABBN_02070:0.0059605,(KBS0714_MOLHKGIG_00057:0.00348725,TT9_LFPAFLNI_00052:0.00294775)n3:0.0008675)n2:0.07292)n1:0.18872)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000358_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000358_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b7f15365e254faee16d8269b8033e55c0d23e57
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000358_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000359_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000359_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46574cb73e6bdbd4d49f4ac2edcb2928f288284
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000359_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000361_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000361_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d7a4b45d273a0d39f94715a87fffc6dfb61101a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000361_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01218:1.06784,((KBS0714_MOLHKGIG_00050:0.0088175,(SA211_MHAAABBN_02063:0.0249295,TT9_LFPAFLNI_00045:0.0049915)n3:0.0151135)n2:0.121476,AS2_ACLBLIBL_00353:0.0869967)n1:1.06784)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000367_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000367_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..557605db10b0b78d5018645caacd3af18c8edbdf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000367_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00302:0.0298454,((TT9_LFPAFLNI_00034:0.006956,(SA211_MHAAABBN_02052:0.0054225,KBS0714_MOLHKGIG_00039:1.87355e-07)n3:0.001227)n2:0.037334,AS2_ACLBLIBL_00361:0.0770592)n1:0.0298454)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000369_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000369_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8931d7addc99b4f3eeb9f13717fb08f3ec29da77
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000369_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00463:0.0911221,(AS2_ACLBLIBL_00365:0.0831979,((KBS0714_MOLHKGIG_00033:0.00232437,SA211_MHAAABBN_02050:0.00134563)n3:0.00166137,TT9_LFPAFLNI_00032:0.00323862)n2:0.102689)n1:0.0911221)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000370_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000370_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9336b0245b7b5b24cb9f06e18d9c9c8133a91186
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000370_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00304:0.0689017,(AS2_ACLBLIBL_00366:0.0167207,(KBS0714_MOLHKGIG_00032:1.73089e-07,(TT9_LFPAFLNI_00031:0.0031745,SA211_MHAAABBN_02049:0.0031645)n3:0.00243291)n2:0.00984753)n1:0.0689017)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000373_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000373_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc98d6d63cd37b7aaec5db9483196cc618eb75a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000373_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00356:0.0813447,(AS2_ACLBLIBL_00374:0.0161337,(TT9_LFPAFLNI_00022:0.00156202,(KBS0714_MOLHKGIG_00022:0.0022418,SA211_MHAAABBN_02040:0.0005712)n3:0.00181848)n2:0.00680201)n1:0.0813447)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000375_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000375_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a89074cd54fc26763d6cc6f941487d6a6ef9c203
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000375_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00358:0.168914,(AS2_ACLBLIBL_00376:0.08046,(KBS0714_MOLHKGIG_00020:0.0184562,(SA211_MHAAABBN_02038:0.0140411,TT9_LFPAFLNI_00020:0.0160869)n3:0.0117008)n2:0.0605274)n1:0.168914)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000376_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000376_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7d38690e7829729809fa9ae18963e4b93495e91
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000376_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00359:0.287674,(AS2_ACLBLIBL_00377:0.318581,(SA211_MHAAABBN_02037:0.0501554,(TT9_LFPAFLNI_00019:0.0382884,KBS0714_MOLHKGIG_00019:0.0362956)n3:0.0156731)n2:0.181801)n1:0.287674)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000377_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000377_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22c033df1371019b361475b4be9f9af2038eab34
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000377_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00360:0.0552901,((SA211_MHAAABBN_02036:0.00180337,(TT9_LFPAFLNI_00018:0.00718937,KBS0714_MOLHKGIG_00018:0.00467363)n3:0.00055513)n2:0.0391986,AS2_ACLBLIBL_00379:0.0499389)n1:0.0552901)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000378_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000378_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dbf2bc6a18595c44f7e0314f0c52784f02a0cff4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000378_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00361:0.126291,(AS2_ACLBLIBL_00380:0.0785126,(TT9_LFPAFLNI_00017:4.04251e-07,(KBS0714_MOLHKGIG_00017:0.00942187,SA211_MHAAABBN_02035:0.00361612)n3:0.00215538)n2:0.0588314)n1:0.126291)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000380_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000380_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..662ee3655e5de2c61fdf5f16c86400af6953e555
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000380_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00363:0.0100082,(AS2_ACLBLIBL_00382:0.0270835,(KBS0714_MOLHKGIG_00015:0,(SA211_MHAAABBN_02033:0,TT9_LFPAFLNI_00015:0)n3:0)n2:0.0339395)n1:0.0100082)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000382_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000382_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9405010a99ced20487ddc779f57407ef5e75d812
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000382_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02182:0.0364264,(AS2_ACLBLIBL_00385:0.205152,(TT9_LFPAFLNI_00613:0.0134259,(KBS0714_MOLHKGIG_00643:0.00611774,SA211_MHAAABBN_00380:0.00964126)n3:0.00565511)n2:0.0538028)n1:0.0364264)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000383_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000383_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8f085d2fabd361ec06774beff5ecaf21ccbe4d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000383_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02181:0.142065,(((SA211_MHAAABBN_02029:0.0139413,KBS0714_MOLHKGIG_00011:0.00520267)n3:0.00164457,TT9_LFPAFLNI_00011:0.00024798)n2:0.0717949,AS2_ACLBLIBL_00386:0.0743763)n1:0.142065)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000386_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000386_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db7b317db943b7191f476d725ef891d89a8ea883
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000386_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00408:0.143531,(KD337_16_NAFOICDF_02192:4.16729e-07,KD337_16_NAFOICDF_02193:0.0311216)n2:0.00345795)n1:0.0800832,(KBS0714_MOLHKGIG_00636:0.00151917,TT9_LFPAFLNI_00595:0.00199583)n3:0.299053)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000387_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000387_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50a16d94ddcbefc32b772571f2a42583d2187b38
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000387_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00367:0.365113,((KBS0714_MOLHKGIG_00009:0.0219218,(TT9_LFPAFLNI_00009:0,SA211_MHAAABBN_02014:0)n3:0.00299325)n2:0.0733957,AS2_ACLBLIBL_00415:0.0509737)n1:0.365113)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000388_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000388_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4ef9b055e1a038ced056701e3a95e1d46f75224
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000388_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00369:0.14419,(AS2_ACLBLIBL_00417:0.064871,((TT9_LFPAFLNI_00007:0,SA211_MHAAABBN_02012:0)n3:0.002371,KBS0714_MOLHKGIG_00007:4.45212e-07)n2:0.0919605)n1:0.14419)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000389_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000389_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfdab7ba68cbfca28bbf3d829beda81a36fd12d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000389_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00370:0.0489391,(((SA211_MHAAABBN_02011:0.00117137,TT9_LFPAFLNI_00006:0.00028863)n3:0.00216863,KBS0714_MOLHKGIG_00006:0.00543937)n2:0.0306456,AS2_ACLBLIBL_00418:0.0437689)n1:0.0489391)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000395_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000395_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d118daad1648f975f97a1658daf45d2fec4f53b7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000395_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00377:0.0111542,(((KBS0714_MOLHKGIG_02312:5e-07,SA211_MHAAABBN_02005:5e-07)n3:0,TT9_LFPAFLNI_02253:5e-07)n2:0.029689,AS2_ACLBLIBL_00424:0.0144475)n1:0.0111542)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000396_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000396_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae7cc14854f1dc15fea6065971c8a9893d178b46
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000396_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00378:0.270615,(AS2_ACLBLIBL_00425:0.0801053,((TT9_LFPAFLNI_02252:0,SA211_MHAAABBN_02004:0)n3:0.0187506,KBS0714_MOLHKGIG_02311:0.0269024)n2:0.0249441)n1:0.270615)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000398_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000398_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..029e18c5211fd41a81da5b9f67a0245bd21d4f8e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000398_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00380:0.0636402,((AS2_ACLBLIBL_00427:0.023115,KBS0714_MOLHKGIG_02309:0.004235)n2:0.0190025,(SA211_MHAAABBN_02002:0.002098,TT9_LFPAFLNI_02250:0.004323)n3:0.027939)n1:0.0636402)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000400_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000400_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64881a9cf8c8bb3121d10eff1d97e6098f2c8920
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000400_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00382:0.136052,((SA211_MHAAABBN_02000:3.52331e-07,(KBS0714_MOLHKGIG_02307:0.00659232,TT9_LFPAFLNI_02248:3.52331e-07)n3:0.00321032)n2:0.0294119,AS2_ACLBLIBL_00429:0.042089)n1:0.136052)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000402_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000402_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9edc4366ca89b368c70fba8c61b8c2df2e94a033
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000402_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00385:0.043949,(((SA211_MHAAABBN_01997:0,KBS0714_MOLHKGIG_02304:0)n3:0,TT9_LFPAFLNI_02245:0)n2:0.04794,AS2_ACLBLIBL_00433:0.016439)n1:0.043949)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000403_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000403_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9465636ac11a6e04126d76b518a04a3da25239b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000403_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00387:0.332545,(((SA211_MHAAABBN_01995:0.0327827,TT9_LFPAFLNI_02243:0.0432932)n3:0.035178,KBS0714_MOLHKGIG_02302:0.078317)n2:0.044299,AS2_ACLBLIBL_00435:0.684919)n1:0.332545)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000404_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000404_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3c7034081a007ba79a991d2d7cea18ea0b0520e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000404_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000405_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000405_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..282a28a81481bfc75407f2c6c479f43a479d2c9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000405_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00390:0.0595124,((SA211_MHAAABBN_01992:0.00752905,(TT9_LFPAFLNI_02240:0.00044642,KBS0714_MOLHKGIG_02299:0.00164758)n3:0.00358965)n2:0.0339096,AS2_ACLBLIBL_00437:0.0312942)n1:0.0595124)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000409_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000409_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..725de889d50a7360df9fd853a1303088842478c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000409_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00396:0.144744,(AS2_ACLBLIBL_00443:0.0865318,((SA211_MHAAABBN_01986:0.00666999,TT9_LFPAFLNI_02234:0.00018101)n3:0.00276019,KBS0714_MOLHKGIG_02293:0.010834)n2:0.0660446)n1:0.144744)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000412_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000412_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5222caa93175937e272976a5a77cfa32c2096e15
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000412_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000414_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000414_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..098148d0db158958df8f754843dfe7545214959a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000414_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00400:0.0034245,(KBS0714_MOLHKGIG_02290:0,(AS2_ACLBLIBL_00448:0,(SA211_MHAAABBN_01982:0,TT9_LFPAFLNI_02230:0)n3:0)n2:0)n1:0.0034245)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000416_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000416_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f992feb99442d3159414fe537693802f8c0b595c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000416_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00403:0.113218,((SA211_MHAAABBN_01978:0.0133456,(KBS0714_MOLHKGIG_02287:0.00491238,TT9_LFPAFLNI_02226:0.00741662)n3:0.00565987)n2:0.0193109,AS2_ACLBLIBL_00450:0.0309519)n1:0.113218)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000418_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000418_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a7fee8df691db375480289f563e51323c87d96b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000418_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000419_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000419_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e5e77160b7812c014b4baab35c61e0cc99b678a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000419_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00406:0.00823084,(((KBS0714_MOLHKGIG_02282:0.00138017,SA211_MHAAABBN_01973:0.00089383)n3:0.00166114,TT9_LFPAFLNI_02221:0.00352144)n2:0.00185304,AS2_ACLBLIBL_00454:0.0116443)n1:0.00823084)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000421_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000421_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be2d53592aa216c29a993df380b662012634e5f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000421_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000422_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000422_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad307da7562fa898e73415cacadcbb9de10c93e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000422_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000425_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000425_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52f0b9ad6f7163ecdfd078f71f772a64fe49ac85
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000425_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00431:0.0023425,(((KBS0714_MOLHKGIG_02255:0.008158,SA211_MHAAABBN_01955:3.3945e-08)n3:1.8e-05,TT9_LFPAFLNI_02186:3.3945e-08)n2:0.004685,AS2_ACLBLIBL_00476:0.016435)n1:0.0023425)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000426_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000426_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0dd07a88d59bb3db3fcd3be21bd1c50c78da2ce5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000426_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000428_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000428_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f77cda6683fa4cd0c4f63cf5d3cce873ed9fa29
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000428_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000429_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000429_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e27d74b897310f6cd2e3233a158f7a35f33f5324
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000429_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000430_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000430_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c9c01674de82d1b896fbc9c13f805fdc3566f62
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000430_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000432_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000432_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f099273c02992b8f729527fa2a3e0590a77c33ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000432_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000437_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000437_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b1dde2ee290c56ad19049c76bdc2fb2603074b0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000437_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000441_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000441_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e1d939a51633b63f5b4f7e48a43adddacf62a4d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000441_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000444_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000444_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65554aa0e3de0123f9d0b4de69e380315e58fea1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000444_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000445_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000445_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1968ea1dd6c56b08dd40bb7c4a1200a102311eda
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000445_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000446_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000446_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98a494ece7dd83c6f278824148f5b9206c19ff88
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000446_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000447_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000447_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99a70ab9e3b7acc4c59b07d3cb51e811a2832395
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000447_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000449_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000449_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c15225b74220e9136e559a88dfc30d242b66a8e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000449_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00484:0.1516,(AS2_ACLBLIBL_00557:0.0300423,(TT9_LFPAFLNI_02134:4.13626e-07,(SA211_MHAAABBN_01903:0,KBS0714_MOLHKGIG_02189:0)n3:0.00201006)n2:0.0790533)n1:0.1516)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000451_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000451_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a53093990645909b7bb340ef115783f6ec39d641
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000451_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00489:0.157424,((KBS0714_MOLHKGIG_02186:0.0119796,(SA211_MHAAABBN_01900:0.00660587,TT9_LFPAFLNI_02131:0.0222391)n3:0.00984927)n2:0.0788012,AS2_ACLBLIBL_00563:0.0837685)n1:0.157424)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000453_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000453_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb4a421fe43874bdb27362e88106fb680929548c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000453_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00492:0.332187,(AS2_ACLBLIBL_00567:0.414034,(SA211_MHAAABBN_01897:0.0140314,(KBS0714_MOLHKGIG_02183:0.0179063,TT9_LFPAFLNI_02128:0.00907769)n3:0.0107896)n2:0.374686)n1:0.332187)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000454_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000454_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5c463f3f9f2f2c2b2b3a8fd3d8c4d89ce37e283
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000454_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00495:0.0870779,(((KBS0714_MOLHKGIG_02182:0.0167531,TT9_LFPAFLNI_02127:0.0162849)n3:0.0137751,SA211_MHAAABBN_01896:0.0184184)n2:0.18591,AS2_ACLBLIBL_00568:0.250662)n1:0.0870779)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000456_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000456_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dd1d5a7397dd66c49ec6549a6370992b749091f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000456_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00499:0.190788,(AS2_ACLBLIBL_00572:0.0903155,(TT9_LFPAFLNI_02125:0.023907,(SA211_MHAAABBN_01894:0.0109217,KBS0714_MOLHKGIG_02180:0.0008853)n3:0.01058)n2:0.0796765)n1:0.190788)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000457_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000457_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..905439318c180160dffe7a913e609f9b3cea87eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000457_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00500:0.129466,((TT9_LFPAFLNI_02124:0.00237187,(KBS0714_MOLHKGIG_02179:0.00088087,SA211_MHAAABBN_01893:0.00336213)n3:0.00722562)n2:0.0248476,AS2_ACLBLIBL_00573:0.0489676)n1:0.129466)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000460_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000460_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4e45606b24b086c9609acd20553d93f83b35253
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000460_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00503:0.119857,(AS2_ACLBLIBL_00576:0.313277,(KBS0714_MOLHKGIG_02176:0.00323551,(SA211_MHAAABBN_01890:0.0151043,TT9_LFPAFLNI_02121:8.21949e-07)n3:0.00244349)n2:0.248209)n1:0.119857)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000462_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000462_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7d9a3d1da54463886afc12376846185c93b7d47
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000462_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00506:0.142663,((TT9_LFPAFLNI_02118:0.00066293,(SA211_MHAAABBN_01887:0,KBS0714_MOLHKGIG_02173:0)n3:0.00661607)n2:0.0410471,AS2_ACLBLIBL_00579:0.0389445)n1:0.142663)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000463_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000463_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6182ee937edbd744d37e932c5b652879b029d1b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000463_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00508:0.134179,(AS2_ACLBLIBL_00582:0.0717363,(TT9_LFPAFLNI_02115:0.00451434,(KBS0714_MOLHKGIG_02170:0.00464858,SA211_MHAAABBN_01884:0.00532542)n3:0.00257916)n2:0.0799355)n1:0.134179)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000465_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000465_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..beddcaa05d31bee7a79ea5a96bd4d05496475834
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000465_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00512:0.0715941,(AS2_ACLBLIBL_00585:0.106958,(TT9_LFPAFLNI_02112:0.0301421,(KBS0714_MOLHKGIG_02167:0.00440563,SA211_MHAAABBN_01881:0.00823937)n3:0.00966538)n2:0.0394414)n1:0.0715941)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000466_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000466_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac77b6ded7737e5f043c067233c2a15af4ccc1f2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000466_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00695:0.0102557,AS2_ACLBLIBL_00586:0.189345)n1:0.0175386,(TT9_LFPAFLNI_02027:0.0157592,(SA211_MHAAABBN_01793:0,KBS0714_MOLHKGIG_02088:0)n3:0.0119758)n2:0.0175386)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000467_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000467_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..132cf637e839ddb4b536144ef95fde06a54a2323
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000467_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00516:0.239751,(AS2_ACLBLIBL_00593:0.163586,(KBS0714_MOLHKGIG_02164:0.0283865,(SA211_MHAAABBN_01878:0,TT9_LFPAFLNI_02109:0)n3:0.0272425)n2:0.203696)n1:0.239751)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000468_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000468_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f7640fa1e0e1d7ec46752df002641f0ed6af641
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000468_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00517:0.117594,((TT9_LFPAFLNI_02108:0,(KBS0714_MOLHKGIG_02163:0.0121127,SA211_MHAAABBN_01877:4.63644e-07)n3:0.00045266)n2:0.0984491,AS2_ACLBLIBL_00594:0.117894)n1:0.117594)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000470_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000470_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41107da5ee939bfb49348323241d9d66a0f22409
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000470_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00521:0.16495,(AS2_ACLBLIBL_00599:0.260236,(TT9_LFPAFLNI_02103:0.041724,(SA211_MHAAABBN_01872:0.00178412,KBS0714_MOLHKGIG_02159:7.70284e-07)n3:0.0176285)n2:0.119022)n1:0.16495)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000472_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000472_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d85cc91d87adde5098ca79cc11123954781fc05d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000472_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00523:0.0498803,(((KBS0714_MOLHKGIG_02157:0.002325,TT9_LFPAFLNI_02100:0.00047)n3:0.00232275,SA211_MHAAABBN_01870:3.29248e-07)n2:0.105565,AS2_ACLBLIBL_00601:0.118887)n1:0.0498803)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000475_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000475_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a73443a8ab3e1213f5731239191cedaa2e83c14c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000475_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00535:0.237174,(AS2_ACLBLIBL_00611:0.098459,(TT9_LFPAFLNI_02094:0.0048605,(KBS0714_MOLHKGIG_02151:0.00630825,SA211_MHAAABBN_01864:7.70958e-07)n3:0.006222)n2:0.181582)n1:0.237174)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000476_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000476_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a48ce6604ebf9b2f93efb5b80a934ca9859623a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000476_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00536:0.156013,(AS2_ACLBLIBL_00612:0.0786337,((SA211_MHAAABBN_01863:0,KBS0714_MOLHKGIG_02150:0)n3:0.0166929,TT9_LFPAFLNI_02093:0.00532307)n2:0.047085)n1:0.156013)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000477_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000477_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..806940feb1055c90ae876d6bcf323855c3b177e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000477_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00537:0.165504,(AS2_ACLBLIBL_00613:0.081979,((KBS0714_MOLHKGIG_02149:0.006175,TT9_LFPAFLNI_02092:0.006834)n3:0.0084275,SA211_MHAAABBN_01862:0.0138045)n2:0.0656465)n1:0.165504)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000482_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000482_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f64598de5b4453a4a70ee40bb70f033e992e841
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000482_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00550:0.0771124,((KBS0714_MOLHKGIG_02146:0.236242,AS2_ACLBLIBL_00626:0.75663)n2:0.0751747,(SA211_MHAAABBN_01853:5e-07,TT9_LFPAFLNI_02083:5e-07)n3:0.178862)n1:0.0771124)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000489_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000489_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f51eac84ce6347f4ed4acd253a85cd1d041ca54
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000489_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000490_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000490_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e91677ba17b502aca47dafb64ef9d10c42d0e2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000490_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000491_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000491_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..762cbd3a2ef7641345f52fcf1007b0122d90abb0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000491_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000492_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000492_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e506e84c4ea2a69bb855fc7c8a2fe04a15d93fe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000492_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00563:0.0274086,(AS2_ACLBLIBL_00647:0.0349327,(SA211_MHAAABBN_01841:0.00521025,(TT9_LFPAFLNI_02071:0.00176025,KBS0714_MOLHKGIG_02133:0.00457175)n3:0.00754575)n2:0.0172677)n1:0.0274086)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000498_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000498_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..561dab07f0c5012161d3031e8656865e1c693157
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000498_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00569:0.0146936,((KBS0714_MOLHKGIG_02127:0.00839138,TT9_LFPAFLNI_02065:0.00894162)n2:0.0170374,(AS2_ACLBLIBL_00653:0.0229414,SA211_MHAAABBN_01835:0.0103076)n3:0.0129669)n1:0.0146936)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000501_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000501_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8929853a1a58f8c731b0bf246ea7df59cf9fb07b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000501_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00574:0.00306478,((TT9_LFPAFLNI_02061:0,SA211_MHAAABBN_01831:0)n2:0.0143324,(KBS0714_MOLHKGIG_02123:0.014131,AS2_ACLBLIBL_00656:0.076938)n3:0.0017835)n1:0.00306478)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000503_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000503_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef54d1734a468cfcdb7c2bf591f1815986284340
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000503_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00577:0.136405,(AS2_ACLBLIBL_00660:0.13226,(KBS0714_MOLHKGIG_02120:0,(TT9_LFPAFLNI_02058:0,SA211_MHAAABBN_01828:0)n3:0)n2:0.146739)n1:0.136405)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000504_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000504_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2030f66ebe987e45e3490955e70395e3202946cb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000504_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00578:0.175483,(AS2_ACLBLIBL_00661:0.147724,((SA211_MHAAABBN_01827:0.00553907,KBS0714_MOLHKGIG_02119:0.00894793)n3:0.0529827,TT9_LFPAFLNI_02057:0.0205144)n2:0.13647)n1:0.175483)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000506_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000506_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e57fd4ed6318c5bbd57e7d91959725897370afa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000506_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00580:0.303535,(AS2_ACLBLIBL_00663:0.176381,(TT9_LFPAFLNI_02055:0.0585539,(SA211_MHAAABBN_01825:0.0114864,KBS0714_MOLHKGIG_02117:9.70509e-07)n3:0.00157063)n2:0.117963)n1:0.303535)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000509_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000509_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..925e4224c0ea3796b64fffef8a2180db8531ba10
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000509_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00583:0.113998,(AS2_ACLBLIBL_00667:0.165378,((KBS0714_MOLHKGIG_02113:0.00808838,SA211_MHAAABBN_01820:0.00909462)n3:0.0096924,TT9_LFPAFLNI_02051:0.0225881)n2:0.0425768)n1:0.113998)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000510_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000510_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9aa189fac81e185aa009e330c0af848f4a1a2536
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000510_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00585:0.0646648,((SA211_MHAAABBN_01817:0.00768015,(KBS0714_MOLHKGIG_02110:0.0016003,TT9_LFPAFLNI_02050:0.0526747)n3:0.00123337)n2:0.0762407,AS2_ACLBLIBL_00668:0.0576993)n1:0.0646648)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000512_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000512_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0e930fa3bcde1700c5e72784d1aeabb71c13928
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000512_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00588:0.40298,(AS2_ACLBLIBL_00672:0.563457,((KBS0714_MOLHKGIG_02107:0,SA211_MHAAABBN_01814:0)n3:0.002922,TT9_LFPAFLNI_02047:0.000138)n2:0.0519055)n1:0.40298)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000513_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000513_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f956e7a23e33e7dd00c720c5f6dc1f4a92809be6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000513_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00589:0.178026,(AS2_ACLBLIBL_00673:0.0723338,(TT9_LFPAFLNI_02046:0.00369677,(KBS0714_MOLHKGIG_02106:0.00404856,SA211_MHAAABBN_01813:5.65619e-07)n3:0.00397323)n2:0.125969)n1:0.178026)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000516_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000516_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a3d5506732c4c473adbc00d231fdc0e1d53a24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000516_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00591:0.437372,(AS2_ACLBLIBL_00676:0.154523,(TT9_LFPAFLNI_02043:0.0139545,(SA211_MHAAABBN_01810:5e-07,KBS0714_MOLHKGIG_02103:5e-07)n3:0.007187)n2:0.194646)n1:0.437372)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000517_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000517_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7120769171b831548363075abe30ddb8b61dd02c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000517_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00592:0.360011,(((KBS0714_MOLHKGIG_02102:0,SA211_MHAAABBN_01809:0)n3:0.004058,TT9_LFPAFLNI_02042:0.002681)n2:0.313765,AS2_ACLBLIBL_00677:0.182725)n1:0.360011)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000519_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000519_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd2607a16d4bc78be4464af4ef638d86fe62d269
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000519_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00598:0.0140756,(TT9_LFPAFLNI_02034:0.157963,((AS2_ACLBLIBL_00683:0.143989,SA211_MHAAABBN_01803:0.0332296)n3:0.0228466,KBS0714_MOLHKGIG_02095:0.0186004)n2:0.0124416)n1:0.0140756)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000520_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000520_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0a3a4b5e296352da8982f2ea7d7132c785de890
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000520_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00686:0.00552938,((KD337_16_NAFOICDF_00413:0.169521,KD337_16_NAFOICDF_00937:2.17161)n3:0.19721,KD337_16_NAFOICDF_00602:0.0359394)n2:0.00399326)n1:0.00718044,KBS0714_MOLHKGIG_02092:0.0120606)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000521_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000521_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0832298246a4606bd9ce50c143b1d89d65e5577c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000521_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00606:0.00357525,(AS2_ACLBLIBL_00696:0.0241295,((KBS0714_MOLHKGIG_02087:0,SA211_MHAAABBN_01792:0)n3:0.00886208,TT9_LFPAFLNI_02026:0.00480492)n2:0.001522)n1:0.00357525)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000525_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000525_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75158620788dbb87d5909d025f3c43fd3175b6d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000525_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00610:0.00624025,((TT9_LFPAFLNI_02022:0.004154,(SA211_MHAAABBN_01788:0,KBS0714_MOLHKGIG_02083:0)n3:0.000352)n2:0.0140935,AS2_ACLBLIBL_00700:0.0056155)n1:0.00624025)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000527_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000527_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..362b22278fd28e5ae0159700a190f57e4395dffd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000527_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00613:0.0023015,((TT9_LFPAFLNI_02019:0,KBS0714_MOLHKGIG_02081:0)n2:0.000653,(AS2_ACLBLIBL_00703:0.01249,SA211_MHAAABBN_01785:1.7085e-08)n3:1.3e-05)n1:0.0023015)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000528_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000528_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01b7d35fd75e786338b07f1cd66ccd52f39eab28
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000528_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00614:0.00914882,(KBS0714_MOLHKGIG_02080:0.0189964,((SA211_MHAAABBN_01784:0.00637583,TT9_LFPAFLNI_02018:0.00590517)n3:0.00738002,AS2_ACLBLIBL_00704:0.313757)n2:0.00481981)n1:0.00914882)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000529_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000529_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00d4aca2372db036657fea1e2b99598e6f32a69e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000529_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00726:0.0480613,(((SA211_MHAAABBN_01761:5.27865e-07,KBS0714_MOLHKGIG_02055:0.00703239)n3:0.00093563,TT9_LFPAFLNI_01989:0.165346)n2:0.161136,AS2_ACLBLIBL_00711:0.0976693)n1:0.0480613)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000531_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000531_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10c7c4222e08f482fbff6057f43d6e3d2b766f0b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000531_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00554:0.0334218,(AS2_ACLBLIBL_00716:0.272102,(SA211_MHAAABBN_01849:0.0103934,(KBS0714_MOLHKGIG_02141:0.0164669,TT9_LFPAFLNI_02079:0.0188281)n3:0.00685957)n2:0.0516655)n1:0.0334218)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000532_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000532_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd7db3a69fa99c1219e1eee2cd1b5f3726a40008
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000532_tree.txt
@@ -0,0 +1 @@
+((SA211_MHAAABBN_01768:1.40313e-06,(AS2_ACLBLIBL_00729:0.722077,(AS2_ACLBLIBL_02365:1.40313e-06,AS2_ACLBLIBL_00728:0.613883)n3:0.220027)n2:0.0244474)n1:0.0668459,KBS0714_MOLHKGIG_00608:1.40313e-06)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000533_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000533_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..606aa70236011163906fd55aab3695e37b11133e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000533_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00723:0.261142,((TT9_LFPAFLNI_01994:0.049236,(SA211_MHAAABBN_01764:0.00584625,KBS0714_MOLHKGIG_02058:0.00416675)n3:0.058208)n2:0.146461,AS2_ACLBLIBL_00760:0.259758)n1:0.261142)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000535_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000535_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd07213900c173e8c3ea7ea8a1ee1e5c3feeb7b5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000535_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00728:0.0669595,(AS2_ACLBLIBL_00764:0.115221,(KBS0714_MOLHKGIG_02056:0.013587,(SA211_MHAAABBN_01762:0,TT9_LFPAFLNI_01990:0)n3:0.00653)n2:0.147236)n1:0.0669595)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000537_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000537_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72bffe585a7de96c1418b067a65d66e53ca1f1bd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000537_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00740:0.0925033,((TT9_LFPAFLNI_01986:4.75602e-07,(KBS0714_MOLHKGIG_02052:0.00075462,SA211_MHAAABBN_01758:0.00822437)n3:0.00662412)n2:0.169457,AS2_ACLBLIBL_00770:0.106996)n1:0.0925033)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000539_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000539_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35723daf18a2e1c961738f0c0b75d201d938c61f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000539_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00747:0.00278637,((SA211_MHAAABBN_01743:0,TT9_LFPAFLNI_01971:0)n2:0.0125582,(AS2_ACLBLIBL_00780:0.219094,KBS0714_MOLHKGIG_02036:0.0118763)n3:0.00619975)n1:0.00278637)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000541_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000541_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1ab67d808cb27f5d0fecbd98eaf1eceb1cef1b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000541_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00782:0.63827,(TT9_LFPAFLNI_00966:0.00046134,(KBS0714_MOLHKGIG_01022:1.67565e-06,(SA211_MHAAABBN_00736:0.41306,SA211_MHAAABBN_00737:0.472242)n3:0.0524713)n2:0.224787)n1:0.0815558)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000542_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000542_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13a5f3ec7201f9f0b6953506e2e41dd16f20ca4d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000542_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00749:0.00306873,((TT9_LFPAFLNI_01969:0.00493973,AS2_ACLBLIBL_00783:0.0498343)n2:0.00132862,(SA211_MHAAABBN_01741:0.00179267,KBS0714_MOLHKGIG_02034:0.00087033)n3:0.00481337)n1:0.00306873)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000543_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000543_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4024cb6ecde30c8f775402a0d03ae4f5ca16083
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000543_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01226:0.406074,(AS2_ACLBLIBL_00787:0.0180615,(SA211_MHAAABBN_01740:0,(KBS0714_MOLHKGIG_02033:0,TT9_LFPAFLNI_01968:0)n3:0)n2:0.0375705)n1:0.406074)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000544_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000544_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b17a8fde0361c8850bbc324b5918442841c946fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000544_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00752:0.0618273,(((TT9_LFPAFLNI_01965:0,KBS0714_MOLHKGIG_02028:0)n3:0,SA211_MHAAABBN_01737:0)n2:0.0308025,AS2_ACLBLIBL_00791:0.163077)n1:0.0618273)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000546_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000546_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6aa874ec135f5fceb86580ec1acbcba8fdb5f1c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000546_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00754:0.0124128,((KBS0714_MOLHKGIG_02026:0.0112996,(TT9_LFPAFLNI_01963:5e-07,SA211_MHAAABBN_01735:5e-07)n3:0.00685889)n2:0.0445157,AS2_ACLBLIBL_00793:0.217167)n1:0.0124128)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000548_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000548_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91bb844f07995659e5571878f2ae60fab8ec117b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000548_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02090:0.275297,((SA211_MHAAABBN_01733:0.00244024,(AS2_ACLBLIBL_00795:0.00258306,TT9_LFPAFLNI_01961:0.00219794)n3:0.00259959)n2:0.00482681,KBS0714_MOLHKGIG_02024:0.00472317)n1:0.275297)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000549_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000549_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed410d0b315b765f6d0d7a669e16f7b1de14a48f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000549_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00757:0.0471815,(AS2_ACLBLIBL_00796:0.04009,((KBS0714_MOLHKGIG_02023:0.00220988,TT9_LFPAFLNI_01960:0.00357512)n3:0.00050346,SA211_MHAAABBN_01732:0.00463585)n2:0.00621387)n1:0.0471815)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000552_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000552_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78cc287317eea46ec6b9e02d24276cfba8d6418f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000552_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000557_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000557_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba1a19d09c9bb7cf6f9c83db56a1e0247279dbbc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000557_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00768:0.057628,(KBS0714_MOLHKGIG_02011:0.010488,(TT9_LFPAFLNI_01949:0.00757013,(AS2_ACLBLIBL_00831:0.0399325,SA211_MHAAABBN_01721:0.00588653)n3:0.00944387)n2:0.0101904)n1:0.057628)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000559_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000559_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f831414613d6664649c3c13283750ed375b2788d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000559_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000562_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000562_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..593c6e7d4e4f43ff834c7f26f15fdae9868e6a91
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000562_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00773:0.72074,(AS2_ACLBLIBL_00836:0.259116,(KBS0714_MOLHKGIG_02006:0.0386622,(SA211_MHAAABBN_01716:0.0216073,TT9_LFPAFLNI_01944:0.0234967)n3:0.0123223)n2:0.256954)n1:0.72074)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000564_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000564_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86b41f465a10d30afb608d7cfaf1da87d82d9af5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000564_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00776:0.107832,(((TT9_LFPAFLNI_01941:0.0155326,KBS0714_MOLHKGIG_02003:0.00355338)n3:0.00660338,SA211_MHAAABBN_01713:0.0102176)n2:0.0459429,AS2_ACLBLIBL_00839:0.0347524)n1:0.107832)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000565_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000565_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9890d85b3df630195494bf44a084cc65882b3922
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000565_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00793:0.191623,(AS2_ACLBLIBL_00857:0.072361,(SA211_MHAAABBN_01694:0,(TT9_LFPAFLNI_01926:0,KBS0714_MOLHKGIG_02000:0)n3:0)n2:0.105949)n1:0.191623)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000569_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000569_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bac9070593a18ae50b4d8186b883961849d706b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000569_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00801:0.00896025,(AS2_ACLBLIBL_00863:0.0828825,(SA211_MHAAABBN_01688:1.44155e-07,(TT9_LFPAFLNI_01920:0.0006105,KBS0714_MOLHKGIG_01994:0.0081095)n3:0.00204537)n2:0.0327629)n1:0.00896025)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000571_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000571_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d9d140c12269e00d6bb0f9192cdca6629b941e9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000571_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00803:0.00450393,(AS2_ACLBLIBL_00865:0.0337431,(TT9_LFPAFLNI_01918:0.00451412,(KBS0714_MOLHKGIG_01992:0.00655537,SA211_MHAAABBN_01686:0.00897363)n3:0.00434088)n2:0.0151159)n1:0.00450393)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000573_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000573_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0cb4bdfdfb8490a94af55f3f25fd4064885591be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000573_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000576_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000576_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df599370e3b251c76dfda2d4e31fdc5b745ae30f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000576_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000578_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000578_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5adacfbc6617d5e0f0be0369a264cd6bbfe91f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000578_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000580_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000580_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc582dc340eb3e9528b9fe153c62230a8267765d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000580_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000587_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000587_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2e8fd04b1b9f303fd1e7483a5c539d444318b33
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000587_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00831:0.248113,(AS2_ACLBLIBL_00890:0.0404498,(KBS0714_MOLHKGIG_01969:0.0113955,(TT9_LFPAFLNI_01895:0.00501164,SA211_MHAAABBN_01663:0.00697336)n3:0.0071955)n2:0.0292243)n1:0.248113)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000590_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000590_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..869c6357fad4744ef8d14160c9bb50ddedd86955
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000590_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00439:0.941098,KD337_16_NAFOICDF_00834:0.786482)n1:0.140983,((KBS0714_MOLHKGIG_01963:2.45418e-06,AS2_ACLBLIBL_00894:0.426642)n3:0.0820626,TT9_LFPAFLNI_01889:0.0111989)n2:0.140983)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000591_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000591_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..746e77f67b5691d1e155b0527d5dc100dd8edaca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000591_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00838:0.00698081,(KBS0714_MOLHKGIG_01620:2.09328,(AS2_ACLBLIBL_00900:0.00802088,(SA211_MHAAABBN_01648:0.0183961,TT9_LFPAFLNI_01879:0.0128489)n3:0.00705612)n2:0.0120771)n1:0.00698081)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000600_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000600_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20b247c12455d3e67f50058e0a4d6cba2fddfdd6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000600_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00856:0.086818,(AS2_ACLBLIBL_00922:0.084768,(SA211_MHAAABBN_01633:0.0122904,(KBS0714_MOLHKGIG_01937:0,TT9_LFPAFLNI_01856:0)n3:0.00540665)n2:0.0783348)n1:0.086818)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000602_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000602_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0f39a5713720209bbdc2945db417c46349c96f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000602_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00858:0.0729493,(((SA211_MHAAABBN_01631:0.00036288,KBS0714_MOLHKGIG_01935:0.00347412)n3:0.00149263,TT9_LFPAFLNI_01854:0.00331538)n2:0.124716,AS2_ACLBLIBL_00924:0.16532)n1:0.0729493)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000603_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000603_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97f8d281e4201f19141da91d88e4ae40ab140445
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000603_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00859:0.0922208,(AS2_ACLBLIBL_00925:0.234168,(SA211_MHAAABBN_01630:0.0142157,(KBS0714_MOLHKGIG_01934:0.0057235,TT9_LFPAFLNI_01853:0.0049635)n3:0.0137138)n2:0.131931)n1:0.0922208)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000604_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000604_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3374473d748b9fa4f35eed3fbefc3e4d8fd471e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000604_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00860:0.0997561,(AS2_ACLBLIBL_00926:0.127617,(TT9_LFPAFLNI_01852:0.00708956,(KBS0714_MOLHKGIG_01933:0.0204677,SA211_MHAAABBN_01629:0.00496732)n3:0.00481044)n2:0.0888807)n1:0.0997561)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000606_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000606_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fff499d1c08a93650255db46362bc404a26720bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000606_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00862:0.0615251,(AS2_ACLBLIBL_00928:0.130447,(KBS0714_MOLHKGIG_01930:4.07955e-07,(TT9_LFPAFLNI_01849:0.0081525,SA211_MHAAABBN_01626:4.07955e-07)n3:0.0006245)n2:0.14693)n1:0.0615251)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000608_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000608_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d64979a8bc0bb281d1c6ca3059b1bdbfb8a16f87
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000608_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00863:0.133122,(AS2_ACLBLIBL_00931:0.125805,(TT9_LFPAFLNI_01847:0.00897662,(KBS0714_MOLHKGIG_01928:0.0125411,SA211_MHAAABBN_01624:0.00457287)n3:0.00231187)n2:0.112359)n1:0.133122)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000610_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000610_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1d08f93888c44865cfe74796eb96b13a92e5b1d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000610_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00866:0.00927231,(AS2_ACLBLIBL_00935:0.194612,(SA211_MHAAABBN_01622:0.0125581,(KBS0714_MOLHKGIG_01926:2.35145e-07,TT9_LFPAFLNI_01845:0.00470712)n3:0.00040587)n2:0.00473738)n1:0.00927231)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000614_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000614_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a710240b5f95448a37dbfb7f820d79055caed2f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000614_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00875:0.164895,((TT9_LFPAFLNI_01840:0.00318587,(KBS0714_MOLHKGIG_01920:4.67713e-07,SA211_MHAAABBN_01616:0.00770662)n3:0.0128756)n2:0.0384871,AS2_ACLBLIBL_00940:0.0761134)n1:0.164895)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000615_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000615_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..330180d6ba60a03d6b60286c0b764084f4238039
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000615_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00876:0.124405,(AS2_ACLBLIBL_00941:0.0268134,((KBS0714_MOLHKGIG_01919:0.00822213,SA211_MHAAABBN_01615:0.00503588)n3:0.00581763,TT9_LFPAFLNI_01839:0.00035138)n2:0.0198911)n1:0.124405)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000617_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000617_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30cd7d138024c93da79b11be1ab14ca5c8dd970c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000617_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00884:0.0583801,((KBS0714_MOLHKGIG_01911:0.0237263,(SA211_MHAAABBN_01607:0.002844,TT9_LFPAFLNI_01831:0.004029)n3:0.00776325)n2:0.146907,AS2_ACLBLIBL_00943:0.190996)n1:0.0583801)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000619_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000619_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7eba78443ee0f7b345e5978f511907d34b24884
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000619_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00889:0,(AS2_ACLBLIBL_00949:0,((KBS0714_MOLHKGIG_01909:0,TT9_LFPAFLNI_01829:0)n3:0,SA211_MHAAABBN_01605:0)n2:0.013363)n1:0)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000620_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000620_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4360c24616afcc2e6af584c2b042e45e146deaf9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000620_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00890:0.028192,(TT9_LFPAFLNI_01828:0,(KBS0714_MOLHKGIG_01908:0,(SA211_MHAAABBN_01604:0,AS2_ACLBLIBL_00950:0)n3:0)n2:0)n1:0.028192)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000622_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000622_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0416bbaadf982ca9efb24c831ca730f59e77aec8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000622_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00892:0.279151,(AS2_ACLBLIBL_00952:0.15634,((KBS0714_MOLHKGIG_01906:0.0150847,SA211_MHAAABBN_01602:0.0115832)n3:0.0186565,TT9_LFPAFLNI_01826:0.0132205)n2:0.304287)n1:0.279151)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000624_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000624_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0853e15d519c2aecf95c6a1e68c76566035eaa35
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000624_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00894:0.235575,(((SA211_MHAAABBN_01600:0.00060804,TT9_LFPAFLNI_01824:0.0179)n3:0.0484686,KBS0714_MOLHKGIG_01904:0.0314436)n2:0.124695,AS2_ACLBLIBL_00954:0.180192)n1:0.235575)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000627_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000627_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1cedd5b29a41f98ce008f75df97acd0510b3558c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000627_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00897:0.260406,(AS2_ACLBLIBL_00957:0.147347,(SA211_MHAAABBN_01597:0.0294727,(TT9_LFPAFLNI_01821:0,KBS0714_MOLHKGIG_01901:0)n3:0.0540482)n2:0.0952018)n1:0.260406)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000628_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000628_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fffb647d1af226025c04594b4eeec260c4e1b1fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000628_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00898:0.0903457,((KBS0714_MOLHKGIG_01900:0.00393572,(SA211_MHAAABBN_01596:0.00105099,TT9_LFPAFLNI_01820:0.00253101)n3:0.00901136)n2:0.0792111,AS2_ACLBLIBL_00958:0.0378777)n1:0.0903457)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000629_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000629_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b202a935cc03a1597173af93cddd95578c65fa8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000629_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00899:0.204912,(AS2_ACLBLIBL_00959:0.0975982,((KBS0714_MOLHKGIG_01899:0.0310473,TT9_LFPAFLNI_01819:0.00318067)n3:0.0085231,SA211_MHAAABBN_01595:0.00331682)n2:0.0694412)n1:0.204912)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000632_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000632_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f4133c32d0106563d78494ce255ad6319111fa2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000632_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00906:0.11285,(AS2_ACLBLIBL_00968:0.0770092,(SA211_MHAAABBN_01586:0.016045,(KBS0714_MOLHKGIG_01890:0.0069231,TT9_LFPAFLNI_01810:0.0033829)n3:0.022271)n2:0.0364078)n1:0.11285)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000634_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000634_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cad67caf5d271feeb5a2cb30c9b8c0c42db21c56
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000634_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00908:0.192549,(AS2_ACLBLIBL_00970:0.0766031,((SA211_MHAAABBN_01584:0.00739413,TT9_LFPAFLNI_01808:0.00575187)n3:0.0318159,KBS0714_MOLHKGIG_01888:0.0843571)n2:0.0391834)n1:0.192549)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000637_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000637_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ce9cc535afcc638e7f16efff23bf14b7e07532b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000637_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00911:0.155887,(AS2_ACLBLIBL_00973:0.0442653,((TT9_LFPAFLNI_01805:0,KBS0714_MOLHKGIG_01885:0)n3:0.070659,SA211_MHAAABBN_01581:0.028514)n2:0.0514175)n1:0.155887)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000640_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000640_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d6adabeb40867233efa6023a29540c843b511d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000640_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00914:0.130499,((SA211_MHAAABBN_01578:0.0274117,AS2_ACLBLIBL_00976:0.0653133)n2:0.0292693,(TT9_LFPAFLNI_01802:0,KBS0714_MOLHKGIG_01882:0)n3:0.0882195)n1:0.130499)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000641_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000641_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6aff919ab0b3045225e8c04aa4a6c361ca35879
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000641_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00915:0.175588,(AS2_ACLBLIBL_00977:0.0455812,(SA211_MHAAABBN_01577:0.0119525,(TT9_LFPAFLNI_01801:0.0251316,KBS0714_MOLHKGIG_01881:0.00069735)n3:0.011252)n2:0.071394)n1:0.175588)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000642_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000642_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77785e5fb7bf8d70bee383010644d2ee6c250260
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000642_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00919:0.20518,(AS2_ACLBLIBL_00979:0.111673,((SA211_MHAAABBN_01576:0,KBS0714_MOLHKGIG_01880:0)n3:0.011048,TT9_LFPAFLNI_01800:0.008054)n2:0.119899)n1:0.20518)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000644_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000644_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d28574a70c93b1261f72c21ebaa2310a500e6d6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000644_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00922:0.187806,(AS2_ACLBLIBL_00984:0.0188955,(SA211_MHAAABBN_01571:0.0193765,(TT9_LFPAFLNI_01795:0.0147445,KBS0714_MOLHKGIG_01875:0.0011965)n3:0.0079065)n2:0.0066095)n1:0.187806)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000645_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000645_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9452b168714b15b78267137fae4066cbe3f6da75
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000645_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00923:0.144453,(((KBS0714_MOLHKGIG_01874:0.0131455,SA211_MHAAABBN_01570:0.0195795)n3:0.0453545,TT9_LFPAFLNI_01794:0.029707)n2:0.0168285,AS2_ACLBLIBL_00986:0.266956)n1:0.144453)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000646_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000646_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6cc5e9bb0196dea7fc2c745847f737ff135b788
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000646_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00924:0.2674,((KBS0714_MOLHKGIG_01873:0,SA211_MHAAABBN_01569:0)n2:0.0713018,(AS2_ACLBLIBL_00987:0.00402583,TT9_LFPAFLNI_01793:0.0135442)n3:0.0799152)n1:0.2674)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000647_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000647_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad1555337233df1588c43206c4debb26960aa288
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000647_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00925:0.365595,(AS2_ACLBLIBL_00988:0.161375,(TT9_LFPAFLNI_01792:0.0259176,(KBS0714_MOLHKGIG_01872:0.0146361,SA211_MHAAABBN_01568:0.0256169)n3:0.0155284)n2:0.0908789)n1:0.365595)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000653_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000653_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56d322a094141c4cd61a95b9918e9508a18cc152
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000653_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00932:0.0467408,(AS2_ACLBLIBL_00994:0.0709264,(SA211_MHAAABBN_01562:0.00050187,(KBS0714_MOLHKGIG_01866:0.00081512,TT9_LFPAFLNI_01786:0.00604288)n3:0.00342912)n2:0.0424946)n1:0.0467408)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000657_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000657_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ffb89dd5bbd748d47c035d162c60b03a60acff2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000657_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00945:0.0745681,((SA211_MHAAABBN_01558:0.00857625,(TT9_LFPAFLNI_01782:0,KBS0714_MOLHKGIG_01862:0)n3:0.0138958)n2:0.00171975,AS2_ACLBLIBL_00998:0.00743575)n1:0.0745681)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000658_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000658_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e373ecb3fdce522a84760833e44676652e563147
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000658_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_00999:0.173538,AS2_ACLBLIBL_01510:2.07843)n1:0.119564,(SA211_MHAAABBN_01557:0.0340027,(KBS0714_MOLHKGIG_01861:0.02002,TT9_LFPAFLNI_01781:0.015937)n3:0.00997475)n2:0.119564)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000661_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000661_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..873ab6f233aef0e0b27c318d3b317528f5097b3b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000661_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00946:0.113755,(TT9_LFPAFLNI_01780:0.06581,(AS2_ACLBLIBL_01003:0.142256,(SA211_MHAAABBN_01556:0,KBS0714_MOLHKGIG_01860:0)n3:0.0481104)n2:0.0633025)n1:0.113755)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000662_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000662_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80b072be6a6eec30d331c61f15c4a8827b759fdb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000662_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00947:0.0854513,(AS2_ACLBLIBL_01004:0.0552085,(KBS0714_MOLHKGIG_01859:0.00220025,(TT9_LFPAFLNI_01779:0.003786,SA211_MHAAABBN_01555:0.000158)n3:0.00293375)n2:0.0531843)n1:0.0854513)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000665_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000665_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..880d66dbb66f2f963b4417963c6f09bda86ef81a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000665_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00952:0.029797,(AS2_ACLBLIBL_01008:0.057948,(SA211_MHAAABBN_01552:0.0056315,(KBS0714_MOLHKGIG_01856:0.00273125,TT9_LFPAFLNI_01776:0.00201675)n3:0.001994)n2:0.067426)n1:0.029797)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000667_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000667_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5356141cdc6911f1b739f15e6ee1c12900f6a706
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000667_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00956:0.029159,(AS2_ACLBLIBL_01014:0.089398,(KBS0714_MOLHKGIG_01854:0.00242528,(SA211_MHAAABBN_01550:0.0144871,TT9_LFPAFLNI_01774:0.00100194)n3:0.00634672)n2:0.0533744)n1:0.029159)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000668_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000668_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b13be044dbfc0fd4783410897bb7f0245b4e9cc3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000668_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00957:0.0805074,(AS2_ACLBLIBL_01015:0.181893,((SA211_MHAAABBN_01549:0.00656825,TT9_LFPAFLNI_01773:0.00472075)n3:0.00134075,KBS0714_MOLHKGIG_01853:0.00394225)n2:0.133669)n1:0.0805074)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000671_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000671_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..832151d118a202d0f0a805abcd98fd899a028fe3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000671_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00961:0.134197,(((KBS0714_MOLHKGIG_01849:0.00071837,TT9_LFPAFLNI_01769:0.00191663)n3:0.00279163,SA211_MHAAABBN_01545:0.00448038)n2:0.0639981,AS2_ACLBLIBL_01019:0.0560569)n1:0.134197)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000672_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000672_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b399620f4316d8791c53096c6808e968df567b9c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000672_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00962:0.251731,((TT9_LFPAFLNI_01768:0.0349239,(SA211_MHAAABBN_01544:0.0189428,KBS0714_MOLHKGIG_01848:9.08797e-07)n3:0.0255679)n2:0.149715,AS2_ACLBLIBL_01020:0.180707)n1:0.251731)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000673_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000673_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6eb0cc5c16842331189fe8a9f818c2fdec87b6c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000673_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00963:0.195582,(AS2_ACLBLIBL_01021:0.053335,((SA211_MHAAABBN_01543:0,KBS0714_MOLHKGIG_01847:0)n3:0,TT9_LFPAFLNI_01767:0)n2:0.033906)n1:0.195582)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000674_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000674_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f150a7c6a74c1c4a97455ef0936a3c6faf7aa1dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000674_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000675_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000675_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4fc30eb26223dc33510d7a9d6ccb6815387c784c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000675_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000677_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000677_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e30f452a1578161d176ab9a0c6e455809851d43
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000677_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00969:0.0324793,(AS2_ACLBLIBL_01028:0.0691335,(TT9_LFPAFLNI_01761:0,(SA211_MHAAABBN_01537:0,KBS0714_MOLHKGIG_01840:0)n3:0)n2:0.0136845)n1:0.0324793)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000680_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000680_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3de1b9c8bbc2786233a1c306ab2089b7ccd4241f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000680_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00972:0.0324373,(AS2_ACLBLIBL_01031:0.0041365,((SA211_MHAAABBN_01534:0,TT9_LFPAFLNI_01758:0)n3:0,KBS0714_MOLHKGIG_01837:0)n2:0.0029975)n1:0.0324373)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000681_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000681_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e045b59a2f46d1815e40b2241504e1d8d71c5a30
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000681_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00974:0.105457,(AS2_ACLBLIBL_01033:0.0470848,((TT9_LFPAFLNI_01756:0.00096312,SA211_MHAAABBN_01532:0.00291188)n3:0.00519639,KBS0714_MOLHKGIG_01835:0.00284188)n2:0.0298921)n1:0.105457)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000683_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000683_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6c75083beced9f5e113b0a737c3424c4beb1fec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000683_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01055:0.584478,(AS2_ACLBLIBL_01035:0.119902,(SA211_MHAAABBN_01530:0.0428416,(KBS0714_MOLHKGIG_01833:0.0571547,TT9_LFPAFLNI_01754:0.0675473)n3:0.00331738)n2:0.0488679)n1:0.584478)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000684_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000684_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b28c917550e6fbc595938bdfb1c1f2125baed4a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000684_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00976:0.0420614,(AS2_ACLBLIBL_01036:0.0215762,(KBS0714_MOLHKGIG_01832:1.42459e-07,(SA211_MHAAABBN_01529:1.42459e-07,TT9_LFPAFLNI_01753:0.002673)n3:0.00277387)n2:0.0314185)n1:0.0420614)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000688_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000688_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..975b8a5c746f5faead918d4060c9f75f398039e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000688_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00981:0.284374,(AS2_ACLBLIBL_01042:0.242859,(SA211_MHAAABBN_01524:0.0670474,(TT9_LFPAFLNI_01748:0.0105459,KBS0714_MOLHKGIG_01827:0.00831807)n3:0.0173611)n2:0.100665)n1:0.284374)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000689_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000689_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..990b5386022268abd155f103d3f5afaf259cd417
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000689_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00982:0.232937,(((TT9_LFPAFLNI_01747:0,KBS0714_MOLHKGIG_01826:0)n3:0.0164218,SA211_MHAAABBN_01523:0.0270632)n2:0.116576,AS2_ACLBLIBL_01043:0.161542)n1:0.232937)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000691_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000691_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7dec5b3828338aaef9eaf9f6b1eac318b01958d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000691_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00984:0.392088,(AS2_ACLBLIBL_01045:0.471031,(KBS0714_MOLHKGIG_01824:0.0446177,(TT9_LFPAFLNI_01745:0.020465,SA211_MHAAABBN_01521:0.085477)n3:0.0592452)n2:0.0819312)n1:0.392088)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000692_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000692_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa3736e64142f580782e0288dcc28c5100c420ef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000692_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00985:0.0820768,(AS2_ACLBLIBL_01046:0.108027,(SA211_MHAAABBN_01520:0.0129733,(KBS0714_MOLHKGIG_01823:0.00864873,TT9_LFPAFLNI_01744:0.00593627)n3:0.00143175)n2:0.0607534)n1:0.0820768)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000693_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000693_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..323a946908ccbea329f4781218c798caea7a6390
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000693_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00986:0.222856,(((KBS0714_MOLHKGIG_01822:0,TT9_LFPAFLNI_01743:0)n3:0.0455285,SA211_MHAAABBN_01519:0.0139275)n2:0.0393245,AS2_ACLBLIBL_01047:0.073515)n1:0.222856)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000694_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000694_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10a07a30b1bb22a0f4d89fc3ae7045b2c2aa468b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000694_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00987:0.100268,(AS2_ACLBLIBL_01048:0.0560508,(SA211_MHAAABBN_01518:0.0284737,(KBS0714_MOLHKGIG_01821:0,TT9_LFPAFLNI_01742:0)n3:0.0157532)n2:0.0669213)n1:0.100268)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000695_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000695_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..800f2c48bdfe446cb7ae7aa89954039cbe46b1a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000695_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00988:0.0652061,(AS2_ACLBLIBL_01049:0.140884,(SA211_MHAAABBN_01517:0.0184806,(TT9_LFPAFLNI_01741:0.00528488,KBS0714_MOLHKGIG_01820:0.00835912)n3:0.00288137)n2:0.0992789)n1:0.0652061)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000697_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000697_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d53eac53d731a78d9ba6b7a40405b795de55e92b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000697_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00990:0.0700253,(AS2_ACLBLIBL_01052:0.0346273,(KBS0714_MOLHKGIG_01818:0.00363365,(SA211_MHAAABBN_01515:2.38365e-07,TT9_LFPAFLNI_01739:0.0030244)n3:0.0123199)n2:0.0447149)n1:0.0700253)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000699_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000699_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47ff74c419947650b4b98c8c0296b923bd64731f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000699_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00992:0.113366,((TT9_LFPAFLNI_01737:7.59246e-07,(SA211_MHAAABBN_01513:0.0148365,KBS0714_MOLHKGIG_01816:0.0149485)n3:0.0005105)n2:0.295587,AS2_ACLBLIBL_01054:0.207272)n1:0.113366)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000700_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000700_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fa3c3ae532e974d62b28ca1236d570c2ec84fda
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000700_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00994:0.0385899,((TT9_LFPAFLNI_01736:0.00088407,(KBS0714_MOLHKGIG_01815:0.0011144,SA211_MHAAABBN_01512:0.0068356)n3:0.0031471)n2:0.0203676,AS2_ACLBLIBL_01059:0.0215352)n1:0.0385899)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000702_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000702_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc8c2bc924628c226ba828ab0d8c733527413df4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000702_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00996:0.086342,(((TT9_LFPAFLNI_01734:0.0082275,KBS0714_MOLHKGIG_01813:0.0072585)n3:0.001727,SA211_MHAAABBN_01510:0.001212)n2:0.0468415,AS2_ACLBLIBL_01061:0.064426)n1:0.086342)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000703_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000703_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b466dc9695aedb3d83bf0ee5882bbe9bff30eb90
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000703_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00997:0.023303,(TT9_LFPAFLNI_01733:0,(KBS0714_MOLHKGIG_01812:0,(SA211_MHAAABBN_01509:0,AS2_ACLBLIBL_01062:0)n3:0)n2:0)n1:0.023303)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000704_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000704_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e8204897b05fa0bf65f8fa88c559c0ca512866e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000704_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00998:0.0981481,((KBS0714_MOLHKGIG_01811:0.00970098,(SA211_MHAAABBN_01508:0.0006557,TT9_LFPAFLNI_01732:0.0162463)n3:0.0206488)n2:0.0322274,AS2_ACLBLIBL_01063:0.0876908)n1:0.0981481)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000705_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000705_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c49daa12c318e82930e5a18805ad430efbfb748
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000705_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00999:0.381302,(AS2_ACLBLIBL_01064:0.216251,(TT9_LFPAFLNI_01731:0.00736137,(SA211_MHAAABBN_01507:0.00361123,KBS0714_MOLHKGIG_01810:0.0227768)n3:0.0406206)n2:0.300538)n1:0.381302)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000707_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000707_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82167d5d0a823457bf62c8035b231004a16c3e43
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000707_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01005:0.238311,((KBS0714_MOLHKGIG_01804:0.00991583,TT9_LFPAFLNI_01725:0.0446352)n2:0.205503,(SA211_MHAAABBN_01501:0.0133247,AS2_ACLBLIBL_01069:0.0166253)n3:0.127796)n1:0.238311)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000710_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000710_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61ccfc972943ddfefb764f69509442f8497ace94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000710_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01008:0.0029971,(TT9_LFPAFLNI_01722:0.0179658,((SA211_MHAAABBN_01498:0.0105163,AS2_ACLBLIBL_01072:0.0181587)n3:0.0409167,KBS0714_MOLHKGIG_01801:0.0124754)n2:0.00393217)n1:0.0029971)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000712_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000712_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..967cac3cdfe2fbc84e547801b975daf288d51af0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000712_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000713_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000713_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3008b6cb492a961afe140b1938ef0bbc45e1d29e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000713_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000716_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000716_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a958b89c2902a3f95036a2caaa0924731a4599c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000716_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01017:0.0540346,(AS2_ACLBLIBL_01094:0.0328689,((TT9_LFPAFLNI_01713:0.00400537,SA211_MHAAABBN_01491:0.00568863)n3:0.00147387,KBS0714_MOLHKGIG_01784:0.00045663)n2:0.0180979)n1:0.0540346)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000718_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000718_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7cb9765a2281658f5f195942e8ed07ef384c6fc7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000718_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01019:0.0595786,((TT9_LFPAFLNI_01711:0.0121266,(KBS0714_MOLHKGIG_01782:0.00396188,SA211_MHAAABBN_01489:0.00280013)n3:0.00427238)n2:0.0777639,AS2_ACLBLIBL_01096:0.0729609)n1:0.0595786)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000720_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000720_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52eda380c3b8550147c2aaef5a9a555e97c8a01d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000720_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01024:0.148114,(AS2_ACLBLIBL_01100:0.114341,(KBS0714_MOLHKGIG_01777:0.0197754,(SA211_MHAAABBN_01484:0.00144113,TT9_LFPAFLNI_01706:0.00683887)n3:0.00349961)n2:0.119779)n1:0.148114)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000721_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000721_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c132c8c021ca41ad774c1fe56b84ed2c60cedce5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000721_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01025:0.0798682,(AS2_ACLBLIBL_01101:0.0546247,(KBS0714_MOLHKGIG_01776:0.00434776,(TT9_LFPAFLNI_01705:0.00163959,SA211_MHAAABBN_01483:0.00110641)n3:0.00448174)n2:0.0528709)n1:0.0798682)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000722_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000722_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbd9bb749f507e25da8516c98a1c63b0e5a6b733
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000722_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01026:0.0855669,(AS2_ACLBLIBL_01102:0.116289,(TT9_LFPAFLNI_01704:0.00571928,(KBS0714_MOLHKGIG_01775:3.42721e-07,SA211_MHAAABBN_01482:0.00506929)n3:0.00700272)n2:0.0381149)n1:0.0855669)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000724_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000724_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..182e12a05b898568d9b580ae5084677c532c3b49
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000724_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01029:0.0335474,(AS2_ACLBLIBL_01104:0.0446513,(KBS0714_MOLHKGIG_01773:0.0111728,(SA211_MHAAABBN_01480:1.78686e-07,TT9_LFPAFLNI_01702:0.00604675)n3:0.00669425)n2:0.0431648)n1:0.0335474)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000725_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000725_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9176ab9546fcc70399aa41b9fd8f898435a5272a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000725_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01031:0.0749265,(AS2_ACLBLIBL_01105:0.072901,(TT9_LFPAFLNI_01701:0.017632,(KBS0714_MOLHKGIG_01772:0,SA211_MHAAABBN_01479:0)n3:0.003116)n2:0.0797205)n1:0.0749265)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000726_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000726_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57cdef260ef4d8cdd2032b017727e6126d5441f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000726_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01033:0.10473,(AS2_ACLBLIBL_01107:0.0432399,(KBS0714_MOLHKGIG_01770:0.00963613,(SA211_MHAAABBN_01477:0.0103611,TT9_LFPAFLNI_01699:0.00334288)n3:0.00164587)n2:0.0690059)n1:0.10473)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000727_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000727_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75dae4db97a8228ebde2dc4504f819fc4c01176a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000727_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01034:0.20691,(AS2_ACLBLIBL_01108:0.0965015,((SA211_MHAAABBN_01476:0,TT9_LFPAFLNI_01698:0)n3:0.00718787,KBS0714_MOLHKGIG_01769:0.0178921)n2:0.0643035)n1:0.20691)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000728_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000728_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94c5ccc96a6a3fa1322aa55efefe3a1e241a6fb7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000728_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01035:0.0455679,(AS2_ACLBLIBL_01109:0.00016025,(TT9_LFPAFLNI_01697:1.06319e-07,(KBS0714_MOLHKGIG_01768:0.004586,SA211_MHAAABBN_01475:0.000438)n3:0.000488)n2:0.009999)n1:0.0455679)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000730_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000730_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e904a1003642b4949f0a1cb5f2cbf8fde410a6d1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000730_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000731_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000731_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41c584bb2ed6fbf1044f1e9f336e795646efc342
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000731_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000735_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000735_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..442baf81f669443874ab1c897bd73b615c0b0899
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000735_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01043:0.108049,(AS2_ACLBLIBL_01118:0.0741615,(TT9_LFPAFLNI_01688:0.016029,(KBS0714_MOLHKGIG_01759:0,SA211_MHAAABBN_01466:0)n3:0.019998)n2:0.0543482)n1:0.108049)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000737_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000737_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5b4a8407b568fe0fa3f240d992513d0139908ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000737_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000738_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000738_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53c191a2959a9a47fe4fab4ea0c47481480e4012
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000738_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01048:0.129282,(AS2_ACLBLIBL_01123:0.051338,(SA211_MHAAABBN_01461:3.93027e-07,(KBS0714_MOLHKGIG_01754:3.93027e-07,TT9_LFPAFLNI_01683:0.0146377)n3:0.00032475)n2:0.0688123)n1:0.129282)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000739_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000739_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3992c95811184fd812f1a780ab3f83a6e9d7b8cb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000739_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01049:0.0982919,(((SA211_MHAAABBN_01460:0,KBS0714_MOLHKGIG_01753:0)n3:0.00673754,TT9_LFPAFLNI_01682:0.00832946)n2:0.0672167,AS2_ACLBLIBL_01124:0.0795002)n1:0.0982919)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000740_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000740_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f048a868f3b5d65d4f143ef3b13ad115b0066840
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000740_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01050:0.0426378,(((KBS0714_MOLHKGIG_01752:0,SA211_MHAAABBN_01459:0)n3:0.0171268,TT9_LFPAFLNI_01681:0.00376922)n2:0.0484572,AS2_ACLBLIBL_01125:0.0583745)n1:0.0426378)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000743_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000743_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29843cb6ade10063dca980813d1de1eb94c12dd0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000743_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01053:0.038773,(AS2_ACLBLIBL_01128:0.025872,(TT9_LFPAFLNI_01678:0,(KBS0714_MOLHKGIG_01749:0,SA211_MHAAABBN_01456:0)n3:0)n2:0.009166)n1:0.038773)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000744_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000744_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb34417a40bc49e320248de12937cf84a3adf14b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000744_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000745_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000745_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd555d6de290b5f507ef5c4359f2ba870a79f49c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000745_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000746_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000746_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98fde1dbe7cf4f460607ec901d4a77af0931a495
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000746_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000748_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000748_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..291546717f2099ae77b08457ba7756ab9d76bae0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000748_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000749_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000749_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb99ba559ac59eaece90554de82bafeb9effe42b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000749_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000750_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000750_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09c466215a9df347369d0a861a20efc6c63aec84
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000750_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01064:0.134743,(((SA211_MHAAABBN_01449:0,KBS0714_MOLHKGIG_01742:0)n3:0.00534956,TT9_LFPAFLNI_01671:0.00099144)n2:0.0504495,AS2_ACLBLIBL_01135:0.0856343)n1:0.134743)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000752_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000752_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fab42163c84c517c5703120d0abf0ca41455fc9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000752_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01066:0.0236524,(AS2_ACLBLIBL_01137:0.0311673,(SA211_MHAAABBN_01447:0.00049125,(KBS0714_MOLHKGIG_01740:0.0005855,TT9_LFPAFLNI_01669:0.0023405)n3:0.00279975)n2:0.0248837)n1:0.0236524)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000755_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000755_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f874678cdccae06f7dde8ef5bbd427256961dde
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000755_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01070:0.0773542,((TT9_LFPAFLNI_01666:0.0102662,(KBS0714_MOLHKGIG_01737:0.00951275,SA211_MHAAABBN_01444:0.00798225)n3:0.00804675)n2:0.0552503,AS2_ACLBLIBL_01141:0.0315375)n1:0.0773542)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000757_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000757_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbb2c3a04423d395acd4272b9a4967981ffccdd4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000757_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01073:0.135231,(((KBS0714_MOLHKGIG_01734:0,TT9_LFPAFLNI_01663:0)n3:0.00882552,SA211_MHAAABBN_01441:0.00085748)n2:0.0313705,AS2_ACLBLIBL_01144:0.0701583)n1:0.135231)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000760_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000760_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78bce3ea6513f3af2155dd8ffad397c5b9e1a583
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000760_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01076:0.0437403,(AS2_ACLBLIBL_01147:0.0067795,(TT9_LFPAFLNI_01660:0.0017125,(KBS0714_MOLHKGIG_01731:1.13664e-07,SA211_MHAAABBN_01438:0.00474425)n3:0.001679)n2:0.0114975)n1:0.0437403)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000761_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000761_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6255d02396ea05b0c4a9b5b18ceeb07c9e68db00
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000761_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01077:0.0313274,(((TT9_LFPAFLNI_01659:0,SA211_MHAAABBN_01437:0)n3:0.00109825,KBS0714_MOLHKGIG_01730:0.00525075)n2:0.0152772,AS2_ACLBLIBL_01148:0.00634125)n1:0.0313274)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000763_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000763_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04846a61791f2db1282ebd37ba58ce87f8f9b3b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000763_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01079:0.0137077,(AS2_ACLBLIBL_01150:0.0135525,(TT9_LFPAFLNI_01657:0,(SA211_MHAAABBN_01435:0,KBS0714_MOLHKGIG_01728:0)n3:0)n2:0.0085085)n1:0.0137077)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000765_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000765_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58af5e668fd16a62da08fde09c9f6f2d8997be59
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000765_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01082:0.00208325,(AS2_ACLBLIBL_01152:0.0041665,(KBS0714_MOLHKGIG_01726:0.0020705,(TT9_LFPAFLNI_01655:0,SA211_MHAAABBN_01433:0)n3:0.0020705)n2:0.0062615)n1:0.00208325)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000767_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000767_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..798570b54de840d49c105690715bf2e71139729c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000767_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01084:0.0142437,(AS2_ACLBLIBL_01154:0.0184975,((TT9_LFPAFLNI_01653:0,KBS0714_MOLHKGIG_01724:0)n3:0.00016114,SA211_MHAAABBN_01431:0.00131386)n2:0.0252208)n1:0.0142437)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000768_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000768_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e8f83f2e850a9fa9e64dc8991b91c145c072f07
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000768_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01085:0.00799725,(((KBS0714_MOLHKGIG_01723:3.3437e-08,SA211_MHAAABBN_01430:0.0033065)n3:9.5e-05,TT9_LFPAFLNI_01652:3.3437e-08)n2:0.0088445,AS2_ACLBLIBL_01155:0.0053855)n1:0.00799725)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000770_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000770_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..421882ff83e5a8c5ebb9b6ad153c6bb9ab02742f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000770_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01087:0.144241,(AS2_ACLBLIBL_01157:0.0988845,(SA211_MHAAABBN_01428:0.0065465,(KBS0714_MOLHKGIG_01721:0,TT9_LFPAFLNI_01650:0)n3:0.0099015)n2:0.156066)n1:0.144241)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000772_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000772_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24199ecb504b2910fd11d650891c0238093ab5c6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000772_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01089:0.0112275,(AS2_ACLBLIBL_01159:0.012184,(KBS0714_MOLHKGIG_01719:5.49495e-08,(TT9_LFPAFLNI_01648:5.49495e-08,SA211_MHAAABBN_01426:0.011124)n3:3e-05)n2:0.0092165)n1:0.0112275)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000774_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000774_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa57293fc1f562b03481fadb7be78a30c209db78
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000774_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000775_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000775_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6abeeef066352ba8e753f6e1f74e4771535cf227
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000775_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01092:0.006358,((KBS0714_MOLHKGIG_01716:0,SA211_MHAAABBN_01423:0)n2:-0,(AS2_ACLBLIBL_01162:0,TT9_LFPAFLNI_01645:0)n3:0)n1:0.006358)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000777_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000777_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3427ce02810996993ad50283a3e7f03b7f7cee04
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000777_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000781_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000781_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10a588a8dc72f8c48c90125d1332f6e954276fa2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000781_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01098:0.0707762,(((SA211_MHAAABBN_01417:0,TT9_LFPAFLNI_01639:0)n3:0,KBS0714_MOLHKGIG_01710:0)n2:0.0149235,AS2_ACLBLIBL_01168:0.0019785)n1:0.0707762)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000788_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000788_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..577c4f372ecc9c5b362e6fa2c46fb3d9a58de9cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000788_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000789_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000789_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1a41ce30e7e1238cbe3fa78bec31e982c032984
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000789_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01106:0.0403012,(AS2_ACLBLIBL_01176:0.0105235,(TT9_LFPAFLNI_01631:0,(KBS0714_MOLHKGIG_01702:0,SA211_MHAAABBN_01409:0)n3:0)n2:0.0174515)n1:0.0403012)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000791_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000791_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b20632ec6c8f5541d628803cde4a06b6814c0675
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000791_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000794_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000794_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4360fe1ff473daf367a83e582e4e896fa45550c6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000794_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000799_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000799_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5d5f40473f80325a9ddaddaec61470a28aa5cf6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000799_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000801_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000801_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..675880ba47cf19c60bd71ef58f752bc485b16601
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000801_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000802_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000802_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..457ec2eddad1c6d602cca89f2478d052f19a2443
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000802_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01119:0.0185613,(((KBS0714_MOLHKGIG_01689:0,TT9_LFPAFLNI_01618:0)n3:0.00541351,SA211_MHAAABBN_01396:0.00453649)n2:0.0147203,AS2_ACLBLIBL_01189:0.0374665)n1:0.0185613)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000803_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000803_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..069198e21d2ed84b612d624d7c61f1247fcaf14c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000803_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01120:0.113383,(KBS0714_MOLHKGIG_01688:0.047134,((AS2_ACLBLIBL_01190:0.682369,SA211_MHAAABBN_01392:0.0506683)n3:0.028843,TT9_LFPAFLNI_01617:0.0848741)n2:0.110229)n1:0.113383)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000805_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000805_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3542ef561a566c90380669fabadca66dbc733821
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000805_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01123:0.412955,(AS2_ACLBLIBL_01193:0.150101,(SA211_MHAAABBN_01389:-0,(TT9_LFPAFLNI_01614:0,KBS0714_MOLHKGIG_01685:0)n3:0)n2:0.240997)n1:0.412955)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000807_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000807_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe6a2bde10148c68f4cd1e2cfc52fa7e23630404
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000807_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01125:0.10162,(AS2_ACLBLIBL_01196:0.046702,(TT9_LFPAFLNI_01611:3.28283e-07,(KBS0714_MOLHKGIG_01682:3.28283e-07,SA211_MHAAABBN_01386:0.00343575)n3:0.00043075)n2:0.0753372)n1:0.10162)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000814_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000814_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d474f7e66e08f3c54e5fa0a16e21516ffc4c3da8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000814_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01133:0.162989,(AS2_ACLBLIBL_01205:0.0567192,(TT9_LFPAFLNI_01603:0.0184625,(KBS0714_MOLHKGIG_01673:4.77156e-07,SA211_MHAAABBN_01378:0.0102671)n3:0.0203495)n2:0.045653)n1:0.162989)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000815_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000815_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..716960657043aa529afb765d78fe8b7315d3ef0e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000815_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01134:0.110902,(AS2_ACLBLIBL_01206:0.0278053,(TT9_LFPAFLNI_01602:0.00611861,(SA211_MHAAABBN_01377:0.0099694,KBS0714_MOLHKGIG_01672:0.0029336)n3:0.00388739)n2:0.0365262)n1:0.110902)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000816_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000816_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20d298122dab550c7f5f257fbcf13da6beda6e90
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000816_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01135:0.165539,((KBS0714_MOLHKGIG_01671:0.0133452,TT9_LFPAFLNI_01601:0.0303948)n2:0.006388,(AS2_ACLBLIBL_01207:0.10657,SA211_MHAAABBN_01376:0.0214105)n3:0.004433)n1:0.165539)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000819_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000819_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..988d3ce5514699434cb56cd40a4b3a9ed23801c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000819_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01137:0.0491501,(AS2_ACLBLIBL_01226:0.105306,((TT9_LFPAFLNI_01598:0.00705604,KBS0714_MOLHKGIG_01668:0.00702296)n3:0.003699,SA211_MHAAABBN_01373:0.007834)n2:0.0554725)n1:0.0491501)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000820_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000820_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..232fce56f7c56217d64615594771af150592cff5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000820_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01138:0.152817,(AS2_ACLBLIBL_01227:0.0677895,(KBS0714_MOLHKGIG_01667:0.02678,(TT9_LFPAFLNI_01597:0,SA211_MHAAABBN_01372:0)n3:0.012493)n2:0.0501145)n1:0.152817)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000821_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000821_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f856c4a602e9a4eee45c21ac14ed915b4a1a0dca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000821_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01139:0.0656121,(AS2_ACLBLIBL_01228:0.0189978,((TT9_LFPAFLNI_01596:0.00420096,SA211_MHAAABBN_01371:0.00850104)n3:0.00675705,KBS0714_MOLHKGIG_01666:0.00680513)n2:0.0127816)n1:0.0656121)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000823_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000823_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0f9354c55dfcd1dcddf7cd2ef5712eb97b8e476
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000823_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01141:0.057254,(((KBS0714_MOLHKGIG_01664:0.003374,SA211_MHAAABBN_01369:0.008232)n3:0.00247387,TT9_LFPAFLNI_01594:0.00428944)n2:0.205024,AS2_ACLBLIBL_01230:0.065407)n1:0.057254)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000827_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000827_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a635a45d69f6651bd3c3b3ad653792359213437
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000827_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000829_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000829_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..035fc63f65bd302c7e75d23175c729f4c9db5487
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000829_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000831_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000831_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8035b2bd8105b79fac7708c58b1ad8040ffc83e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000831_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000832_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000832_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..930d7d50d69907d060d7cafd6131ec2670e6dff2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000832_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000834_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000834_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7af9c7fc81dff8523a2f7ac633d8ebfed91253dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000834_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000837_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000837_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84712cb8c2c55500cf04abcb33723b8f776a3988
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000837_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000840_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000840_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0118427c3934e8e5d5ab7bda6cb0eb2a3451ba93
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000840_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000842_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000842_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e6e1459988f2a1b6cbf846529847b54e5e0b8d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000842_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000846_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000846_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a46d8a501362aa603e4835f1913c869ce42e10b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000846_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000847_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000847_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66f93095f1dfd9ef3a3e069104e52010337f14c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000847_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000848_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000848_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2ca6722e03e85ce9af9054df2383229871b1bd2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000848_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000850_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000850_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00341b51c8acece306746b44e83e7135ef8c8d23
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000850_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01171:0.167345,(AS2_ACLBLIBL_01262:0.323372,(KBS0714_MOLHKGIG_01633:0.00959438,(TT9_LFPAFLNI_01562:0.0241684,SA211_MHAAABBN_01338:0.00375462)n3:0.00928662)n2:0.339895)n1:0.167345)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000851_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000851_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f27ee3eaef5ce75bb47abc9f1f7f067eb83f17e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000851_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01172:0.0377041,((KBS0714_MOLHKGIG_01632:0.00764363,(TT9_LFPAFLNI_01561:0.00676988,SA211_MHAAABBN_01337:0.00751613)n3:0.00306238)n2:0.0154459,AS2_ACLBLIBL_01263:0.0390219)n1:0.0377041)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000852_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000852_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb41cd7db07de76b36f69fd6aad2d506d1cec689
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000852_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01174:0.144277,(AS2_ACLBLIBL_01266:0.0665898,(SA211_MHAAABBN_01335:0.00705658,(KBS0714_MOLHKGIG_01630:0.01713,TT9_LFPAFLNI_01559:0.00618305)n3:0.00462642)n2:0.054886)n1:0.144277)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000858_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000858_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1693f1f1f89ed73bcce6b9bad56593e45d356b9c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000858_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01193:0.0118404,((KBS0714_MOLHKGIG_01610:0.0140191,(TT9_LFPAFLNI_01536:0.0135136,SA211_MHAAABBN_01321:0.00255237)n3:0.00545587)n2:0.00580788,AS2_ACLBLIBL_01288:0.108176)n1:0.0118404)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000860_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000860_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b67cd220d0283d03ef9004df9c9adb8a728ffa4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000860_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01200:0.00513084,((SA211_MHAAABBN_01314:0.00023829,(KBS0714_MOLHKGIG_01602:0,TT9_LFPAFLNI_01529:0)n3:0.00354371)n2:0.0104644,AS2_ACLBLIBL_01292:0.0820363)n1:0.00513084)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000861_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000861_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c4971a5f5f776e203a31b9a6c07d630f8d6b122
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000861_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01202:0.00746525,(AS2_ACLBLIBL_01293:0.0159385,((TT9_LFPAFLNI_01527:0.00341104,SA211_MHAAABBN_01312:0.00312496)n3:0.0288907,KBS0714_MOLHKGIG_01600:0.00152683)n2:0.0485751)n1:0.00746525)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000863_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000863_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ec38b1ec18afd2e77613208b99bcd996c77929d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000863_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01204:1.02118e-06,(AS2_ACLBLIBL_01295:0.969055,(TT9_LFPAFLNI_01525:0.003955,(KBS0714_MOLHKGIG_01598:0,SA211_MHAAABBN_01310:0)n3:0.02893)n2:0.033708)n1:1.02118e-06)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000864_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000864_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9766363d57f73e1686d8907ae383daf886396d49
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000864_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01207:0.0358353,((TT9_LFPAFLNI_01524:0.00739041,(SA211_MHAAABBN_01309:5e-07,KBS0714_MOLHKGIG_01597:5e-07)n3:0.00470609)n2:0.0484998,AS2_ACLBLIBL_01298:0.0501403)n1:0.0358353)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000865_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000865_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69c38d392d6d3e65c2aa7fa360350deb066e8c25
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000865_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01219:0.0690377,((TT9_LFPAFLNI_01518:0.0297646,(KBS0714_MOLHKGIG_01591:0,SA211_MHAAABBN_01303:0)n3:0.00619038)n2:0.10692,AS2_ACLBLIBL_01300:0.101504)n1:0.0690377)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000866_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000866_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92b79c52252551e28d3f37c3ab79714c599a5d17
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000866_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01214:0.0136031,(((KBS0714_MOLHKGIG_01595:0.0155835,AS2_ACLBLIBL_01301:0.37702)n3:0.00546294,SA211_MHAAABBN_01307:0.0149343)n2:0.00264618,TT9_LFPAFLNI_01522:0.0209158)n1:0.0136031)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000868_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000868_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..069f75507c62f355f6c464c03d96397a5f8fb3ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000868_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01231:0.213217,((SA211_MHAAABBN_01300:0.0155569,(TT9_LFPAFLNI_01516:0.001335,KBS0714_MOLHKGIG_01589:0.001335)n3:0.0123661)n2:0.0242039,AS2_ACLBLIBL_01333:0.03087)n1:0.213217)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000869_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000869_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..342344488b0a125e97d3f838fe8a814e87944c0f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000869_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01233:0.203687,(AS2_ACLBLIBL_01335:0.300913,((SA211_MHAAABBN_01298:0.00263968,TT9_LFPAFLNI_01514:7.16811e-07)n3:0.00121794,KBS0714_MOLHKGIG_01587:0.00206074)n2:0.00267284)n1:0.203687)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000870_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000870_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c83ae68b3088c5790210fd1351151709b6f6b101
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000870_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01236:0.00202983,(AS2_ACLBLIBL_01343:0.194919,(KBS0714_MOLHKGIG_01580:0.012971,(SA211_MHAAABBN_01290:2.36207e-07,TT9_LFPAFLNI_01507:0.00516042)n3:0.0113779)n2:0.00843002)n1:0.00202983)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000871_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000871_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..486d25dad1078fe0dbaf2e6b731ef4144ec0ad5f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000871_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01237:0.00745394,(AS2_ACLBLIBL_01344:0.0943231,(SA211_MHAAABBN_01289:1.12307e-07,(TT9_LFPAFLNI_01506:1.12307e-07,KBS0714_MOLHKGIG_01579:0.00132062)n3:0.00017662)n2:0.00193162)n1:0.00745394)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000872_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000872_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..405cd66c6045f94ccba59baad886961fefa08c6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000872_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000873_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000873_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8492c56b641deb3d1e7506091000ac0ead27db87
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000873_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01239:0.0598827,((TT9_LFPAFLNI_01504:0.00619025,(SA211_MHAAABBN_01287:0.00533375,KBS0714_MOLHKGIG_01577:0.00535225)n3:0.0118312)n2:0.0428878,AS2_ACLBLIBL_01346:0.109865)n1:0.0598827)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000875_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000875_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..caf71988d6d2334d4494c38736c8cc5f26af6362
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000875_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01242:0.0582184,((SA211_MHAAABBN_01285:8.96086e-07,(TT9_LFPAFLNI_01502:0.0043325,KBS0714_MOLHKGIG_01575:8.96086e-07)n3:0.0013245)n2:0.120951,AS2_ACLBLIBL_01349:0.65569)n1:0.0582184)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000877_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000877_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39c79f341215a0dc80c1cb7112d2f0a4b7d2242a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000877_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01244:0.0580182,(((KBS0714_MOLHKGIG_01573:0.00077194,TT9_LFPAFLNI_01500:0.00681306)n3:0.00356095,SA211_MHAAABBN_01283:0.00416975)n2:0.0510753,AS2_ACLBLIBL_01351:0.0368487)n1:0.0580182)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000878_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000878_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26ff38abba1a024a4288965e930e67faf18c7042
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000878_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01245:0.119778,(AS2_ACLBLIBL_01352:0.0412672,((TT9_LFPAFLNI_01499:0.00857691,KBS0714_MOLHKGIG_01572:0.0167821)n3:0.0108002,SA211_MHAAABBN_01282:0.00695633)n2:0.0513509)n1:0.119778)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000881_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000881_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e38f2f247f1f926467ff2f5839c9a6020a0397
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000881_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000882_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000882_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6753695cce124af42df7101e415bce39aa30fba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000882_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000883_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000883_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb02b2a7e2d282dc84df69957df0fecad2ee68d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000883_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000885_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000885_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63cf9899dd8bba701dd84ae02639236247e4a797
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000885_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01253:0.0160816,(AS2_ACLBLIBL_01362:0.0594098,(TT9_LFPAFLNI_01491:0.00046549,(KBS0714_MOLHKGIG_01564:0.00080649,SA211_MHAAABBN_01274:0.00245451)n3:0.00075651)n2:0.0143193)n1:0.0160816)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000886_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000886_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a711b63c379997acbe179220c567bea9fc99948
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000886_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01255:0.0256123,(((SA211_MHAAABBN_01272:0,KBS0714_MOLHKGIG_01562:0)n3:0.00193237,TT9_LFPAFLNI_01489:0.00657863)n2:0.0292339,AS2_ACLBLIBL_01364:0.00543533)n1:0.0256123)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000887_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000887_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a53b4111e7ff220abb87db979135bb7da6f4d9d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000887_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01256:0.0751743,(((TT9_LFPAFLNI_01488:0.00951679,SA211_MHAAABBN_01271:0.00332121)n3:0.00742121,KBS0714_MOLHKGIG_01561:0.00388513)n2:0.0477256,AS2_ACLBLIBL_01365:0.0414763)n1:0.0751743)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000888_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000888_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eabf4bbed31d085994a3fb122b9f7a7d8382ffd1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000888_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01257:0.0275318,((TT9_LFPAFLNI_01487:0.00071496,(KBS0714_MOLHKGIG_01560:0.00535108,SA211_MHAAABBN_01270:0.00106092)n3:0.00158204)n2:0.0126455,AS2_ACLBLIBL_01366:0.0182755)n1:0.0275318)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000889_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000889_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cec426b03e44c13ef165a2648c4e84b3d048b2c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000889_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01258:0.0450953,((SA211_MHAAABBN_01268:0.00696588,(TT9_LFPAFLNI_01485:2.16881e-07,KBS0714_MOLHKGIG_01558:0.00417551)n3:0.00213564)n2:0.0831578,AS2_ACLBLIBL_01367:0.0303465)n1:0.0450953)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000893_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000893_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4e2c21db1fa6008b78ecfb946f39ad1fbf62904
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000893_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01262:0.0561189,(((KBS0714_MOLHKGIG_01554:0.00052025,TT9_LFPAFLNI_01481:0.00228775)n3:0.019286,SA211_MHAAABBN_01264:0.007392)n2:0.0652575,AS2_ACLBLIBL_01371:0.0638173)n1:0.0561189)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000896_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000896_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13fa4e36769023c5e301dfd0c37c16757f382c4f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000896_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01265:0.203624,((TT9_LFPAFLNI_01478:0.0687933,(KBS0714_MOLHKGIG_01551:0.0235107,SA211_MHAAABBN_01261:0.0155323)n3:0.0214402)n2:0.249168,AS2_ACLBLIBL_01374:0.202714)n1:0.203624)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000897_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000897_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f63cc3e09522c5d6d464a8bc5118986645745e94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000897_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01266:0.0276076,((SA211_MHAAABBN_01260:6.85001e-08,(AS2_ACLBLIBL_01375:0.0139411,KBS0714_MOLHKGIG_01550:6.85001e-08)n3:0.00065613)n2:0.00065613,TT9_LFPAFLNI_01477:6.85001e-08)n1:0.0276076)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000898_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000898_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43da143b0cd5967efd3df4dd953c7bea9060c8c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000898_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000901_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000901_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ea6e9d831d9275d3ab0427f3dbdf3d7a10234e1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000901_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000902_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000902_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4675738e78266cb48855a469d9a4d1ae4aa8a848
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000902_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01272:0.0799717,(AS2_ACLBLIBL_01381:0.0281575,(TT9_LFPAFLNI_01471:0.00686224,(SA211_MHAAABBN_01254:0,KBS0714_MOLHKGIG_01544:0)n3:0.00284976)n2:0.0408959)n1:0.0799717)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000905_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000905_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a8c7f454782d2a0814de51a097596c2bc31ba7b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000905_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01275:0.0644698,(AS2_ACLBLIBL_01384:0.0487863,((SA211_MHAAABBN_01251:0.00177743,KBS0714_MOLHKGIG_01541:0.00161657)n3:0.00468346,TT9_LFPAFLNI_01468:0.0125934)n2:0.0457944)n1:0.0644698)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000906_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000906_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12a78a4d3cf69f5ffd70c6167a1b09a8a5458a34
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000906_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000908_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000908_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..feb1468d697c22b8d16204ff08ef2c5b3beee29e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000908_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01279:0.0725081,(((SA211_MHAAABBN_01247:0.002274,KBS0714_MOLHKGIG_01537:0.008371)n3:0.00518275,TT9_LFPAFLNI_01464:0.00549375)n2:0.0376833,AS2_ACLBLIBL_01388:0.0501648)n1:0.0725081)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000909_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000909_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2c3a155944b4962ea55906dcd4b2d0b6860edba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000909_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000911_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000911_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ced93f4f70c5e52ffb8535a64442ec74e796cb8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000911_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000913_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000913_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..abbb494c499f3c39ab56a6a1e3fbaf0a3d64f38d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000913_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01284:0.0703065,(((TT9_LFPAFLNI_01459:0,SA211_MHAAABBN_01242:0)n3:0,KBS0714_MOLHKGIG_01532:0)n2:0.041709,AS2_ACLBLIBL_01393:0.054417)n1:0.0703065)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000916_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000916_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..477eb9f950ebeb5e4cdb0990a0b70a841dccbdcf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000916_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000919_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000919_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f41f673944881308e7f6318c5ab6f78f09f6fcb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000919_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000920_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000920_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd33a967ddb9d7fbff2ce2aae9d97bacf5494ebc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000920_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000923_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000923_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a51a77d698897b46f6782636a931f812824e8164
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000923_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000924_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000924_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb81fd26d07ab46b2dd197ba512a4f05a5d48cf0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000924_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000925_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000925_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0043d2b569f4f522d0c20630087e0680137bd94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000925_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01304:0.146994,((KBS0714_MOLHKGIG_01520:0.00937391,(SA211_MHAAABBN_01229:0.00222334,TT9_LFPAFLNI_01447:0.00347466)n3:0.00529875)n2:0.0549566,AS2_ACLBLIBL_01405:0.0804718)n1:0.146994)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000926_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000926_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcf20a1933d8899ff5cb8ab305e13a7465a53a51
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000926_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01305:0.21617,(((TT9_LFPAFLNI_01446:0.0082245,SA211_MHAAABBN_01228:0.0126335)n3:0.0060195,KBS0714_MOLHKGIG_01519:0.0187705)n2:0.041166,AS2_ACLBLIBL_01406:0.14232)n1:0.21617)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000927_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000927_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edea581f6edef7e55c52da7b03a866787b30bb3d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000927_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01306:0.245649,(AS2_ACLBLIBL_01407:0.075563,((KBS0714_MOLHKGIG_01518:0.0014455,SA211_MHAAABBN_01227:8.75e-05)n3:0.008374,TT9_LFPAFLNI_01445:0.0082235)n2:0.0744285)n1:0.245649)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000929_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000929_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c2361581a1c12bb304d8f4b154261e829e185d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000929_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01308:0.518656,((TT9_LFPAFLNI_01443:0.000276,(SA211_MHAAABBN_01225:1.43455e-06,KBS0714_MOLHKGIG_01516:0.0082855)n3:0.01733)n2:0.128922,AS2_ACLBLIBL_01409:0.243316)n1:0.518656)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000930_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000930_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64b6868af09d63b26ba1e32e1e3986bca3d4acc8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000930_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01309:0.252343,((TT9_LFPAFLNI_01442:0.0521567,(KBS0714_MOLHKGIG_01515:0,SA211_MHAAABBN_01224:0)n3:0.0605133)n2:0.11116,AS2_ACLBLIBL_01410:0.275023)n1:0.252343)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000933_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000933_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c8f92a2088a1bd548d1221d382fd27579fdf31f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000933_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01314:0.244994,(AS2_ACLBLIBL_01415:0.0201922,(KBS0714_MOLHKGIG_01487:0.0020171,(SA211_MHAAABBN_01219:0.00032882,TT9_LFPAFLNI_01437:0.00140718)n3:0.0023309)n2:0.0350842)n1:0.244994)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000935_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000935_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51ca73346a1400b96d25083675b304fe8b1831dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000935_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01317:0.239103,(AS2_ACLBLIBL_01417:0.0952066,(KBS0714_MOLHKGIG_01485:0.0343046,(SA211_MHAAABBN_01217:0.0158144,TT9_LFPAFLNI_01435:0.00287663)n3:0.0253429)n2:0.166547)n1:0.239103)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000937_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000937_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ebf4a2bb1b6d649e12fbb48bfb94acbf0ab4a13
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000937_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01319:0.102223,(AS2_ACLBLIBL_01419:0.0281474,(KBS0714_MOLHKGIG_01483:0.0449194,(TT9_LFPAFLNI_01433:0.0118361,SA211_MHAAABBN_01215:8.088e-05)n3:0.0139191)n2:0.0495236)n1:0.102223)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000938_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000938_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c1d8baaa44294c61e17efb639a3d1a79499d3df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000938_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01320:0.208485,(AS2_ACLBLIBL_01420:0.100321,(KBS0714_MOLHKGIG_01482:0.012257,(TT9_LFPAFLNI_01432:0.00488625,SA211_MHAAABBN_01214:0.00535375)n3:0.0059685)n2:0.136088)n1:0.208485)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000939_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000939_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd06041d666bcb553a561dbd3fae46674eae337b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000939_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01321:0.0884834,(AS2_ACLBLIBL_01421:0.178176,(SA211_MHAAABBN_01213:0.00711025,(TT9_LFPAFLNI_01431:0,KBS0714_MOLHKGIG_01481:0)n3:0.00798975)n2:0.0695082)n1:0.0884834)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000942_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000942_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..743596bf137580a3a541b84dc6d8827b4612cc2a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000942_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01324:0.0892218,(AS2_ACLBLIBL_01424:0.175867,(SA211_MHAAABBN_01210:0,(TT9_LFPAFLNI_01428:0,KBS0714_MOLHKGIG_01478:0)n3:0)n2:0.11632)n1:0.0892218)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000947_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000947_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad0140a73a7dc74a2b1c7ad308f7dd3e5fd61892
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000947_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01331:0.043805,(AS2_ACLBLIBL_01429:0.026791,((TT9_LFPAFLNI_01421:0,KBS0714_MOLHKGIG_01471:0)n3:0.0133745,SA211_MHAAABBN_01203:0.0068235)n2:0.020505)n1:0.043805)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000951_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000951_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec6c76f6ea101e3f2064c1a4decec579b019aee5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000951_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01337:0.0561768,(AS2_ACLBLIBL_01434:0.0296654,((TT9_LFPAFLNI_01416:0.00339512,KBS0714_MOLHKGIG_01466:0.00294888)n3:0.00214138,SA211_MHAAABBN_01198:0.00638763)n2:0.0201119)n1:0.0561768)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000952_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000952_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81ef7b1b80f9a74bfa3be0bfd1657c741631b5a2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000952_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01338:0.281984,(AS2_ACLBLIBL_01435:0.249465,((TT9_LFPAFLNI_01415:9.90473e-07,KBS0714_MOLHKGIG_01465:0.00802707)n3:0.0110141,SA211_MHAAABBN_01197:0.00997298)n2:0.1481)n1:0.281984)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000953_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000953_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee47c9df696ef9d17be4a60391ccefb1b813c2fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000953_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01339:0.27268,(AS2_ACLBLIBL_01436:0.310518,(SA211_MHAAABBN_01196:0.0138032,(KBS0714_MOLHKGIG_01464:0,TT9_LFPAFLNI_01414:0)n3:0.00779575)n2:0.271988)n1:0.27268)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000954_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000954_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dd7f8d64bded8373728c18ac77e424c49f4d453
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000954_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01340:0.245295,(AS2_ACLBLIBL_01437:0.147388,((SA211_MHAAABBN_01195:0.0174201,TT9_LFPAFLNI_01413:8.54328e-07)n3:0.00926714,KBS0714_MOLHKGIG_01463:0.00253096)n2:0.189132)n1:0.245295)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000956_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000956_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8e2abfd37cce691243d815077e75958d85a7fc5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000956_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01342:0.214724,((SA211_MHAAABBN_01193:0.00545285,(KBS0714_MOLHKGIG_01461:0.00728263,TT9_LFPAFLNI_01411:0.00014337)n3:0.00682875)n2:0.063286,AS2_ACLBLIBL_01439:0.148072)n1:0.214724)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000958_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000958_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43493581dbc39d9dca3f021ac0b39b28db4bff4d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000958_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01344:0.136339,(AS2_ACLBLIBL_01441:0.0855205,(TT9_LFPAFLNI_01409:0,(KBS0714_MOLHKGIG_01459:0,SA211_MHAAABBN_01191:0)n3:0)n2:0.0659275)n1:0.136339)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000960_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000960_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..895dc15bca41548a1203c10dbad024cb6e9670e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000960_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01346:0.380194,(((SA211_MHAAABBN_01189:0,TT9_LFPAFLNI_01407:0)n3:0.0238191,KBS0714_MOLHKGIG_01457:0.0001499)n2:0.712728,AS2_ACLBLIBL_01443:0.074493)n1:0.380194)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000964_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000964_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7db2fbff0a5692719556326a406cf397da68d61e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000964_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01351:0.128862,((AS2_ACLBLIBL_01447:0.27853,SA211_MHAAABBN_01184:0.083786)n2:0.065551,(KBS0714_MOLHKGIG_01452:0.0142983,TT9_LFPAFLNI_01402:0.0311687)n3:0.100092)n1:0.128862)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000965_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000965_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab7b408a8bd553b982cabba35468dbf9291d7e74
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000965_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000974_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000974_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b00c7e36f99de7caca62a6fee9160343ef3a906
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000974_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01367:0.119504,((SA211_MHAAABBN_01171:0.00737513,(TT9_LFPAFLNI_01389:0.00115538,KBS0714_MOLHKGIG_01439:0.00118463)n3:0.00402787)n2:0.0694319,AS2_ACLBLIBL_01459:0.0882456)n1:0.119504)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000976_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000976_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c491d9c35670c769be9a490ffe40971787deddfe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000976_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01369:0.0826316,((TT9_LFPAFLNI_01387:0.00923049,(KBS0714_MOLHKGIG_01437:0.00632438,SA211_MHAAABBN_01169:0.00566762)n3:0.00258057)n2:0.0943359,AS2_ACLBLIBL_01461:0.0625228)n1:0.0826316)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000977_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000977_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4ab37a53a7624f110045451bae3cc2fd19298d2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000977_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01370:0.0754519,(AS2_ACLBLIBL_01462:0.0628262,(TT9_LFPAFLNI_01386:0.00349547,(SA211_MHAAABBN_01168:2.61642e-07,KBS0714_MOLHKGIG_01436:0.0027942)n3:0.00178103)n2:0.0402097)n1:0.0754519)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000978_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000978_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e36b812b5a3e69ccbd3f337e66f1c94783ffece
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000978_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01371:0.101838,((TT9_LFPAFLNI_01385:0.00404287,(SA211_MHAAABBN_01167:0.00142063,KBS0714_MOLHKGIG_01435:0.00288338)n3:0.00335463)n2:0.0763746,AS2_ACLBLIBL_01463:0.0906956)n1:0.101838)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000979_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000979_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf8ef49d58b634559ddb19b496460258662a59c1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000979_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01372:0.06126,(AS2_ACLBLIBL_01464:0.041451,(KBS0714_MOLHKGIG_01434:0.000526,(SA211_MHAAABBN_01166:0,TT9_LFPAFLNI_01384:0)n3:0.005957)n2:0.037807)n1:0.06126)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000980_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000980_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e37bd4063de60a74be08cf24c7ff1498056d7d3a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000980_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01373:0.10571,(AS2_ACLBLIBL_01465:0.044557,((KBS0714_MOLHKGIG_01433:0,SA211_MHAAABBN_01165:0)n3:0,TT9_LFPAFLNI_01383:0)n2:0.034083)n1:0.10571)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000981_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000981_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3493091d8e2527b277cf6ed996b515f4d2ecf4f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000981_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01374:0.252228,(AS2_ACLBLIBL_01467:0.159597,(KBS0714_MOLHKGIG_01432:0.0709459,(SA211_MHAAABBN_01164:0.00413737,TT9_LFPAFLNI_01382:0.0256626)n3:0.0411156)n2:0.13454)n1:0.252228)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000983_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000983_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6e86c9f45608c461599adb76742279fa232df36
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000983_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01376:0.0453426,((SA211_MHAAABBN_01162:0.00347187,(KBS0714_MOLHKGIG_01430:0.00295087,TT9_LFPAFLNI_01380:0.00128413)n3:0.00344513)n2:0.0232811,AS2_ACLBLIBL_01469:0.0309569)n1:0.0453426)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000985_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000985_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a33960f5aeaa46bf1fcec8c03a9de51bf131d1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000985_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01378:0.0682051,(AS2_ACLBLIBL_01471:0.0535699,((KBS0714_MOLHKGIG_01428:2.31107e-07,TT9_LFPAFLNI_01378:0.00193438)n3:0.00339063,SA211_MHAAABBN_01159:0.00653587)n2:0.0295061)n1:0.0682051)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000986_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000986_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..568b21f7e8d062120a02d44266f0748609c2cbfe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000986_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01383:0.171649,(AS2_ACLBLIBL_01475:0.145134,((SA211_MHAAABBN_01155:5e-07,TT9_LFPAFLNI_01374:5e-07)n3:0.0140642,KBS0714_MOLHKGIG_01424:0.0663043)n2:0.124958)n1:0.171649)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000987_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000987_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d20e5cce986f637b7f4d2664279b3dca857e159
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000987_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01384:0.151379,((KBS0714_MOLHKGIG_01423:0.0239469,(TT9_LFPAFLNI_01373:0,SA211_MHAAABBN_01154:0)n3:0.0067341)n2:0.122703,AS2_ACLBLIBL_01476:0.0985457)n1:0.151379)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000991_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000991_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4f6deb5777a3e4016935c554b4228a03de107ef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000991_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01388:0.0902883,(AS2_ACLBLIBL_01480:0.0493365,((TT9_LFPAFLNI_01369:0.0091447,KBS0714_MOLHKGIG_01419:0.0056083)n3:0.0205422,SA211_MHAAABBN_01150:0.01051)n2:0.0219772)n1:0.0902883)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000992_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000992_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e26356e4790e4952b81a40bede6fcbcf1f63a713
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000992_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01389:0.140287,(TT9_LFPAFLNI_01368:0.037877,(KBS0714_MOLHKGIG_01418:0.0272753,(SA211_MHAAABBN_01149:0.00787925,AS2_ACLBLIBL_01481:0.0139968)n3:0.0133963)n2:0.0257927)n1:0.140287)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000994_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000994_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bab7e47c855f70b29ddaee4a59800fef6adb239
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0000994_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01391:0.00694169,((TT9_LFPAFLNI_01365:4.038e-05,(SA211_MHAAABBN_01146:0.00340038,KBS0714_MOLHKGIG_01415:0.00400363)n3:0.0115506)n2:0.0192096,AS2_ACLBLIBL_01484:0.0221166)n1:0.00694169)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001003_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001003_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15239bb45569df53e2ecd803a53a921e600c8493
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001003_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01407:0.100179,(((KBS0714_MOLHKGIG_01380:2.42542e-07,SA211_MHAAABBN_01100:0.00645636)n3:0.00057236,TT9_LFPAFLNI_01335:0)n2:0.0192568,AS2_ACLBLIBL_01512:0.0164707)n1:0.100179)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001006_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001006_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57a105b5ab771b27689fecc64fdc464e5862a7bb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001006_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01410:0.218076,(AS2_ACLBLIBL_01515:0.0838669,(TT9_LFPAFLNI_01332:0.0106484,(KBS0714_MOLHKGIG_01377:6.20542e-07,SA211_MHAAABBN_01097:0.0162001)n3:0.00437613)n2:0.0697016)n1:0.218076)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001008_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001008_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f97619eb31ce7a6fbfb2ae2b6dda0405424932c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001008_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01412:0.0544799,(AS2_ACLBLIBL_01517:0.00330813,(KBS0714_MOLHKGIG_01375:0.00253813,(SA211_MHAAABBN_01095:0.00123637,TT9_LFPAFLNI_01330:0.00320263)n3:0.00312537)n2:0.00297788)n1:0.0544799)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001009_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001009_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f49c921ad31593e92206b029728708f58f08378
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001009_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01413:0.105316,(((TT9_LFPAFLNI_01329:0.002042,SA211_MHAAABBN_01094:2.5e-05)n3:0.0088195,KBS0714_MOLHKGIG_01374:0.0335125)n2:0.0739625,AS2_ACLBLIBL_01518:0.054526)n1:0.105316)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001012_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001012_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6209706f11c006f4439eb19b20daa10f5ca36d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001012_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01417:0.0586091,(AS2_ACLBLIBL_01521:0.0639978,(SA211_MHAAABBN_01091:0.0348072,(TT9_LFPAFLNI_01326:0.00633425,KBS0714_MOLHKGIG_01371:0.00334575)n3:0.0143128)n2:0.0159577)n1:0.0586091)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001015_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001015_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6633edf8ad08ad8586378560ce040ee138bb498
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001015_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01421:0.0984574,(AS2_ACLBLIBL_01526:0.0961252,(TT9_LFPAFLNI_01322:3.56822e-07,(SA211_MHAAABBN_01087:0,KBS0714_MOLHKGIG_01367:0)n3:0.00970175)n2:0.0541273)n1:0.0984574)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001016_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001016_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..633c43f1507cba8dfe94033766af6a610865f5b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001016_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01422:0.135331,((TT9_LFPAFLNI_01321:0.00661777,(SA211_MHAAABBN_01086:0.0274439,KBS0714_MOLHKGIG_01366:0.00671107)n3:0.00370733)n2:0.127609,AS2_ACLBLIBL_01527:0.107895)n1:0.135331)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001018_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001018_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..004b3a20c56c85c0a9eca1a5bacd17a19e1854a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001018_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01424:0.333052,(((TT9_LFPAFLNI_01319:0,KBS0714_MOLHKGIG_01364:0)n3:0,SA211_MHAAABBN_01084:0)n2:0.214751,AS2_ACLBLIBL_01529:0.216338)n1:0.333052)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001020_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001020_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b63fa48e056e242caa9d9293921c6e30e15c5744
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001020_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01426:0.0739527,(AS2_ACLBLIBL_01531:0.0432307,(SA211_MHAAABBN_01082:0.00320321,(TT9_LFPAFLNI_01317:0,KBS0714_MOLHKGIG_01362:0)n3:0.00807779)n2:0.0193734)n1:0.0739527)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001023_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001023_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a24cccb7a654f1a3888afee68555b9b056461c26
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001023_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01429:0.118196,(AS2_ACLBLIBL_01534:0.106684,((KBS0714_MOLHKGIG_01359:0.00634909,TT9_LFPAFLNI_01314:0.00381591)n3:0.00844093,SA211_MHAAABBN_01079:0.0222543)n2:0.0848966)n1:0.118196)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001024_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001024_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..972712843c0ccffab5657058b4260082549f7447
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001024_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01430:0.0540396,(((TT9_LFPAFLNI_01313:0.00016239,KBS0714_MOLHKGIG_01358:0.00302861)n3:0.00296114,SA211_MHAAABBN_01078:0.00379509)n2:0.0598206,AS2_ACLBLIBL_01535:0.326034)n1:0.0540396)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001028_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001028_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6de39604be1cdcc77570c83b27759bfcd2c2c7f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001028_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01435:0.0819744,(((KBS0714_MOLHKGIG_01353:0.004012,SA211_MHAAABBN_01073:0.000888)n3:0.0038485,TT9_LFPAFLNI_01308:0.003521)n2:0.061275,AS2_ACLBLIBL_01539:0.0528173)n1:0.0819744)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001030_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001030_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6902558904bd6a5853c9e9e4edab4a359eaec69
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001030_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01437:0.0294913,(((TT9_LFPAFLNI_01306:0.0101985,SA211_MHAAABBN_01071:0.0172975)n3:0.007241,KBS0714_MOLHKGIG_01351:0.01248)n2:0.029388,AS2_ACLBLIBL_01541:0.0372375)n1:0.0294913)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001031_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001031_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bda40fd436b7454740d8a486e6bc6cc29ccf443
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001031_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01438:0.219977,((TT9_LFPAFLNI_01305:0.0280973,(KBS0714_MOLHKGIG_01350:0.0166325,SA211_MHAAABBN_01070:0.0188345)n3:0.00338525)n2:0.104604,AS2_ACLBLIBL_01542:0.165392)n1:0.219977)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001032_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001032_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1a069404ceba49d9bd28327e993ae36bdf6765c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001032_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01439:0.130387,(((TT9_LFPAFLNI_01304:0.0129186,KBS0714_MOLHKGIG_01349:0.0151054)n3:0.00193482,SA211_MHAAABBN_01069:0.0130393)n2:0.128818,AS2_ACLBLIBL_01543:0.104325)n1:0.130387)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001033_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001033_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd0fabe49c7aa455e5b82009eeb5a4f22dac89e2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001033_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01440:0.154355,(AS2_ACLBLIBL_01544:0.149449,((SA211_MHAAABBN_01068:0.022151,KBS0714_MOLHKGIG_01348:0.010787)n3:0.025844,TT9_LFPAFLNI_01303:0.019078)n2:0.0978135)n1:0.154355)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001036_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001036_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d02a30ec82707cad0702984aa4740bdf20249c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001036_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01443:0.141233,(AS2_ACLBLIBL_01547:0.0900038,(TT9_LFPAFLNI_01300:0.00801216,(KBS0714_MOLHKGIG_01345:0.002469,SA211_MHAAABBN_01065:0.000898)n3:0.00465784)n2:0.0721466)n1:0.141233)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001038_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001038_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1caeca15d00da9895fdea9bf79e89efaa3ebee7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001038_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01445:0.0364207,((SA211_MHAAABBN_01063:0.0023463,(KBS0714_MOLHKGIG_01343:0.00134021,TT9_LFPAFLNI_01298:0.00096979)n3:0.00145414)n2:0.0117665,AS2_ACLBLIBL_01549:0.0155817)n1:0.0364207)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001039_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001039_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7aa0c7861c9ee942e0e4d8cb6cc3f50c3a489e86
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001039_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01446:0.03606,(AS2_ACLBLIBL_01550:0.033598,((KBS0714_MOLHKGIG_01342:0,SA211_MHAAABBN_01062:0)n3:0,TT9_LFPAFLNI_01297:0)n2:0.024513)n1:0.03606)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001040_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001040_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bffd6190ca0b9db955d18b73051e55142af442f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001040_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01448:0.0518463,((SA211_MHAAABBN_01060:0.0002003,(KBS0714_MOLHKGIG_01340:0.00766536,TT9_LFPAFLNI_01295:0.00119464)n3:0.00214572)n2:0.0237729,AS2_ACLBLIBL_01552:0.0325905)n1:0.0518463)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001043_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001043_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdf0f62eef1288fee9c590934ec87d806ee439f2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001043_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01451:0.0451938,((SA211_MHAAABBN_01057:0.00162819,(TT9_LFPAFLNI_01292:0.00332052,KBS0714_MOLHKGIG_01336:0.00552748)n3:0.0103856)n2:0.0140379,AS2_ACLBLIBL_01555:0.0149733)n1:0.0451938)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001044_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001044_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fb0c23edc5ae8ccd515dbb1bcc936ecd5e69419
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001044_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01452:0.132961,(AS2_ACLBLIBL_01556:0.0535076,(KBS0714_MOLHKGIG_01335:0.0141666,(SA211_MHAAABBN_01056:0.0124369,TT9_LFPAFLNI_01291:0.00242613)n3:0.00410937)n2:0.0397439)n1:0.132961)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001045_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001045_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45ffd37082277f79687d70a6538dd8a544ec650b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001045_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01454:0.0479646,(((SA211_MHAAABBN_01054:0,KBS0714_MOLHKGIG_01333:0)n3:0.00133525,AS2_ACLBLIBL_01558:0.00547975)n2:0.00144975,TT9_LFPAFLNI_01289:0.0130297)n1:0.0479646)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001046_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001046_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15b7d657f65ec85384b6e620a6380a0cda752f52
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001046_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01455:0.124025,(TT9_LFPAFLNI_01288:0.111989,((KBS0714_MOLHKGIG_01332:0,SA211_MHAAABBN_01053:0)n3:0,AS2_ACLBLIBL_01559:0)n2:0.1212)n1:0.124025)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001048_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001048_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ff0da9199b99001b7674f385564934ac6dfb0f2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001048_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01457:0.0363324,((SA211_MHAAABBN_01051:0.00260425,(TT9_LFPAFLNI_01286:0,KBS0714_MOLHKGIG_01330:0)n3:0.00110875)n2:0.00150325,AS2_ACLBLIBL_01561:0.0142072)n1:0.0363324)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001050_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001050_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..087960996643d51fad3e5d752d739f1061e9a771
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001050_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01459:0.472936,((TT9_LFPAFLNI_01284:0.0307877,(SA211_MHAAABBN_01049:0.00254475,KBS0714_MOLHKGIG_01328:0.0108492)n3:0.0185562)n2:0.0209247,AS2_ACLBLIBL_01563:0.0579078)n1:0.472936)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001051_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001051_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f23aeba4c6bbfa89e78df9baecfe726113eaf6a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001051_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01460:0.0550306,(TT9_LFPAFLNI_01283:0.00552175,(SA211_MHAAABBN_01048:0.00784825,(AS2_ACLBLIBL_01564:0,KBS0714_MOLHKGIG_01327:0)n3:0.00096275)n2:0.00110825)n1:0.0550306)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001053_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001053_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..395437150d7cdb4d4edc4fa364423362eb0931c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001053_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01462:0.0058055,(AS2_ACLBLIBL_01566:0.02486,((TT9_LFPAFLNI_01281:4.13398e-08,KBS0714_MOLHKGIG_01325:0.00162425)n3:0.00105775,SA211_MHAAABBN_01046:0.00118325)n2:0.00150875)n1:0.0058055)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001054_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001054_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c0223ec7fd3cefa2ff539a7db51d5867531fde3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001054_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01463:0.0991342,((SA211_MHAAABBN_01045:0.00354919,(KBS0714_MOLHKGIG_01324:0.0087235,TT9_LFPAFLNI_01280:0.0072605)n3:0.00536596)n2:0.0396397,AS2_ACLBLIBL_01567:0.0922125)n1:0.0991342)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001056_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001056_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6469b5a58ad056da479b2f779d06aaec1831144
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001056_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01465:0.42203,(((KBS0714_MOLHKGIG_01322:0.00111462,TT9_LFPAFLNI_01278:0.0209294)n3:0.0177446,SA211_MHAAABBN_01043:0.0391379)n2:0.344355,AS2_ACLBLIBL_01569:0.541672)n1:0.42203)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001059_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001059_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db0a7f03b8ef46012e5447ed330ac5e95814cdf4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001059_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01468:0.0376795,((TT9_LFPAFLNI_01275:0.0019004,(KBS0714_MOLHKGIG_01319:0.0166975,SA211_MHAAABBN_01040:0.00193249)n3:0.00097742)n2:0.00452603,AS2_ACLBLIBL_01572:0.021729)n1:0.0376795)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001060_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001060_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c299796b9483f957ed79d9b68fce90896d02f096
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001060_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01470:0.0802503,((KBS0714_MOLHKGIG_01318:0.00070729,(TT9_LFPAFLNI_01274:0.00797131,SA211_MHAAABBN_01039:0.00227769)n3:0.0141782)n2:0.0259797,AS2_ACLBLIBL_01574:0.0248243)n1:0.0802503)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001064_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001064_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20e11420847ccb5bb3c7fa0c6e11c000f8f2018a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001064_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01476:0.053415,((SA211_MHAAABBN_01035:0.003343,TT9_LFPAFLNI_01270:0.003476)n2:0.154133,(KBS0714_MOLHKGIG_01312:0,AS2_ACLBLIBL_01580:0)n3:0.063052)n1:0.053415)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001075_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001075_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37e2b8648dab9a454d323b2c8401619747d37159
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001075_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01488:0.221508,(AS2_ACLBLIBL_01592:0.061121,((SA211_MHAAABBN_01023:0,KBS0714_MOLHKGIG_01300:0)n3:0,TT9_LFPAFLNI_01258:0)n2:0.129964)n1:0.221508)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001081_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001081_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd61e9019ca3023249ba06b15f70d2f370a6e2f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001081_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01494:0.0627583,(AS2_ACLBLIBL_01598:0.0312284,((KBS0714_MOLHKGIG_01287:0.00196963,SA211_MHAAABBN_01006:1.882e-07)n3:0.00074238,TT9_LFPAFLNI_01245:0.00269962)n2:0.0261039)n1:0.0627583)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001082_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001082_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d804df7f87679029c65dacc303d0cce085d13969
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001082_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01495:0.196987,(AS2_ACLBLIBL_01599:0.0618447,(KBS0714_MOLHKGIG_01286:0.0139262,(SA211_MHAAABBN_01005:0,TT9_LFPAFLNI_01244:0)n3:0.0155558)n2:0.0906383)n1:0.196987)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001084_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001084_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c8f748f1cb7b769558c1ffd54557df6bc106ef4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001084_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01498:0.184628,(AS2_ACLBLIBL_01602:0.15881,((TT9_LFPAFLNI_01241:0,SA211_MHAAABBN_01002:0)n3:0.0331489,KBS0714_MOLHKGIG_01283:0.00718313)n2:0.0957512)n1:0.184628)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001085_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001085_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37e8044511c92ddb3c9e4f5a1a1c1298a2acce32
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001085_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01499:0.354634,((KBS0714_MOLHKGIG_01282:0.0164287,(TT9_LFPAFLNI_01240:0,SA211_MHAAABBN_01001:0)n3:0.00852833)n2:0.147695,AS2_ACLBLIBL_01603:0.134845)n1:0.354634)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001088_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001088_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d7c75d2ef8b0408c13c077e59d1670d916fd5a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001088_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01501:0.125398,((KBS0714_MOLHKGIG_01280:6.93717e-07,(TT9_LFPAFLNI_01238:6.93717e-07,SA211_MHAAABBN_00999:0.00374981)n3:0.00185364)n2:0.0597585,AS2_ACLBLIBL_01606:0.378173)n1:0.125398)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001091_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001091_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd98027fa7cc2028d3c89297272fcf00920b0409
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001091_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01505:0.116697,(((TT9_LFPAFLNI_01235:0,SA211_MHAAABBN_00996:0)n3:0.00579775,KBS0714_MOLHKGIG_01277:0.0123392)n2:0.0923367,AS2_ACLBLIBL_01610:0.0946967)n1:0.116697)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001092_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001092_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9a5de14097f6718ddfd56f9a5e9cb45a1e00153
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001092_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01506:0.0926075,(AS2_ACLBLIBL_01611:0.080588,(KBS0714_MOLHKGIG_01276:0.004336,(SA211_MHAAABBN_00995:5.85e-05,TT9_LFPAFLNI_01234:0.0010755)n3:0.0049595)n2:0.060638)n1:0.0926075)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001093_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001093_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7cb0b64bf038d5b31e82656a214d83173049ad22
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001093_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01507:0.036105,(AS2_ACLBLIBL_01612:0.082044,(KBS0714_MOLHKGIG_01275:0,(SA211_MHAAABBN_00994:0,TT9_LFPAFLNI_01233:0)n3:0)n2:0.048586)n1:0.036105)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001095_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001095_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2442a737b3dfa1c62e9c558fbbcd5a0c3109486
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001095_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01509:0.0964124,(AS2_ACLBLIBL_01614:0.0649543,((TT9_LFPAFLNI_01231:0,SA211_MHAAABBN_00992:0)n3:0.00152725,KBS0714_MOLHKGIG_01273:0.00097275)n2:0.0711708)n1:0.0964124)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001096_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001096_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7a119d50bf220fa889ba59eba3ebb871c7c95cf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001096_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01511:0.288714,(AS2_ACLBLIBL_01616:0.140381,(TT9_LFPAFLNI_01229:8.84081e-07,(SA211_MHAAABBN_00990:8.84081e-07,KBS0714_MOLHKGIG_01271:0.00771788)n3:0.00160188)n2:0.160155)n1:0.288714)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001102_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001102_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee1af091c225a584f40e0047bb7576504adaa3f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001102_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01517:0.0531033,(AS2_ACLBLIBL_01622:0.0301423,(KBS0714_MOLHKGIG_01265:0.00457276,(TT9_LFPAFLNI_01223:0,SA211_MHAAABBN_00984:0)n3:0.00792524)n2:0.0289462)n1:0.0531033)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001106_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001106_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..73c543c5ec38e7c7a8eafd378fa4596c999fbebb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001106_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01524:0.0497308,(AS2_ACLBLIBL_01627:0.171319,(KBS0714_MOLHKGIG_01261:4.03676e-07,(SA211_MHAAABBN_00980:0,TT9_LFPAFLNI_01219:0)n3:0.00189558)n2:0.131099)n1:0.0497308)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001107_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001107_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c115ab53c26c566d2cfc0a03e8cc07302d84bfcd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001107_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01526:0.0633173,(AS2_ACLBLIBL_01628:0.0674285,((TT9_LFPAFLNI_01217:0,SA211_MHAAABBN_00978:0)n3:0.003981,KBS0714_MOLHKGIG_01259:0.00337)n2:0.055792)n1:0.0633173)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001108_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001108_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11fbfb58e9421364856f3f84998a3ef177bcbca4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001108_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01527:0.295216,(AS2_ACLBLIBL_01629:0.189386,((SA211_MHAAABBN_00977:0,KBS0714_MOLHKGIG_01258:0)n3:0,TT9_LFPAFLNI_01216:0)n2:0.269757)n1:0.295216)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001109_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001109_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43935b57362b5b82740fe2c8bb99c128ed1b70c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001109_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01528:0.00141463,((KBS0714_MOLHKGIG_01257:1.03432e-08,(SA211_MHAAABBN_00976:0,TT9_LFPAFLNI_01215:0)n3:0.00282625)n2:0.00534025,AS2_ACLBLIBL_01630:1.03432e-08)n1:0.00141463)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001110_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001110_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..060cf79a68aee67c5588feb41fbc3c27ff74e5ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001110_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01529:0.476764,(AS2_ACLBLIBL_01632:0.191984,(KBS0714_MOLHKGIG_01256:0,(SA211_MHAAABBN_00975:0,TT9_LFPAFLNI_01214:0)n3:0)n2:0.33738)n1:0.476764)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001111_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001111_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bedd7124db131663a8936134adb77dfe3e797f1d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001111_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01530:0.0268202,(AS2_ACLBLIBL_01633:0.0409356,((TT9_LFPAFLNI_01213:0.00088188,SA211_MHAAABBN_00974:1.34074e-07)n3:0.00461313,KBS0714_MOLHKGIG_01255:0.00929437)n2:0.0247176)n1:0.0268202)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001112_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001112_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d8c4d7fc51e418b0042d8a8bdf96aa4350947b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001112_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01531:0.159041,((AS2_ACLBLIBL_01634:0.11078,KBS0714_MOLHKGIG_01254:0.0220883)n2:0.0192457,(TT9_LFPAFLNI_01212:4.93971e-07,SA211_MHAAABBN_00973:0.0116193)n3:0.0139063)n1:0.159041)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001114_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001114_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c9301df9012fd53f74a6aa137f77ac2c790eb9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001114_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01534:0.02649,((KBS0714_MOLHKGIG_01251:0.00318175,(SA211_MHAAABBN_00970:0.00060725,TT9_LFPAFLNI_01209:0.00130175)n3:0.00514325)n2:0.0313208,AS2_ACLBLIBL_01637:0.022498)n1:0.02649)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001116_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001116_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..027fc6514f7f4b455dddcacb128275daad5b13c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001116_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01536:0.0564038,(AS2_ACLBLIBL_01639:0.0400945,((SA211_MHAAABBN_00968:0,TT9_LFPAFLNI_01207:0)n3:0.000336,KBS0714_MOLHKGIG_01249:0.004939)n2:0.0365415)n1:0.0564038)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001117_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001117_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7af7024f18fbbe3c2c25d31ff506bbe4e398414
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001117_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01537:0.0277312,(AS2_ACLBLIBL_01640:0.0157355,((TT9_LFPAFLNI_01206:0,KBS0714_MOLHKGIG_01248:0)n3:0,SA211_MHAAABBN_00967:0)n2:0.0542235)n1:0.0277312)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001118_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001118_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27f9cea4beb8c6467bcd8ed5f3b009c8660bac7e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001118_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01538:0.0449512,(AS2_ACLBLIBL_01641:0.0256435,(KBS0714_MOLHKGIG_01247:0,(SA211_MHAAABBN_00966:0,TT9_LFPAFLNI_01205:0)n3:0)n2:0.0220595)n1:0.0449512)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001120_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001120_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ebc3fe251e183c8216a3ca35ec6591514da4c77
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001120_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01540:0.092703,(((KBS0714_MOLHKGIG_01245:0,SA211_MHAAABBN_00964:0)n3:0.001668,TT9_LFPAFLNI_01203:0.006336)n2:0.011915,AS2_ACLBLIBL_01643:0.034329)n1:0.092703)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001122_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001122_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1b9da053d43bca02957587f89fd7825491bbcdc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001122_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01543:0.0744745,(AS2_ACLBLIBL_01646:0.031977,(SA211_MHAAABBN_00961:0.002074,(KBS0714_MOLHKGIG_01242:5e-07,TT9_LFPAFLNI_01200:5e-07)n3:0.0036735)n2:0.029471)n1:0.0744745)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001123_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001123_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..640cabcb468f7e8c87a4137297e2dfb14ee61ad7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001123_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01544:0.0302028,(((KBS0714_MOLHKGIG_01241:0,TT9_LFPAFLNI_01199:0)n3:0.0002375,SA211_MHAAABBN_00960:0.0007095)n2:0.017533,AS2_ACLBLIBL_01647:0.0209355)n1:0.0302028)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001126_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001126_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2afdf6cd5e139a1bd63f7e80fcc175938ba074a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001126_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01547:0.0867667,(AS2_ACLBLIBL_01650:0.0312087,(TT9_LFPAFLNI_01196:2.51334e-07,(SA211_MHAAABBN_00957:0,KBS0714_MOLHKGIG_01238:0.002378)n3:0.00047936)n2:0.0442135)n1:0.0867667)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001128_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001128_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3db4e61f6e445897b87055628b853572b42b18e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001128_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01549:0.12282,(((TT9_LFPAFLNI_01194:0.0013795,SA211_MHAAABBN_00955:4.16187e-07)n3:0.015219,KBS0714_MOLHKGIG_01236:0.0160055)n2:0.0445915,AS2_ACLBLIBL_01652:0.0934798)n1:0.12282)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001129_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001129_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5508c11a0060a8e5d731486501cbdb7efe4b56f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001129_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01550:0.0628819,(AS2_ACLBLIBL_01653:0.0273362,((KBS0714_MOLHKGIG_01235:0.00393495,SA211_MHAAABBN_00954:1.76514e-07)n3:0.00043111,TT9_LFPAFLNI_01193:0.00224284)n2:0.0169625)n1:0.0628819)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001130_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001130_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b519f4b68ef80f05f1707272d06d62dc8afcacc8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001130_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01551:0.145814,(AS2_ACLBLIBL_01654:0.0576804,((KBS0714_MOLHKGIG_01234:0.00460038,SA211_MHAAABBN_00953:0.00538762)n3:0.0119279,TT9_LFPAFLNI_01192:0.0141166)n2:0.0492029)n1:0.145814)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001131_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001131_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99fc73003373e8e44a5791fb560d1637e28043a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001131_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01552:0.116355,(AS2_ACLBLIBL_01655:0.192157,((KBS0714_MOLHKGIG_01233:0.040229,SA211_MHAAABBN_00952:0.029887)n3:0.00795638,TT9_LFPAFLNI_01191:0.0201283)n2:0.143576)n1:0.116355)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001134_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001134_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..096f70d6904ad2a86e7b0bb835451e18131a545e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001134_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01555:0.199734,((KBS0714_MOLHKGIG_01230:0.00527456,(SA211_MHAAABBN_00949:0,TT9_LFPAFLNI_01188:0)n3:0.00566444)n2:0.0181677,AS2_ACLBLIBL_01658:0.0628182)n1:0.199734)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001135_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001135_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82dc04271258e00cc556ac194f051d9126822cec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001135_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01556:0.281169,(AS2_ACLBLIBL_01659:0.380747,(KBS0714_MOLHKGIG_01229:0.17824,(SA211_MHAAABBN_00948:0.0253067,TT9_LFPAFLNI_01187:0.00191226)n3:0.0813176)n2:0.221541)n1:0.281169)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001137_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001137_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d54f962b6602abcf1651ab0ace242db8abb8321
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001137_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01558:0.0889217,(AS2_ACLBLIBL_01661:0.0448727,(KBS0714_MOLHKGIG_01227:0.00367166,(SA211_MHAAABBN_00946:0,TT9_LFPAFLNI_01185:0)n3:0.00679234)n2:0.0469939)n1:0.0889217)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001140_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001140_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1dd3a86806bba40fe247d7c3eaaa07292e7e0d01
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001140_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01561:0.0321533,(AS2_ACLBLIBL_01664:0.0133493,((TT9_LFPAFLNI_01182:0.00046577,SA211_MHAAABBN_00943:0.00244823)n3:0.00383651,KBS0714_MOLHKGIG_01224:0.00588041)n2:0.0149276)n1:0.0321533)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001141_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001141_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00271dc3357bcf49a38fc2e31f0335d650f72648
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001141_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01563:0.209612,(((TT9_LFPAFLNI_01180:0.00594816,KBS0714_MOLHKGIG_01222:5.32653e-07)n3:0.00053116,SA211_MHAAABBN_00941:0)n2:0.0541386,AS2_ACLBLIBL_01666:0.0533415)n1:0.209612)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001143_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001143_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..630ba3a3a995bd4c810b1861f070271186c19945
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001143_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01565:0.075929,(((KBS0714_MOLHKGIG_01220:0.00500644,TT9_LFPAFLNI_01178:0.00142456)n3:0.00601526,SA211_MHAAABBN_00939:0.00043161)n2:0.0478671,AS2_ACLBLIBL_01668:0.04644)n1:0.075929)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001144_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001144_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e8c273db1f587d6e6fd4fc5fc43deda59bc88c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001144_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01566:0.108589,(AS2_ACLBLIBL_01669:0.0496665,(TT9_LFPAFLNI_01177:0.002738,(KBS0714_MOLHKGIG_01219:0,SA211_MHAAABBN_00938:0)n3:0.000879)n2:0.0331405)n1:0.108589)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001145_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001145_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d5bcf9367337857a902d04063751ee8bab8ef06
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001145_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01567:0.125053,(AS2_ACLBLIBL_01670:0.0807845,((TT9_LFPAFLNI_01176:4.18023e-07,SA211_MHAAABBN_00937:0.003308)n3:0.00643225,KBS0714_MOLHKGIG_01218:0.00286475)n2:0.0745813)n1:0.125053)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001146_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001146_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a34652f750a5b7e328da0f86e509bcea0ee14a5e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001146_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01568:0.0848813,(AS2_ACLBLIBL_01671:0.0557555,((TT9_LFPAFLNI_01174:0,KBS0714_MOLHKGIG_01217:0)n3:0,SA211_MHAAABBN_00936:0)n2:0.0805055)n1:0.0848813)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001147_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001147_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ff6098751d06f5667e495b66fa8efd30a42e34b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001147_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001149_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001149_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5be9189718b0e3daf091d6d2f4908dae2013c230
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001149_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001150_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001150_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66b5fc7feb4cd050441fa529a8d02d0c895f36e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001150_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01572:0.0365114,(AS2_ACLBLIBL_01675:0.0184211,(SA211_MHAAABBN_00932:0.00267863,(KBS0714_MOLHKGIG_01213:0.00083387,TT9_LFPAFLNI_01170:4.313e-05)n3:0.00347487)n2:0.0272884)n1:0.0365114)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001157_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001157_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fc25ffc22dfdcbd1f8eb81ed472b9c157ff460b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001157_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01580:0.0850972,(((KBS0714_MOLHKGIG_01205:0.0187438,TT9_LFPAFLNI_01162:0.00500224)n3:0.00263839,SA211_MHAAABBN_00924:0.00753985)n2:0.0164935,AS2_ACLBLIBL_01682:0.0179375)n1:0.0850972)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001158_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001158_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4b9684e4f9451c74d77894a05fb9e7e56cc4138
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001158_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01581:0.0148287,(AS2_ACLBLIBL_01683:0.00334963,(SA211_MHAAABBN_00923:0.00666587,(KBS0714_MOLHKGIG_01204:0.0208519,TT9_LFPAFLNI_01161:0.00316912)n3:0.00079113)n2:0.0133321)n1:0.0148287)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001161_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001161_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4866eed9e08b5a91b9abe7ed1be70faffb8ebda
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001161_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01584:0.0492802,(AS2_ACLBLIBL_01687:0.0110875,(TT9_LFPAFLNI_01154:0.00539175,(KBS0714_MOLHKGIG_01200:0.0113848,SA211_MHAAABBN_00920:0.00107025)n3:0.00259625)n2:0.00421825)n1:0.0492802)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001164_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001164_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b4df721ebccc1a52f1f4ac653448937b493e6a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001164_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01587:0.0496772,((KBS0714_MOLHKGIG_01197:0.00439681,(SA211_MHAAABBN_00917:0,TT9_LFPAFLNI_01151:0)n3:0.00011119)n2:0.0631383,AS2_ACLBLIBL_01690:0.0517957)n1:0.0496772)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001166_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001166_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91ff476e6311c0a2a10542fd65ffaefeaa82b397
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001166_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01590:0.278451,(AS2_ACLBLIBL_01692:0.268741,(TT9_LFPAFLNI_01149:0.0217027,(SA211_MHAAABBN_00915:0.0189621,KBS0714_MOLHKGIG_01195:0.0213929)n3:0.00719581)n2:0.188156)n1:0.278451)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001168_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001168_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b03a5195d1d65dffc65f7afc5bd4b00076604dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001168_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01594:0.284292,(AS2_ACLBLIBL_01695:0.0962423,(SA211_MHAAABBN_00912:0.0114285,(TT9_LFPAFLNI_01143:0.00106925,KBS0714_MOLHKGIG_01193:0.0113328)n3:0.0081195)n2:0.117665)n1:0.284292)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001170_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001170_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..735842bdc580f31827383d6627eafb3d107e71e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001170_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01596:0.220674,(AS2_ACLBLIBL_01697:0.0665802,(SA211_MHAAABBN_00910:0.00504153,(KBS0714_MOLHKGIG_01191:0,TT9_LFPAFLNI_01141:0)n3:0.00463547)n2:0.138442)n1:0.220674)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001172_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001172_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45e215be291458b0126947bc7343937fd2e942fe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001172_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01598:0.0932116,((KBS0714_MOLHKGIG_01189:0,TT9_LFPAFLNI_01139:0)n2:0.00415175,(AS2_ACLBLIBL_01699:0.0277856,SA211_MHAAABBN_00908:2.21173e-07)n3:0.00281825)n1:0.0932116)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001175_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001175_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a7dfad3dc533e794335728ac17968c3ddb2a2c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001175_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01601:0.100424,(AS2_ACLBLIBL_01702:0.0420896,(SA211_MHAAABBN_00905:0.0135961,(TT9_LFPAFLNI_01136:0.00161487,KBS0714_MOLHKGIG_01186:3.21447e-07)n3:0.0106719)n2:0.0529364)n1:0.100424)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001176_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001176_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..134fce3ecabf33091cdeef9b0e38aedaaf2e7f69
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001176_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01602:0.195508,(AS2_ACLBLIBL_01703:0.0732155,(SA211_MHAAABBN_00904:0.00462543,(TT9_LFPAFLNI_01135:0,KBS0714_MOLHKGIG_01185:0)n3:0.00928157)n2:0.055479)n1:0.195508)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001177_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001177_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f714b3a0eb77308f9a6e03387346b880ea61d108
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001177_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01603:0.281003,(AS2_ACLBLIBL_01704:0.117273,(KBS0714_MOLHKGIG_01184:0,(SA211_MHAAABBN_00903:0,TT9_LFPAFLNI_01134:0)n3:0)n2:0.0697365)n1:0.281003)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001180_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001180_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f81b2014d65b6b114698c0cd43e2d696f5fa8a20
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001180_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01607:0.0807321,((SA211_MHAAABBN_00899:0.00114738,(TT9_LFPAFLNI_01130:0.00189287,KBS0714_MOLHKGIG_01180:0.0112061)n3:0.00184662)n2:0.0288351,AS2_ACLBLIBL_01709:0.0534089)n1:0.0807321)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001184_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001184_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40d1da5075d5b2972fe0fee296fb7f68a5bb091a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001184_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01611:0.134486,(((SA211_MHAAABBN_00895:0.002076,KBS0714_MOLHKGIG_01176:0.000986)n3:0.00170225,TT9_LFPAFLNI_01126:0.00887425)n2:0.00299025,AS2_ACLBLIBL_01713:0.0102495)n1:0.134486)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001187_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001187_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80a232067e529bbacceb72acb2e1efc568ff9e75
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001187_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01614:0.243944,((KBS0714_MOLHKGIG_01173:0.0139588,(TT9_LFPAFLNI_01123:0.0065625,SA211_MHAAABBN_00892:0.0099225)n3:0.0197538)n2:0.147211,AS2_ACLBLIBL_01716:0.154627)n1:0.243944)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001188_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001188_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63966b35ef07619a77c634638fb4cfb3d848b6e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001188_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01615:0.101623,(AS2_ACLBLIBL_01717:0.157383,((SA211_MHAAABBN_00891:0.0137319,KBS0714_MOLHKGIG_01172:0.0217351)n3:0.00419337,TT9_LFPAFLNI_01122:0.0261981)n2:0.133686)n1:0.101623)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001190_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001190_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc6e5f37170c7c31fa7f0d4d0408a731d53ce87e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001190_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01617:0.0780991,(((KBS0714_MOLHKGIG_01170:0,TT9_LFPAFLNI_01120:0)n3:0.00106275,SA211_MHAAABBN_00889:0.00605025)n2:0.0586228,AS2_ACLBLIBL_01719:0.0634217)n1:0.0780991)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001191_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001191_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7012e0ef1cfaf19a72a7d69f0322e389f90319c1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001191_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01618:0.0346023,(AS2_ACLBLIBL_01720:0.0348035,((TT9_LFPAFLNI_01119:0,SA211_MHAAABBN_00888:0)n3:0,KBS0714_MOLHKGIG_01169:0)n2:0.0739665)n1:0.0346023)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001192_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001192_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ce0cae4f871a10951cd6d326c6a9bfc1c69c12
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001192_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01619:0.0472573,(AS2_ACLBLIBL_01721:0.0336045,((KBS0714_MOLHKGIG_01168:0,TT9_LFPAFLNI_01118:0)n3:0,SA211_MHAAABBN_00887:0)n2:0.0170745)n1:0.0472573)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001193_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001193_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c2d5f9810fae54a91bca5b95e7c3f5c83abc72f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001193_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01620:0.0397845,(AS2_ACLBLIBL_01722:0.084802,(TT9_LFPAFLNI_01117:0.0032155,(SA211_MHAAABBN_00886:0,KBS0714_MOLHKGIG_01167:0)n3:0.0032155)n2:0.0822745)n1:0.0397845)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001195_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001195_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bebd8739bdaa21765c5a897a64815b601a1754ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001195_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001196_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001196_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27f5ca786ebc72330a44addf6f939c392007100d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001196_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01624:0.192072,((TT9_LFPAFLNI_01113:0.00634795,(SA211_MHAAABBN_00882:0.0150563,KBS0714_MOLHKGIG_01163:0.00853366)n3:0.0088838)n2:0.107503,AS2_ACLBLIBL_01727:0.123701)n1:0.192072)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001200_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001200_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92c7ea7df1efc1aaa98771e7564d815d3b7dea25
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001200_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01629:0.0663517,(AS2_ACLBLIBL_01731:0.0301507,((KBS0714_MOLHKGIG_01158:0,TT9_LFPAFLNI_01108:0)n3:0.00114603,SA211_MHAAABBN_00877:0.00011797)n2:0.0406927)n1:0.0663517)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001204_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001204_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f47d7441a6cd2aae5b49d8bdd3b2ed2d7f6036b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001204_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01633:0.00585475,(((TT9_LFPAFLNI_01103:0,SA211_MHAAABBN_00872:0)n3:0,KBS0714_MOLHKGIG_01153:0)n2:0.0086455,AS2_ACLBLIBL_01738:0.0086455)n1:0.00585475)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001206_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001206_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0649d053fdf587fc5fc59a02996b7453c214cbd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001206_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01636:0.0950491,(AS2_ACLBLIBL_01742:0.0650418,(KBS0714_MOLHKGIG_01150:3.35996e-07,(SA211_MHAAABBN_00869:0,TT9_LFPAFLNI_01100:0)n3:0.0100534)n2:0.07151)n1:0.0950491)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001207_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001207_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a0a594f434154b0ff9e384d764d9363c4caa42c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001207_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01637:0.134595,(AS2_ACLBLIBL_01743:0.0599527,(KBS0714_MOLHKGIG_01149:0.00204429,(TT9_LFPAFLNI_01099:0,SA211_MHAAABBN_00868:0)n3:0.00171871)n2:0.0350064)n1:0.134595)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001208_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001208_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dca881c9d4986306d1475cd09b09348b0cc8252
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001208_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01638:0.0268168,((KBS0714_MOLHKGIG_01148:0.011067,(TT9_LFPAFLNI_01098:0,SA211_MHAAABBN_00867:0)n3:0.009462)n2:0.0254015,AS2_ACLBLIBL_01744:0.0432665)n1:0.0268168)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001213_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001213_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c19def5551e74b12283fce04974952e3dea9cbd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001213_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01645:0.0194262,(AS2_ACLBLIBL_01751:0.00160254,((TT9_LFPAFLNI_01091:0,SA211_MHAAABBN_00860:0)n3:0.0128645,KBS0714_MOLHKGIG_01141:0.0026345)n2:0.002914)n1:0.0194262)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001214_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001214_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2e7a968b7200a57d58443d66400b5b89925101f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001214_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01646:0.0151481,(((TT9_LFPAFLNI_01090:0.00064462,KBS0714_MOLHKGIG_01140:0.00137738)n3:0.00554212,SA211_MHAAABBN_00859:0.00258988)n2:0.0139511,AS2_ACLBLIBL_01752:0.00571987)n1:0.0151481)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001215_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001215_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccebcce63496f688fa6f26daaed3af84150e0fe5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001215_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01647:0.0968801,(AS2_ACLBLIBL_01753:0.0311249,((KBS0714_MOLHKGIG_01139:0.00034663,SA211_MHAAABBN_00858:0.00222237)n3:0.00228963,TT9_LFPAFLNI_01089:0.00510438)n2:0.0369711)n1:0.0968801)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001216_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001216_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4077ad51402bdd1b213fd7f4a5324a7fc2ea8cba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001216_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01648:0.0211285,(AS2_ACLBLIBL_01754:0.014045,((SA211_MHAAABBN_00857:0.00111275,TT9_LFPAFLNI_01088:0.00043725)n3:0.00059575,KBS0714_MOLHKGIG_01138:0.00095425)n2:0.0110393)n1:0.0211285)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001218_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001218_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b67b0bfaff93f6e2385bb8c25ce82f78e13285
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001218_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01650:0.152323,(AS2_ACLBLIBL_01756:0.0771778,(TT9_LFPAFLNI_01086:0.00773675,(KBS0714_MOLHKGIG_01136:0,SA211_MHAAABBN_00855:0)n3:0.00304625)n2:0.0503333)n1:0.152323)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001220_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001220_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c6f27cdfd944004cb02667a2d51126237cce519
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001220_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01652:0.273523,(((KBS0714_MOLHKGIG_01134:0,SA211_MHAAABBN_00853:0)n3:0.00780845,TT9_LFPAFLNI_01084:0.00652255)n2:0.101115,AS2_ACLBLIBL_01758:0.0877803)n1:0.273523)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001221_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001221_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..604e3c92bfdf3396189f30a4b3a830a4da68e115
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001221_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01653:0.0545027,(AS2_ACLBLIBL_01759:0.0417566,(SA211_MHAAABBN_00852:1.8748e-07,(KBS0714_MOLHKGIG_01133:1.8748e-07,TT9_LFPAFLNI_01083:0.00484237)n3:0.00014338)n2:0.0320194)n1:0.0545027)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001223_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001223_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7426311c8aec07b17670392964bdd324839d7d37
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001223_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01655:0.0980753,((TT9_LFPAFLNI_01081:0.000372,(SA211_MHAAABBN_00850:5e-07,KBS0714_MOLHKGIG_01131:5e-07)n3:0.0025265)n2:0.042721,AS2_ACLBLIBL_01761:0.0525805)n1:0.0980753)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001224_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001224_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7344a94ab27a84c751fdc61f5830e5a222297136
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001224_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01656:0.129956,((TT9_LFPAFLNI_01080:0.0005334,(KBS0714_MOLHKGIG_01130:0,SA211_MHAAABBN_00849:0)n3:0.0029116)n2:0.0528356,AS2_ACLBLIBL_01762:0.0764562)n1:0.129956)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001229_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001229_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a46f194ad95d6ecc4bd3bf2f47342390f3ef8d0d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001229_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01661:0.0698233,(AS2_ACLBLIBL_01767:0.0399704,(SA211_MHAAABBN_00844:0.00223513,(TT9_LFPAFLNI_01075:0.00060137,KBS0714_MOLHKGIG_01125:0.00140763)n3:0.0214264)n2:0.0317139)n1:0.0698233)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001230_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001230_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7412de4be250007daacbe4b286fcd3b411a457c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001230_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01662:0.0499143,(AS2_ACLBLIBL_01769:0.0319095,(SA211_MHAAABBN_00843:0.00386625,(TT9_LFPAFLNI_01074:1.67225e-07,KBS0714_MOLHKGIG_01124:0.00153875)n3:0.00206625)n2:0.0280758)n1:0.0499143)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001231_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001231_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9accafcac2be182320447f4e351fa497881f418e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001231_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01663:0.0117897,(AS2_ACLBLIBL_01770:0.0174395,(SA211_MHAAABBN_00842:-0,(KBS0714_MOLHKGIG_01123:0,TT9_LFPAFLNI_01073:0)n3:0)n2:0.0162585)n1:0.0117897)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001232_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001232_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f6824b2e3c22c06dbbc5172f4f7f815431a5cab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001232_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01664:0.0417512,(AS2_ACLBLIBL_01771:0.0226097,(SA211_MHAAABBN_00841:0.00269195,(TT9_LFPAFLNI_01072:0,KBS0714_MOLHKGIG_01122:0)n3:0.00334405)n2:0.0368583)n1:0.0417512)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001233_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001233_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86b409d1cb69988b8e87fd4c32687762ed40043c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001233_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01665:0.107717,(AS2_ACLBLIBL_01772:0.0458857,((TT9_LFPAFLNI_01071:3.18709e-07,KBS0714_MOLHKGIG_01121:0.0109897)n3:0.00579405,SA211_MHAAABBN_00840:0.00445163)n2:0.036665)n1:0.107717)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001236_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001236_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..436bd7918aabf283b8174793784732135b9a4c5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001236_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01670:0.092352,(AS2_ACLBLIBL_01777:0.0294301,((SA211_MHAAABBN_00835:0,TT9_LFPAFLNI_01066:0)n3:0.012513,KBS0714_MOLHKGIG_01116:0.012235)n2:0.0019115)n1:0.092352)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001241_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001241_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64318e90c1871421491e057a325b478d14742ab0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001241_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01676:0.248749,((KBS0714_MOLHKGIG_01109:0.0130059,(SA211_MHAAABBN_00828:0,TT9_LFPAFLNI_01058:0)n3:0.0238411)n2:0.0904335,AS2_ACLBLIBL_01783:0.169468)n1:0.248749)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001245_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001245_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37cc93f9b0ce01af4414fb116d33f234248a5d84
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001245_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001247_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001247_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8a36cfe5e1393c670e4c06e7a9c7816a525f016
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001247_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01684:0.0837747,(AS2_ACLBLIBL_01794:0.0402396,(KBS0714_MOLHKGIG_01101:0.00579437,(TT9_LFPAFLNI_01050:0.00719137,SA211_MHAAABBN_00820:0.00288162)n3:0.00206412)n2:0.0430501)n1:0.0837747)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001248_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001248_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec7eaa422e4ebd5b0fd70c7b3bb4e19bad3fe6b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001248_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01685:0.141901,(AS2_ACLBLIBL_01795:0.0889472,(TT9_LFPAFLNI_01049:0.0234773,(SA211_MHAAABBN_00819:0.0211476,KBS0714_MOLHKGIG_01100:0.00551636)n3:0.00687721)n2:0.10846)n1:0.141901)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001249_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001249_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..463bcb394d5fb8e4b5b695baf44e70e871429354
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001249_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01686:0.0707616,(AS2_ACLBLIBL_01796:0.0237218,((KBS0714_MOLHKGIG_01099:0,SA211_MHAAABBN_00818:0)n3:0.00864823,TT9_LFPAFLNI_01048:0.0535118)n2:0.0922258)n1:0.0707616)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001253_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001253_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8c5ad4bb0d35d255269fc34b864d761b23d420a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001253_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01690:0.185811,(AS2_ACLBLIBL_01800:0.157045,((TT9_LFPAFLNI_01044:5e-07,SA211_MHAAABBN_00814:5e-07)n3:0,KBS0714_MOLHKGIG_01095:5e-07)n2:0.171855)n1:0.185811)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001255_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001255_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe96c600f5f3f89ce949c5af7bb9079c59b55ddc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001255_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01693:0.0982362,(AS2_ACLBLIBL_01804:0.0725485,(TT9_LFPAFLNI_01041:-0,(KBS0714_MOLHKGIG_01092:0,SA211_MHAAABBN_00811:0)n3:0)n2:0.0599835)n1:0.0982362)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001256_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001256_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ba639f56f726b5d3b9403e76140eef9d0c40a60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001256_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01694:0.0385389,(AS2_ACLBLIBL_01805:0.0466722,(KBS0714_MOLHKGIG_01091:0.0040605,(SA211_MHAAABBN_00810:0.003077,TT9_LFPAFLNI_01040:0.002123)n3:0.001669)n2:0.0446555)n1:0.0385389)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001257_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001257_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cad9d7c87bcb2000f90746c956c10e73566afa6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001257_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01695:0.0235698,(AS2_ACLBLIBL_01806:0.278106,((SA211_MHAAABBN_00809:3.70575e-07,KBS0714_MOLHKGIG_01090:0.00138374)n3:0.00281334,TT9_LFPAFLNI_01039:9.84e-05)n2:0.0414006)n1:0.0235698)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001258_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001258_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ad0410155dc7384df3ffd4dd26c840e8cfa66de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001258_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01696:0.0200555,(((TT9_LFPAFLNI_01038:0,SA211_MHAAABBN_00808:0)n3:0,KBS0714_MOLHKGIG_01089:0)n2:0.051496,AS2_ACLBLIBL_01807:0.231876)n1:0.0200555)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001260_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001260_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f32699a09b5a1c8bfc3c82f8c238aecedbd8568
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001260_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01698:0.126853,(AS2_ACLBLIBL_01810:0.026908,((SA211_MHAAABBN_00806:0,TT9_LFPAFLNI_01036:0)n3:0.0162775,KBS0714_MOLHKGIG_01087:0.0110635)n2:0.022982)n1:0.126853)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001267_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001267_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b70df0c1890ebbae85f0e9acec41d4180df55759
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001267_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01705:0.0470337,(AS2_ACLBLIBL_01818:0.0578185,(KBS0714_MOLHKGIG_01080:0.0027795,(TT9_LFPAFLNI_01029:0,SA211_MHAAABBN_00799:0)n3:0.0043225)n2:0.020153)n1:0.0470337)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001268_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001268_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5854dd4059fbfe41805d53baea5ced22e5ba740
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001268_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01706:0.014,(AS2_ACLBLIBL_01819:0.062516,((TT9_LFPAFLNI_01028:0,KBS0714_MOLHKGIG_01079:0)n3:0,SA211_MHAAABBN_00798:0)n2:0.050793)n1:0.014)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001269_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001269_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9a6b08fe6da9973f91a0c78bd8a1716fc065e78
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001269_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01707:0.043913,(((KBS0714_MOLHKGIG_01078:0,TT9_LFPAFLNI_01027:0)n3:0,SA211_MHAAABBN_00797:0)n2:0.003003,AS2_ACLBLIBL_01820:0.003003)n1:0.043913)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001270_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001270_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5619e91aaea1b50987871f77e4edbeb6bfd8f19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001270_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01710:0.0810371,(((SA211_MHAAABBN_00785:0,TT9_LFPAFLNI_01013:0)n3:0.00357701,KBS0714_MOLHKGIG_01066:3.13566e-07)n2:0.0764198,AS2_ACLBLIBL_01821:0.0717158)n1:0.0810371)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001271_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001271_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e61d9e23e31ea874ba09fc1751bbf66804d54d82
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001271_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01713:0.124526,(AS2_ACLBLIBL_01823:0.293622,(SA211_MHAAABBN_00782:0.0122238,(TT9_LFPAFLNI_01010:0.0206237,KBS0714_MOLHKGIG_01063:0.0118353)n3:0.00889625)n2:0.129764)n1:0.124526)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001275_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001275_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d5bc7af33f1f79f426199bd3fceb63cb9d5f411
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001275_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01717:0.185007,(AS2_ACLBLIBL_01827:0.127413,(SA211_MHAAABBN_00778:0.0435182,(KBS0714_MOLHKGIG_01059:0.0136042,TT9_LFPAFLNI_01006:0.0228608)n3:0.00683278)n2:0.0747902)n1:0.185007)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001277_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001277_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ffd6f3f4b19c6ea7439c10f545e2f95969578bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001277_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01719:0.0907338,(AS2_ACLBLIBL_01829:0.0646363,(TT9_LFPAFLNI_01004:0.0109393,(KBS0714_MOLHKGIG_01057:0.00374706,SA211_MHAAABBN_00776:3.2082e-07)n3:0.00591369)n2:0.0544298)n1:0.0907338)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001278_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001278_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53930fca75ba9829bc362c38d46630a5dd5b893b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001278_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01724:0.0448079,(AS2_ACLBLIBL_01834:0.0685562,(SA211_MHAAABBN_00765:0.00169121,(KBS0714_MOLHKGIG_01052:0.00216592,TT9_LFPAFLNI_00993:0.00144508)n3:0.00047479)n2:0.0519369)n1:0.0448079)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001279_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001279_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cdc39f2f0677e0b88585c5e51de55c15ce62f14
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001279_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01725:0.0613065,((SA211_MHAAABBN_00764:0.011151,(TT9_LFPAFLNI_00992:0.0012015,KBS0714_MOLHKGIG_01051:0.0004155)n3:0.0067935)n2:0.0327545,AS2_ACLBLIBL_01835:0.044076)n1:0.0613065)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001280_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001280_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a66c00fafc52ac0229fd979b953acbf5babac367
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001280_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01726:0.0809788,(((SA211_MHAAABBN_00763:0,KBS0714_MOLHKGIG_01050:0)n3:0.001834,TT9_LFPAFLNI_00991:0.001608)n2:0.047936,AS2_ACLBLIBL_01836:0.0564435)n1:0.0809788)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001283_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001283_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f621fd66a844ad76f2033b87495a26fe4b14b4a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001283_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01729:0.151004,(AS2_ACLBLIBL_01841:0.10799,((KBS0714_MOLHKGIG_01047:0.00328867,SA211_MHAAABBN_00760:0.00118033)n3:0.0114735,TT9_LFPAFLNI_00988:0.00716388)n2:0.0774023)n1:0.151004)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001284_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001284_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44c109ed92c78e6fc508d1ebaf67dfb70542d605
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001284_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001285_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001285_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..485e4571c75e9f076328f43e1fff1f2b0f8d48c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001285_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01731:0.0605718,(AS2_ACLBLIBL_01844:0.144525,(TT9_LFPAFLNI_00986:0.00337901,(SA211_MHAAABBN_00758:0.00939047,KBS0714_MOLHKGIG_01045:0.00428253)n3:0.00085699)n2:0.0505365)n1:0.0605718)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001288_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001288_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bffc309d3c8aff10b22832903e9c9f140b30570b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001288_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01737:0.0123621,(AS2_ACLBLIBL_01847:0.0135437,(TT9_LFPAFLNI_00979:0.00120414,(SA211_MHAAABBN_00750:0.00445767,KBS0714_MOLHKGIG_01037:0.00043133)n3:0.00824808)n2:0.00328309)n1:0.0123621)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001289_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001289_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebff2658d4f9a1331f29ead927e29a5583e69310
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001289_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01738:0.00024081,(((KBS0714_MOLHKGIG_01036:0.00891963,SA211_MHAAABBN_00749:3.24459e-08)n3:0.00420138,TT9_LFPAFLNI_00978:0.00580113)n2:0.00030438,AS2_ACLBLIBL_01848:0.0127934)n1:0.00024081)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001290_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001290_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..282ad3bc19471f32264b92be9e32fd6c699f6d0e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001290_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01739:0.00130194,((KBS0714_MOLHKGIG_01035:0.0264156,TT9_LFPAFLNI_00977:0.00235038)n2:0.00111312,(AS2_ACLBLIBL_01849:0.00479312,SA211_MHAAABBN_00748:0.00702288)n3:0.0256656)n1:0.00130194)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001293_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001293_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51be3a426db9ecc4447507d19e87c519b69cae77
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001293_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01745:0.0318493,((TT9_LFPAFLNI_00971:0.00231625,(SA211_MHAAABBN_00742:0.00399925,KBS0714_MOLHKGIG_01027:0.00365775)n3:0.00227775)n2:0.0287262,AS2_ACLBLIBL_01858:0.0261625)n1:0.0318493)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001295_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001295_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..140f2de8f88e0a30c54562ebaa21446d63551d00
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001295_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01750:0.140277,(AS2_ACLBLIBL_01860:0.0176551,((SA211_MHAAABBN_00740:3.47641e-07,KBS0714_MOLHKGIG_01025:0.00214712)n3:0.00057313,TT9_LFPAFLNI_00969:3.47641e-07)n2:0.0478571)n1:0.140277)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001296_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001296_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8e70d8c9f0dc915fb2add5b253e6521276f7072
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001296_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01751:0.0341678,(KBS0714_MOLHKGIG_01024:9.06556e-08,(SA211_MHAAABBN_00739:9.06556e-08,(AS2_ACLBLIBL_01861:0.0228926,TT9_LFPAFLNI_00968:9.06556e-08)n3:0.00057263)n2:0.00057263)n1:0.0341678)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001298_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001298_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..035f30072d8c2ea184d79ff2bc8c0ec6e92ba49e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001298_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01762:0.488496,(AS2_ACLBLIBL_01866:0.517426,(TT9_LFPAFLNI_00965:0.0154658,(KBS0714_MOLHKGIG_01021:0.00255983,SA211_MHAAABBN_00735:0.00730017)n3:0.00809471)n2:0.20239)n1:0.488496)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001300_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001300_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6433449de3c9b7521ca47944eb211054874b840d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001300_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01760:0.235653,(((KBS0714_MOLHKGIG_01019:0.0215467,SA211_MHAAABBN_00733:0.0128453)n3:0.0110623,TT9_LFPAFLNI_00963:0.00810904)n2:0.100931,AS2_ACLBLIBL_01868:0.150292)n1:0.235653)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001307_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001307_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a9331defab51d8c545c209cac583a83642c46f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001307_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01813:0.155277,((TT9_LFPAFLNI_00948:0.015578,(KBS0714_MOLHKGIG_01005:0,SA211_MHAAABBN_00719:0)n3:0.001862)n2:0.0751847,AS2_ACLBLIBL_01885:0.0715993)n1:0.155277)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001308_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001308_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9507f30c00b58dc895be85984517c1f5f546f03
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001308_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01814:0.111453,(((KBS0714_MOLHKGIG_01004:0.00039048,SA211_MHAAABBN_00718:0.00020652)n3:0.00813547,TT9_LFPAFLNI_00947:0.00216675)n2:0.0470501,AS2_ACLBLIBL_01886:0.0561255)n1:0.111453)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001309_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001309_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fe8a997d00d5f3efbbc4145ec0556d8389f2155
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001309_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01815:0.0973774,(((SA211_MHAAABBN_00717:0.00298941,TT9_LFPAFLNI_00946:0.00833959)n3:0.00334952,KBS0714_MOLHKGIG_01003:0.00251078)n2:0.067661,AS2_ACLBLIBL_01887:0.0504892)n1:0.0973774)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001310_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001310_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b997a6a55e2c6ebe8cb1f3f828c52796c54aa706
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001310_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01816:0.055919,(AS2_ACLBLIBL_01888:0.022658,((TT9_LFPAFLNI_00945:0,SA211_MHAAABBN_00716:0)n3:0,KBS0714_MOLHKGIG_01002:0)n2:0.043309)n1:0.055919)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001311_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001311_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3abefb673d9c1c1d7acd9fb351ced9ebbec45474
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001311_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01817:0.032072,(SA211_MHAAABBN_00715:0,(AS2_ACLBLIBL_01889:0,(TT9_LFPAFLNI_00944:0,KBS0714_MOLHKGIG_01001:0)n3:0)n2:0)n1:0.032072)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001312_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001312_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54c1c9cf300a5e1b0c9587f78ee252479d3417cf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001312_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01818:0.0173953,(AS2_ACLBLIBL_01890:0.0106185,(SA211_MHAAABBN_00714:0,(TT9_LFPAFLNI_00943:0,KBS0714_MOLHKGIG_01000:0)n3:0)n2:0.0104905)n1:0.0173953)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001313_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001313_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3c9f3cfbbfa4caaa3d124001679261a471b981c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001313_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01819:0.125269,((TT9_LFPAFLNI_00942:0.0592686,(SA211_MHAAABBN_00713:5e-07,KBS0714_MOLHKGIG_00999:5e-07)n3:0.0356369)n2:0.215691,AS2_ACLBLIBL_01891:0.234628)n1:0.125269)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001315_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001315_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdfa54ead891ec9940100e86319c400f2e453a28
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001315_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01839:0.0824778,(AS2_ACLBLIBL_01893:0.0555415,((TT9_LFPAFLNI_00940:0,KBS0714_MOLHKGIG_00997:0)n3:0,SA211_MHAAABBN_00711:0)n2:0.0255345)n1:0.0824778)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001316_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001316_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9e8a0ce4787d14aa189516049c6293731ce2934
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001316_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01841:0.0631959,(((KBS0714_MOLHKGIG_00995:0.00293675,SA211_MHAAABBN_00709:0.00017025)n3:0.00135311,TT9_LFPAFLNI_00938:0.00368329)n2:0.0566434,AS2_ACLBLIBL_01894:0.227132)n1:0.0631959)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001319_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001319_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6100a0fd0e8bd3585849af4254f7f2cb7fd161fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001319_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01846:0.00484034,(AS2_ACLBLIBL_01899:0.0308043,(KBS0714_MOLHKGIG_00990:0.00410645,(SA211_MHAAABBN_00704:0.00342167,TT9_LFPAFLNI_00933:0.00208833)n3:0.0111231)n2:0.0164105)n1:0.00484034)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001321_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001321_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b25d1be50039bf65051734527ce11f7e6bfa79d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001321_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01848:0.00163744,(AS2_ACLBLIBL_01901:0.00507312,(KBS0714_MOLHKGIG_00988:1.75819e-08,(TT9_LFPAFLNI_00931:1.75819e-08,SA211_MHAAABBN_00702:0.00536387)n3:1.188e-05)n2:0.00388187)n1:0.00163744)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001322_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001322_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ee7baae00da4adae3542eedcac34047c4582717
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001322_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01849:1.19745e-08,((KBS0714_MOLHKGIG_00987:1.19745e-08,(TT9_LFPAFLNI_00930:1.19745e-08,SA211_MHAAABBN_00701:0.0039935)n3:5.5e-06)n2:5.5e-06,AS2_ACLBLIBL_01902:0.0079865)n1:1.19745e-08)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001324_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001324_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cf3f166d775621646190bec28e8f3d95134c3df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001324_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01851:0.00060062,(((TT9_LFPAFLNI_00928:0,KBS0714_MOLHKGIG_00985:0)n3:0.0037075,SA211_MHAAABBN_00699:0.0010755)n2:0.0002285,AS2_ACLBLIBL_01904:0.439624)n1:0.00060062)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001325_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001325_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2ee38ec0e1681561e6efa0a7b72ddd43e802ea5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001325_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01852:0.003779,(AS2_ACLBLIBL_01905:0.01917,(SA211_MHAAABBN_00698:0.006346,(KBS0714_MOLHKGIG_00984:0,TT9_LFPAFLNI_00927:0)n3:0.016694)n2:0.026093)n1:0.003779)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001328_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001328_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2ae4098bd9bb3775d40de242696c4b5426f31fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001328_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01856:0.012876,(AS2_ACLBLIBL_01908:0.29369,(SA211_MHAAABBN_00695:0,(TT9_LFPAFLNI_00924:0,KBS0714_MOLHKGIG_00981:0)n3:0)n2:0.014603)n1:0.012876)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001329_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001329_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..850553f04ca931cffbd55ce23bd59d5650b7a419
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001329_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01857:0.0361423,(((TT9_LFPAFLNI_00923:0,KBS0714_MOLHKGIG_00980:0)n3:0,SA211_MHAAABBN_00694:0)n2:0.334967,AS2_ACLBLIBL_01910:0.0910805)n1:0.0361423)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001330_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001330_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fca9050d1febe6cc059e3a8df40b08c002d73e40
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001330_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01858:0.0196447,(AS2_ACLBLIBL_01911:0.0146785,(SA211_MHAAABBN_00693:-0,(KBS0714_MOLHKGIG_00979:0,TT9_LFPAFLNI_00922:0)n3:0)n2:0.0279595)n1:0.0196447)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001332_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001332_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f79051c959e3166707f69f3356eeaeb1575331e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001332_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01860:0.0393418,(AS2_ACLBLIBL_01913:0.0057255,((SA211_MHAAABBN_00691:0,TT9_LFPAFLNI_00920:0)n3:0.00674525,KBS0714_MOLHKGIG_00977:9.29287e-08)n2:0.00225975)n1:0.0393418)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001335_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001335_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaf23f3d04bc1b4bdfe4277d554990a6045301bf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001335_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01866:0.129603,(AS2_ACLBLIBL_01918:0.103993,(KBS0714_MOLHKGIG_00972:0.0137593,(TT9_LFPAFLNI_00915:0.00176582,SA211_MHAAABBN_00685:0.0186082)n3:0.00353366)n2:0.0888968)n1:0.129603)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001337_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001337_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..743525793ed756fc5d05412aace79a0b4eb1df6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001337_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01869:0.1083,(AS2_ACLBLIBL_01921:0.0706035,(KBS0714_MOLHKGIG_00966:0.00605393,(SA211_MHAAABBN_00679:0.00793703,TT9_LFPAFLNI_00912:0.00914497)n3:0.00179907)n2:0.0778135)n1:0.1083)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001340_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001340_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18d59fbecfff5729187eb8f5f2f5b14a5b21ae61
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001340_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01877:0.122851,(((TT9_LFPAFLNI_00908:0.0142624,KBS0714_MOLHKGIG_00962:0.0190066)n3:0.0317008,SA211_MHAAABBN_00675:0.0334436)n2:0.145908,AS2_ACLBLIBL_01926:0.243102)n1:0.122851)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001342_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001342_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe35f07bd6daf3aa43db3aa9d5c20a4145c97f57
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001342_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01880:0.101067,((SA211_MHAAABBN_00672:0.00558338,(KBS0714_MOLHKGIG_00959:0.00430687,TT9_LFPAFLNI_00905:0.0143151)n3:0.00399962)n2:0.0792476,AS2_ACLBLIBL_01929:0.369999)n1:0.101067)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001344_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001344_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77d6b1912b5376d78fbf7600ae5f26f0c9bc9a36
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001344_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01883:0.0287406,(AS2_ACLBLIBL_01931:0.0891779,(TT9_LFPAFLNI_00902:0.00605012,(SA211_MHAAABBN_00669:0.00642838,KBS0714_MOLHKGIG_00956:0.00215663)n3:0.00255888)n2:0.0111884)n1:0.0287406)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001349_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001349_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ed10a1f602b766363af806bc03a93126ce432be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001349_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01895:0.227585,(AS2_ACLBLIBL_01997:0.340293,(SA211_MHAAABBN_00660:0.0263097,(TT9_LFPAFLNI_00890:0,KBS0714_MOLHKGIG_00941:0)n3:0.00901125)n2:0.0976937)n1:0.227585)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001350_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001350_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a1c8c09c347a6dfc379efc9a3057bb325e38af1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001350_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01896:0.10903,(((KBS0714_MOLHKGIG_00940:0.0126236,TT9_LFPAFLNI_00889:0.0181164)n3:0.00738262,SA211_MHAAABBN_00659:0.0220289)n2:0.105178,AS2_ACLBLIBL_01999:0.112424)n1:0.10903)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001351_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001351_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..329e5ca8baf291c04c1c7a6a93e3e0f83838a5a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001351_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01897:0.162386,((KBS0714_MOLHKGIG_00939:0.00597288,(TT9_LFPAFLNI_00888:0.0200589,AS2_ACLBLIBL_02000:0.44078)n3:0.00897313)n2:0.00609562,SA211_MHAAABBN_00658:0.0153966)n1:0.162386)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001352_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001352_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f93ee5a8c60d26f180597b54f6e1096537ffd44
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001352_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01898:0.425803,(AS2_ACLBLIBL_02001:0.046112,(SA211_MHAAABBN_00657:0.0218447,(TT9_LFPAFLNI_00887:0.0038695,KBS0714_MOLHKGIG_00938:0.0323825)n3:0.0147102)n2:0.12544)n1:0.425803)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001353_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001353_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a0d6a7280b232864fda5b88a59a07c569ddc36d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001353_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001354_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001354_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa8c358c64807e31435881c235cc523ed67d5f5e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001354_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01900:0.133803,(((AS2_ACLBLIBL_02003:0.00603413,SA211_MHAAABBN_00655:0.0131099)n3:0.00406205,TT9_LFPAFLNI_00885:3.02388e-07)n2:0.00496651,KBS0714_MOLHKGIG_00936:0.0076335)n1:0.133803)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001357_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001357_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7256d9b184338e389a469a9570ad9d9a8ef8b3b2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001357_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01903:0.0544554,((TT9_LFPAFLNI_00882:0.00535432,(SA211_MHAAABBN_00652:0.00438715,KBS0714_MOLHKGIG_00933:0.00159785)n3:0.00121917)n2:0.0193353,AS2_ACLBLIBL_02007:0.0186062)n1:0.0544554)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001360_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001360_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7880b1b006f44097704ee6a7f2a33c3b373c86a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001360_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001361_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001361_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b929461400b90f7cc2587010f5b8879cace895d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001361_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001364_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001364_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f1a62ca6a9c91e77b8932db385ecd1ca7fc10c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001364_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01915:0.125222,(AS2_ACLBLIBL_02016:0.0657957,(SA211_MHAAABBN_00644:0.0102804,(KBS0714_MOLHKGIG_00925:0,TT9_LFPAFLNI_00873:0)n3:0.00053063)n2:0.0369668)n1:0.125222)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001365_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001365_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b8b56ff70ae721d0f3284baf88bd5e26ece8c68
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001365_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001367_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001367_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d0d1630f3ffb6cc2a6c78f123fb9cf051c61c62
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001367_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001368_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001368_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69ad2547883700c562764deb64582135bf9de230
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001368_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001369_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001369_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f853a14678e39cd3a74f70b954926c1eb1f94a2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001369_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01920:0.00842132,(((KBS0714_MOLHKGIG_00920:5.33626e-08,SA211_MHAAABBN_00639:0.0133411)n3:9.613e-05,TT9_LFPAFLNI_00868:5.33626e-08)n2:0.0168436,AS2_ACLBLIBL_02021:0.00643137)n1:0.00842132)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001372_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001372_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a489d86d6de8c10c6bec9bd4cd882b972b1e4c60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001372_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01923:0.180475,(AS2_ACLBLIBL_02024:0.110706,(SA211_MHAAABBN_00636:0.0108697,(TT9_LFPAFLNI_00865:0.0219358,KBS0714_MOLHKGIG_00917:0.0230342)n3:0.00513332)n2:0.112366)n1:0.180475)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001373_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001373_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f41a82ac9d993cd10a6659f3f09a39c862bd6309
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001373_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01924:0.144661,(AS2_ACLBLIBL_02026:0.207747,(KBS0714_MOLHKGIG_00916:0.0094233,(SA211_MHAAABBN_00635:0.0131063,TT9_LFPAFLNI_00864:0.00640866)n3:0.0070242)n2:0.130567)n1:0.144661)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001374_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001374_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..634f2a89f6f7b271cfaa73329f14b070d4197cc4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001374_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01925:0.128469,((SA211_MHAAABBN_00634:0.00512858,(TT9_LFPAFLNI_00863:0,KBS0714_MOLHKGIG_00915:0)n3:0.00516242)n2:0.0897245,AS2_ACLBLIBL_02027:0.076348)n1:0.128469)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001377_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001377_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5b73721ee72813279551774f257fb905e18b6e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001377_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01928:0.18585,(((KBS0714_MOLHKGIG_00912:0,TT9_LFPAFLNI_00860:0)n3:0,SA211_MHAAABBN_00631:0)n2:0.0823165,AS2_ACLBLIBL_02030:0.105508)n1:0.18585)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001379_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001379_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d2bf768d2b075988d9a3788139a800fa425e306
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001379_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01930:0.156679,((KBS0714_MOLHKGIG_00910:0.00737662,(TT9_LFPAFLNI_00858:0.00946688,SA211_MHAAABBN_00629:0.00816512)n3:0.00670588)n2:0.0917619,AS2_ACLBLIBL_02032:0.167837)n1:0.156679)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001380_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001380_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bfc621cd0300e2e7d619941680ebc62041e2f1f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001380_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01931:0.0203004,((KBS0714_MOLHKGIG_00909:0.00694213,(SA211_MHAAABBN_00628:0.00434713,TT9_LFPAFLNI_00857:0.00432988)n3:0.00280888)n2:0.00897738,AS2_ACLBLIBL_02033:0.0428751)n1:0.0203004)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001381_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001381_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad3caea2ee8055b41bc191d855790b89c9225dec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001381_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01932:0.0793323,((SA211_MHAAABBN_00627:0.0035905,(TT9_LFPAFLNI_00856:5e-07,KBS0714_MOLHKGIG_00908:5e-07)n3:0.001392)n2:0.069299,AS2_ACLBLIBL_02034:0.0340195)n1:0.0793323)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001382_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001382_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca7277ac7a25f83e6556f5c3ea9e23d82d5c3c11
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001382_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01933:0.154766,(((SA211_MHAAABBN_00626:0.0107291,TT9_LFPAFLNI_00855:0.00537888)n3:0.0134585,KBS0714_MOLHKGIG_00907:0.00804818)n2:0.0678085,AS2_ACLBLIBL_02035:0.069155)n1:0.154766)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001384_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001384_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9037d5208a586bb9958ec9dba446f6ed4ecb0141
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001384_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01935:0.035004,((KBS0714_MOLHKGIG_00905:0.0192835,(TT9_LFPAFLNI_00853:5e-07,SA211_MHAAABBN_00624:5e-07)n3:0.001001)n2:0.0031915,AS2_ACLBLIBL_02037:0.055569)n1:0.035004)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001385_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001385_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a185cd65cfe0a7762320e0586714ce88bff0b4c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001385_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01936:0.0473104,(AS2_ACLBLIBL_02038:0.0200033,(KBS0714_MOLHKGIG_00904:0.009352,(SA211_MHAAABBN_00623:0.00097325,TT9_LFPAFLNI_00852:0.00107775)n3:0.0013685)n2:0.023689)n1:0.0473104)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001389_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001389_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01af0037c3d5da4f694433c72f6b3032daed89e2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001389_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01940:0.254886,(TT9_LFPAFLNI_00846:0.796211,((KBS0714_MOLHKGIG_00895:0.0049595,SA211_MHAAABBN_00617:0.0051095)n3:0.160151,AS2_ACLBLIBL_02042:0.193145)n2:0.252046)n1:0.254886)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001391_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001391_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98d2ee12450f443090b4b54c8e354423177d6f43
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001391_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01942:0.150128,(SA211_MHAAABBN_00619:0.0200641,(AS2_ACLBLIBL_02044:0.00849688,(KBS0714_MOLHKGIG_00897:0.00881963,TT9_LFPAFLNI_00848:0.00707738)n3:0.00093363)n2:0.00547212)n1:0.150128)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001394_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001394_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90be01113eeca6a859cce06052a6cb7632e541c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001394_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01948:0.28047,(AS2_ACLBLIBL_02054:0.105211,(KBS0714_MOLHKGIG_00881:0.0162233,(TT9_LFPAFLNI_00840:0.0132802,SA211_MHAAABBN_00603:0.00785977)n3:0.00037273)n2:0.127705)n1:0.28047)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001398_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001398_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..928f87e66041367fcd143c068a107f2f05ec0a69
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001398_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01952:0.12654,((SA211_MHAAABBN_00599:3.22661e-07,(TT9_LFPAFLNI_00836:0.00684488,KBS0714_MOLHKGIG_00877:3.22661e-07)n3:0.00050187)n2:0.0350584,AS2_ACLBLIBL_02058:0.0281796)n1:0.12654)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001399_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001399_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f13f55c29cea4ed1f715c44e504f23514b2ed39a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001399_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01953:0.0794178,(AS2_ACLBLIBL_02059:0.0329513,(TT9_LFPAFLNI_00835:0.00185178,(SA211_MHAAABBN_00598:0.00502064,KBS0714_MOLHKGIG_00876:0.00255836)n3:0.00236122)n2:0.0541563)n1:0.0794178)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001400_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001400_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2134147b7fdbaa96ed2ff82c25d8d56498df0617
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001400_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01954:0.09113,((TT9_LFPAFLNI_00834:0.000935,(KBS0714_MOLHKGIG_00875:2.90199e-07,SA211_MHAAABBN_00597:0.008373)n3:0.002363)n2:0.0494775,AS2_ACLBLIBL_02060:0.046933)n1:0.09113)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001401_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001401_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad989c59c7d50209ecabeefae3fe66fb834076c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001401_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01955:0.135787,((SA211_MHAAABBN_00596:0.0129528,(KBS0714_MOLHKGIG_00874:0.00845723,TT9_LFPAFLNI_00833:0.00994477)n3:0.00732976)n2:0.028545,AS2_ACLBLIBL_02061:0.0614892)n1:0.135787)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001402_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001402_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f764af36c10e1258db29a741e9b81beaccf94b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001402_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01956:0.106479,(AS2_ACLBLIBL_02062:0.039005,(KBS0714_MOLHKGIG_00873:0.00763059,(TT9_LFPAFLNI_00832:0.0113022,SA211_MHAAABBN_00595:0.0168688)n3:0.00195791)n2:0.0588199)n1:0.106479)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001403_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001403_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdf9c995d9d6d93787f8fd81818b7eff82a1d16a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001403_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01957:0.0838075,(((TT9_LFPAFLNI_00831:0.00773245,KBS0714_MOLHKGIG_00872:0.00537655)n3:0.00321381,SA211_MHAAABBN_00594:0.00702973)n2:0.0219352,AS2_ACLBLIBL_02063:0.074134)n1:0.0838075)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001405_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001405_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5be3a07da5fee9ff7541d7a61334fcd18ef39c8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001405_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01959:0.235144,(AS2_ACLBLIBL_02065:0.0133917,(SA211_MHAAABBN_00592:0.0060825,(TT9_LFPAFLNI_00829:0.0038345,KBS0714_MOLHKGIG_00870:0.0018925)n3:0.0065245)n2:0.0394865)n1:0.235144)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001406_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001406_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..031c99b2a87c867b04ab4814b4b58c97697757d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001406_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01960:0.153517,(AS2_ACLBLIBL_02066:0.0810196,(TT9_LFPAFLNI_00828:0.00138488,(KBS0714_MOLHKGIG_00869:0.00642663,SA211_MHAAABBN_00591:0.00156737)n3:0.00750663)n2:0.0480256)n1:0.153517)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001408_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001408_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d974896cf095f6ff529b3486bb131eee8ab966b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001408_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01962:0.101258,((KBS0714_MOLHKGIG_00867:0.00845287,(SA211_MHAAABBN_00589:0.00616638,TT9_LFPAFLNI_00826:0.00424463)n3:0.00079713)n2:0.0372991,AS2_ACLBLIBL_02068:0.0458999)n1:0.101258)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001410_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001410_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6715d656509f112063cb643458f323415a7655a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001410_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01964:0.0203583,(((KBS0714_MOLHKGIG_00865:7.81363e-08,TT9_LFPAFLNI_00824:0.00388244)n3:0.00025598,SA211_MHAAABBN_00587:0.00250545)n2:0.0152439,AS2_ACLBLIBL_02070:0.0160413)n1:0.0203583)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001411_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001411_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39f3925f226046b874bcdea1a987448a793ba273
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001411_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01965:0.0746794,(AS2_ACLBLIBL_02071:0.0122582,(SA211_MHAAABBN_00586:0.00785097,(KBS0714_MOLHKGIG_00864:0,TT9_LFPAFLNI_00823:0)n3:0.00586903)n2:0.0259275)n1:0.0746794)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001414_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001414_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c8887775e0eaad6631ea3b7d92da36191447e56
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001414_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01968:0.065223,(AS2_ACLBLIBL_02074:0.07858,((KBS0714_MOLHKGIG_00861:0.00284375,SA211_MHAAABBN_00583:2.64735e-07)n3:0.0053825,TT9_LFPAFLNI_00820:0.0026005)n2:0.0450775)n1:0.065223)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001417_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001417_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6aa50b41d477563c0e56ac0b860705edbd70eaa6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001417_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01976:0.0463424,(AS2_ACLBLIBL_02081:0.0507242,(KBS0714_MOLHKGIG_00853:0.00506834,(TT9_LFPAFLNI_00812:0,SA211_MHAAABBN_00575:0)n3:0.00746066)n2:0.0326523)n1:0.0463424)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001420_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001420_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a00898d86063b2ae8e7ee4f5df1b03cd14046193
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001420_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01985:0.0567504,(AS2_ACLBLIBL_02085:0.0384473,((SA211_MHAAABBN_00572:0,TT9_LFPAFLNI_00809:0)n3:0.0315392,KBS0714_MOLHKGIG_00850:0.0164858)n2:0.0211987)n1:0.0567504)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001421_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001421_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7323d972533c1da0f71247d69d00ab866e91f317
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001421_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01986:0.0140026,(AS2_ACLBLIBL_02086:0.0512998,((TT9_LFPAFLNI_00808:0,SA211_MHAAABBN_00571:0)n3:0.00248633,KBS0714_MOLHKGIG_00849:0.00572167)n2:0.0113151)n1:0.0140026)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001422_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001422_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a941adb44359a44728ca5e9c22d36d17025b8593
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001422_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01987:0.0766038,(AS2_ACLBLIBL_02087:0.0248053,((TT9_LFPAFLNI_00807:5e-07,SA211_MHAAABBN_00570:5e-07)n3:0.0013954,KBS0714_MOLHKGIG_00848:0.0029361)n2:0.0561784)n1:0.0766038)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001423_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001423_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c44ef5eccc6c8e213f2b3602f04a624ce9febc68
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001423_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01988:0.0774428,(AS2_ACLBLIBL_02088:0.0371925,((TT9_LFPAFLNI_00806:0,KBS0714_MOLHKGIG_00847:0)n3:0.00040148,SA211_MHAAABBN_00569:0.00096652)n2:0.04165)n1:0.0774428)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001426_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001426_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9f54149777eb5e7cb97f13a8dae306540c2b739
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001426_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01991:0.039713,(((SA211_MHAAABBN_00564:0,KBS0714_MOLHKGIG_00832:0)n3:0,AS2_ACLBLIBL_02092:0)n2:0.000611,TT9_LFPAFLNI_00802:0.005718)n1:0.039713)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001427_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001427_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..247b4929a1602af067e7144de081b3a416652f5f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001427_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01992:0.0679571,(AS2_ACLBLIBL_02093:0.0202309,(KBS0714_MOLHKGIG_00831:0.00504162,(TT9_LFPAFLNI_00801:0.00056938,SA211_MHAAABBN_00563:0.00466762)n3:0.00182588)n2:0.00825337)n1:0.0679571)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001429_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001429_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..440ff6003448f7f2d7fc3e735f383ed81137456f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001429_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01994:0.172581,(AS2_ACLBLIBL_02095:0.103373,((TT9_LFPAFLNI_00796:0.0068335,SA211_MHAAABBN_00559:6.02816e-07)n3:0.00078025,KBS0714_MOLHKGIG_00827:0.0311088)n2:0.115652)n1:0.172581)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001430_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001430_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bddb39ce4d995d9cd6d75cf2ec728d1cc9281fed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001430_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01996:0.0536995,(AS2_ACLBLIBL_02097:0.017255,(SA211_MHAAABBN_00557:1.71657e-07,(KBS0714_MOLHKGIG_00825:0,TT9_LFPAFLNI_00794:0.003008)n3:0.00040869)n2:0.0439948)n1:0.0536995)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001434_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001434_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74ca2e9336c1bd1febf2352d6de04d47be5c6703
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001434_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02001:0.174053,((SA211_MHAAABBN_00552:0.0291131,(KBS0714_MOLHKGIG_00820:0.00241088,TT9_LFPAFLNI_00789:0.00345012)n3:0.0387339)n2:0.344756,AS2_ACLBLIBL_02110:0.278329)n1:0.174053)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001436_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001436_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41f6bf1d12ad69a7e610d5bd0587c8eddebc3594
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001436_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02003:0.138815,(AS2_ACLBLIBL_02112:0.188614,((KBS0714_MOLHKGIG_00818:0.00091075,TT9_LFPAFLNI_00787:0.0170373)n3:0.0019595,SA211_MHAAABBN_00550:0.0015065)n2:0.212708)n1:0.138815)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001438_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001438_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7563de2ed95a417cdff38cc3264df0ba5db21a7d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001438_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02005:0.102227,((KBS0714_MOLHKGIG_00816:0.00423212,(TT9_LFPAFLNI_00785:0.00161188,SA211_MHAAABBN_00548:3.31694e-07)n3:0.00318138)n2:0.0414819,AS2_ACLBLIBL_02114:0.0772071)n1:0.102227)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001442_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001442_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfe0ac2c9931fb97a265e32b27e39f5ba4c5ef61
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001442_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02009:0.208239,(AS2_ACLBLIBL_02118:0.139987,((TT9_LFPAFLNI_00781:0.00119066,SA211_MHAAABBN_00544:0.00302034)n3:0.0053762,KBS0714_MOLHKGIG_00812:0.00255536)n2:0.145126)n1:0.208239)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001443_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001443_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78f7a27677e24639ae915012b72fdbc3ac28b584
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001443_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02010:0.140858,(AS2_ACLBLIBL_02119:0.0614085,(SA211_MHAAABBN_00543:0,(KBS0714_MOLHKGIG_00811:0,TT9_LFPAFLNI_00780:0)n3:0)n2:0.0566385)n1:0.140858)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001445_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001445_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c70d4b90a2cf5cdbaeac85278f3044d8de5f3fd0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001445_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02012:0.214381,(AS2_ACLBLIBL_02121:0.0338951,(KBS0714_MOLHKGIG_00809:0.0018755,(TT9_LFPAFLNI_00778:0,SA211_MHAAABBN_00541:0)n3:0.0038195)n2:0.0026345)n1:0.214381)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001450_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001450_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe2168c0818dd28d2be575b103fe0e90573be041
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001450_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02020:0.118475,(((SA211_MHAAABBN_00534:0.007636,TT9_LFPAFLNI_00770:0.002638)n3:0.00475502,KBS0714_MOLHKGIG_00803:0.0133664)n2:0.109656,AS2_ACLBLIBL_02127:0.0983848)n1:0.118475)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001451_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001451_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bf6f23bf1858cfc6007e4e4df25762fb153264e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001451_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001454_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001454_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..792fbb435c21113cafba8b0f1f8e4c5de3f686fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001454_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001456_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001456_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0007ec66a67259a700d2dbe5e9cb21bbf5d101d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001456_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02026:0.057121,(((TT9_LFPAFLNI_00765:0,SA211_MHAAABBN_00529:0)n3:0.010464,KBS0714_MOLHKGIG_00798:0.004212)n2:0.004223,AS2_ACLBLIBL_02133:0.0138489)n1:0.057121)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001457_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001457_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f363a1fa9d38c3b5bb86c3ee0494bcdfd08865c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001457_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02027:0.0192589,(AS2_ACLBLIBL_02134:0.0170803,(KBS0714_MOLHKGIG_00797:0.001014,(TT9_LFPAFLNI_00764:0.002373,SA211_MHAAABBN_00528:0.00292)n3:0.000572)n2:0.004874)n1:0.0192589)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001459_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001459_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a18b9cdde3a13fc6cb8d11f7f4ae422c951241f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001459_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02029:0.0311673,((KBS0714_MOLHKGIG_00795:0.00263862,(TT9_LFPAFLNI_00762:9.86184e-08,SA211_MHAAABBN_00526:0.00159613)n3:0.00134488)n2:0.0125109,AS2_ACLBLIBL_02136:0.0183864)n1:0.0311673)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001460_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001460_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38812b90da986c2e66e65a61140f86f746f63790
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001460_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02030:0.102,((TT9_LFPAFLNI_00761:0.00131748,(SA211_MHAAABBN_00525:2.69506e-07,KBS0714_MOLHKGIG_00794:0.00495674)n3:0.0146523)n2:0.0226635,AS2_ACLBLIBL_02137:0.0228637)n1:0.102)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001464_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001464_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91d24244cedbec13269127995f2d57745d03d3d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001464_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02034:0.21537,((TT9_LFPAFLNI_00757:0.0758689,(KBS0714_MOLHKGIG_00790:0,SA211_MHAAABBN_00521:0)n3:0.00597112)n2:0.16145,AS2_ACLBLIBL_02141:0.20166)n1:0.21537)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001465_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001465_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2427fbba049028552130078d48f22e4422c7743f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001465_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02035:0.127665,(AS2_ACLBLIBL_02142:0.0848205,(TT9_LFPAFLNI_00756:0.00580827,(KBS0714_MOLHKGIG_00789:0,SA211_MHAAABBN_00520:0)n3:0.00891773)n2:0.102704)n1:0.127665)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001467_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001467_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d909d2d4952fc535650f95e01a3ad1a16cc9623
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001467_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02038:0.0729772,(AS2_ACLBLIBL_02144:0.0402825,(TT9_LFPAFLNI_00753:0.001534,(KBS0714_MOLHKGIG_00786:0,SA211_MHAAABBN_00517:0)n3:0.002103)n2:0.0203835)n1:0.0729772)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001468_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001468_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca9429a3f5c9e73f6617e4794e10f34acf781ec1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001468_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02039:0.119975,((KBS0714_MOLHKGIG_00785:0.0335653,(TT9_LFPAFLNI_00752:0.0191341,SA211_MHAAABBN_00516:0.0278539)n3:0.033572)n2:0.0383148,AS2_ACLBLIBL_02145:0.111234)n1:0.119975)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001469_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001469_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d66e55314f381cf2f3368ca68d588133db10a777
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001469_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02040:0.169257,(AS2_ACLBLIBL_02146:0.0965096,(TT9_LFPAFLNI_00751:0.00777888,(SA211_MHAAABBN_00515:0.00388162,KBS0714_MOLHKGIG_00784:0.0158524)n3:0.00553613)n2:0.0912371)n1:0.169257)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001470_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001470_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68cee7fce623fbf6a7c7b4739579aedd79336776
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001470_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02041:0.0347915,(AS2_ACLBLIBL_02147:0.014508,(TT9_LFPAFLNI_00750:5e-07,(SA211_MHAAABBN_00514:5e-07,KBS0714_MOLHKGIG_00783:5e-07)n3:0)n2:0.0238085)n1:0.0347915)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001472_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001472_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37deafe79b7f76e7af34ecd6ec85d1c27e3f40d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001472_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02043:0.101624,(AS2_ACLBLIBL_02149:0.0224145,(TT9_LFPAFLNI_00748:0.00794875,(KBS0714_MOLHKGIG_00781:0.00282575,SA211_MHAAABBN_00512:0.00255925)n3:0.0164623)n2:0.0103147)n1:0.101624)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001473_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001473_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88d51c19e86d3385d0a57a071c157c4c388cc1f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001473_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02044:0.070256,((SA211_MHAAABBN_00511:0.00185859,(KBS0714_MOLHKGIG_00780:0.00100526,TT9_LFPAFLNI_00747:0.00589874)n3:0.00189351)n2:0.00757573,AS2_ACLBLIBL_02150:0.006455)n1:0.070256)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001474_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001474_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15e57f5d30eef35309d4c3c03712ed380ba03900
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001474_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02046:0.116573,(AS2_ACLBLIBL_02151:0.0215812,((TT9_LFPAFLNI_00746:0.0158048,KBS0714_MOLHKGIG_00779:0.00451623)n3:0.00528582,SA211_MHAAABBN_00510:0.0127697)n2:0.0184477)n1:0.116573)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001475_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001475_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68f27a5a5f6939b6ac9e23e5678034f4de270bac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001475_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02047:0.0790052,(((TT9_LFPAFLNI_00745:0,SA211_MHAAABBN_00509:0)n3:0,KBS0714_MOLHKGIG_00778:0)n2:0.0021065,AS2_ACLBLIBL_02152:0.0078635)n1:0.0790052)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001476_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001476_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4fa493fdaa17cae411f0efab2c6228f89f575ba1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001476_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02048:0.110937,(TT9_LFPAFLNI_00744:0.0020465,(SA211_MHAAABBN_00508:3.02201e-07,(AS2_ACLBLIBL_02153:0.038669,KBS0714_MOLHKGIG_00777:0.010292)n3:0.0140893)n2:0.0152744)n1:0.110937)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001479_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001479_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db2f77112b484be374e46699a5e3e7e93fb118e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001479_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02052:0.140743,(AS2_ACLBLIBL_02157:0.0490044,(SA211_MHAAABBN_00504:0.00138912,(TT9_LFPAFLNI_00740:3.73122e-07,KBS0714_MOLHKGIG_00773:0.00236262)n3:0.00348788)n2:0.0358034)n1:0.140743)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001481_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001481_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..778857701525b03b1bb42bb234e3c04c3f10f95d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001481_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02054:0.018749,((KBS0714_MOLHKGIG_00771:0.00144861,SA211_MHAAABBN_00502:0.00594339)n2:0.00166599,(AS2_ACLBLIBL_02159:0.00900983,TT9_LFPAFLNI_00738:0.00769217)n3:0.00893456)n1:0.018749)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001484_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001484_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35078b7904bfef27811c6552369f86c28e304ea8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001484_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02059:0.0729226,(AS2_ACLBLIBL_02163:0.0617978,(TT9_LFPAFLNI_00730:0.00545513,(SA211_MHAAABBN_00496:0.00440477,KBS0714_MOLHKGIG_00766:0.00708923)n3:0.00475187)n2:0.0513212)n1:0.0729226)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001489_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001489_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97d7d14c28abd20780985e5b4558ee78a9a3ccb5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001489_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02065:0.127943,(AS2_ACLBLIBL_02170:0.304768,(TT9_LFPAFLNI_00724:0.0167591,(SA211_MHAAABBN_00490:0.0130171,KBS0714_MOLHKGIG_00760:0.0170319)n3:0.00689989)n2:0.186929)n1:0.127943)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001490_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001490_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77c44bb2241d0bbbbe3ebb4d1c7083d008021a33
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001490_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02066:0.0759415,(((KBS0714_MOLHKGIG_00759:0,SA211_MHAAABBN_00489:0)n3:0.003412,TT9_LFPAFLNI_00723:0.00413)n2:0.0320635,AS2_ACLBLIBL_02171:0.032173)n1:0.0759415)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001493_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001493_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2947ff5758796a91cb14cc46ba536d943597019c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001493_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02069:0.0695114,(AS2_ACLBLIBL_02174:0.0396492,(SA211_MHAAABBN_00486:0.00440825,(KBS0714_MOLHKGIG_00756:0.00778825,TT9_LFPAFLNI_00720:0.00836575)n3:0.00162325)n2:0.0186942)n1:0.0695114)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001496_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001496_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..020e186c6fc6f3e55e5f2930a5943da119e2344b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001496_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02072:0.0983553,(AS2_ACLBLIBL_02177:0.0481884,(KBS0714_MOLHKGIG_00753:3.05662e-07,(TT9_LFPAFLNI_00717:3.05662e-07,SA211_MHAAABBN_00483:0.00543838)n3:0.00030838)n2:0.0556329)n1:0.0983553)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001499_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001499_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3335a851e8e6aeefb1649e0fc86d1ae052e1a73f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001499_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02075:0.0462402,((KBS0714_MOLHKGIG_00750:0.00516865,(TT9_LFPAFLNI_00714:0.00203849,SA211_MHAAABBN_00480:0.00626751)n3:0.00375656)n2:0.0213458,AS2_ACLBLIBL_02180:0.0278075)n1:0.0462402)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001500_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001500_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5484322f754bac43af62d8bf17501943bc669bce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001500_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02082:0,((KBS0714_MOLHKGIG_00745:0,TT9_LFPAFLNI_00710:0)n2:0,(AS2_ACLBLIBL_02184:0.010725,SA211_MHAAABBN_00476:0.007648)n3:0.001484)n1:0)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001503_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001503_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47cea8d00dc923b995d2af5b92b05d6d0c497ffc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001503_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02085:0.00198233,((KBS0714_MOLHKGIG_00742:0.00032141,(SA211_MHAAABBN_00473:0.00029888,AS2_ACLBLIBL_02187:0.0115741)n3:0.00134862)n2:0.00363109,TT9_LFPAFLNI_00707:0.00395633)n1:0.00198233)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001504_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001504_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3b9918c30d9c7d076b1cf6db8dc49c594944704
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001504_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02086:0.00176019,(SA211_MHAAABBN_00472:0.00140363,((AS2_ACLBLIBL_02188:0.0116881,TT9_LFPAFLNI_00706:2.08314e-08)n3:0.00249138,KBS0714_MOLHKGIG_00741:0.00210562)n2:2.37e-06)n1:0.00176019)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001505_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001505_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5ae31e8206c4c5e803b378ca027880f537856a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001505_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02087:0.0228908,(AS2_ACLBLIBL_02189:0.0179985,(SA211_MHAAABBN_00471:8.70415e-08,(TT9_LFPAFLNI_00705:0,KBS0714_MOLHKGIG_00740:0)n3:0.002583)n2:0.0210935)n1:0.0228908)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001507_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001507_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdbe10deb5016feda3c8fd957d0eac8f3bb6baf8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001507_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02092:0.312927,((TT9_LFPAFLNI_00701:0.00952475,(SA211_MHAAABBN_00468:0,KBS0714_MOLHKGIG_00737:0)n3:0.00391725)n2:0.147251,AS2_ACLBLIBL_02193:0.182531)n1:0.312927)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001508_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001508_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ae662e2909a1ff149055507fab54b6162a4bacf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001508_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02093:0.177901,((SA211_MHAAABBN_00467:0.028098,(KBS0714_MOLHKGIG_00736:0.0108739,TT9_LFPAFLNI_00700:0.0191771)n3:0.015301)n2:0.0818153,AS2_ACLBLIBL_02194:0.0822363)n1:0.177901)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001509_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001509_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d26587494bee9104825d1b3c5a2d97cfecdb232a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001509_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02094:0.161439,(((SA211_MHAAABBN_00466:0,KBS0714_MOLHKGIG_00735:0)n3:0.00595361,TT9_LFPAFLNI_00699:0.00182839)n2:0.0854001,AS2_ACLBLIBL_02195:0.106969)n1:0.161439)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001510_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001510_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa914d69d430d938ef17a3e581d243f291dca608
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001510_tree.txt
@@ -0,0 +1 @@
+((SA211_MHAAABBN_02232:0.673447,(AS2_ACLBLIBL_02198:1.5088,AS2_ACLBLIBL_02196:0.929004)n2:0.0275186)n1:0.491682,(AS2_ACLBLIBL_02372:0.0479534,SA211_MHAAABBN_00303:0.0218486)n3:0.491682)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001512_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001512_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98d634e66ff0cd116853624df5b8ba26ed1adc7f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001512_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02096:0.0894878,(AS2_ACLBLIBL_02220:0.0288064,(TT9_LFPAFLNI_00697:0.0118369,(SA211_MHAAABBN_00464:0.00689288,KBS0714_MOLHKGIG_00733:0.00238912)n3:0.00447612)n2:0.0476901)n1:0.0894878)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001513_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001513_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d9fccf3901087f8110f9f1aa248a36d3dc7d9f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001513_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02097:0.0591568,((TT9_LFPAFLNI_00696:0.00117493,(SA211_MHAAABBN_00463:0,KBS0714_MOLHKGIG_00732:0)n3:0.00073207)n2:0.023011,AS2_ACLBLIBL_02221:0.0399803)n1:0.0591568)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001516_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001516_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27127230012c3aedaf8bb06165783dcbf76e9bf9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001516_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02102:0.150767,((SA211_MHAAABBN_00459:0.00584837,(KBS0714_MOLHKGIG_00728:0,TT9_LFPAFLNI_00692:0)n3:0.00863363)n2:0.0992681,AS2_ACLBLIBL_02229:0.0650397)n1:0.150767)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001518_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001518_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8eb97ae1475be31da1c4fcd1615f569089bb7dea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001518_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02104:0.176697,(AS2_ACLBLIBL_02232:0.052853,(SA211_MHAAABBN_00457:0,(TT9_LFPAFLNI_00690:0,KBS0714_MOLHKGIG_00726:0)n3:0)n2:0.127221)n1:0.176697)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001520_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001520_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf9265c613b19ea31e73c77033193a19f24edb7a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001520_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02106:0.289512,(((TT9_LFPAFLNI_00688:0,KBS0714_MOLHKGIG_00724:0)n3:0,SA211_MHAAABBN_00455:0)n2:0.124133,AS2_ACLBLIBL_02234:0.103054)n1:0.289512)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001521_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001521_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b328a8bd2327176b67434120939946d5b2edfc9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001521_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02107:0.093993,(((TT9_LFPAFLNI_00687:0.00426475,KBS0714_MOLHKGIG_00723:0.00492125)n3:0.008153,SA211_MHAAABBN_00454:0.0171335)n2:0.053627,AS2_ACLBLIBL_02235:0.050226)n1:0.093993)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001523_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001523_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c443ff366c8b8ef1eb6f11b0e0bf2d54084df942
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001523_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02109:0.0574228,(AS2_ACLBLIBL_02237:0.0182295,(SA211_MHAAABBN_00452:0,(TT9_LFPAFLNI_00685:0,KBS0714_MOLHKGIG_00721:0)n3:0)n2:0.0185585)n1:0.0574228)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001525_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001525_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee5e3b79a098b984730a5d7fe8e29d1b729581ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001525_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02111:0.0229428,(((TT9_LFPAFLNI_00683:0.00370663,KBS0714_MOLHKGIG_00719:6.30931e-08)n3:3.863e-05,SA211_MHAAABBN_00450:6.30931e-08)n2:0.00162312,AS2_ACLBLIBL_02239:0.0119164)n1:0.0229428)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001526_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001526_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16127a5ab288776aa3a6e21e513d9cd9eabc1d37
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001526_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02112:0.0794003,(AS2_ACLBLIBL_02240:0.0374455,(SA211_MHAAABBN_00449:0.00893158,(KBS0714_MOLHKGIG_00718:0,TT9_LFPAFLNI_00682:0)n3:0.0113784)n2:0.034428)n1:0.0794003)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001529_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001529_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78198bdf2dc2ca51e79bcd8662702f5a8e2018c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001529_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02115:0.0482854,(((TT9_LFPAFLNI_00679:0.00329744,SA211_MHAAABBN_00446:7.356e-05)n3:0.00440174,KBS0714_MOLHKGIG_00715:0.00565349)n2:0.027334,AS2_ACLBLIBL_02243:0.0331222)n1:0.0482854)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001530_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001530_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f691e03e10b9b5a69d7a2ccdf9a066b9a5d2acc9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001530_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02116:0.0391154,((SA211_MHAAABBN_00445:0.00405989,(KBS0714_MOLHKGIG_00714:0.00575374,TT9_LFPAFLNI_00678:0.00065226)n3:0.0038251)n2:0.0648598,AS2_ACLBLIBL_02244:0.0516372)n1:0.0391154)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001531_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001531_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c83d6d2d5183203fe156b74115355c81763474cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001531_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02118:0.0073245,(((SA211_MHAAABBN_00444:0,TT9_LFPAFLNI_00677:0)n3:0.103566,KBS0714_MOLHKGIG_00710:0.26989)n2:0.246693,AS2_ACLBLIBL_02245:0.055586)n1:0.0073245)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001532_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001532_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1ab5911db83a50b18a6bc35423552fcca991012
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001532_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02119:0.00951019,(AS2_ACLBLIBL_02246:0.0111906,((SA211_MHAAABBN_00443:3.0004e-07,TT9_LFPAFLNI_00676:0.00606913)n3:0.0136781,KBS0714_MOLHKGIG_00709:0.00747538)n2:0.2427)n1:0.00951019)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001533_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001533_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..203e15632bc78d3b62f2b2b61597d4218d396de1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001533_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02121:0.00704894,(AS2_ACLBLIBL_02249:0.167687,(SA211_MHAAABBN_00442:0.00380038,(TT9_LFPAFLNI_00675:0.00509312,KBS0714_MOLHKGIG_00708:0.00516987)n3:0.00290613)n2:0.00136812)n1:0.00704894)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001535_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001535_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10d3bbd7152d7271e25bdabb61ace794e6c329d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001535_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02123:0.0208869,(AS2_ACLBLIBL_02251:0.0718552,((TT9_LFPAFLNI_00673:0,KBS0714_MOLHKGIG_00706:0)n3:0.00012875,SA211_MHAAABBN_00440:0.00283425)n2:0.0234532)n1:0.0208869)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001536_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001536_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..984f5390e7175a638618c2284cbc835a77185a04
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001536_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02124:0.147719,((KBS0714_MOLHKGIG_00705:0.0714246,(TT9_LFPAFLNI_00672:0.0194991,SA211_MHAAABBN_00439:0.0215279)n3:0.0402989)n2:0.188224,AS2_ACLBLIBL_02252:0.22782)n1:0.147719)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001537_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001537_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77baf4cc34581e7770dd30d398920afa9219f1a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001537_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02125:0.0376135,(AS2_ACLBLIBL_02253:0.014369,(SA211_MHAAABBN_00438:1.00671e-07,(KBS0714_MOLHKGIG_00704:1.00671e-07,TT9_LFPAFLNI_00671:0.00224175)n3:1.975e-05)n2:0.00885275)n1:0.0376135)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001538_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001538_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47874d9e4ee0e31b7325278a09e0e142f9998de2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001538_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02126:0.0984478,(AS2_ACLBLIBL_02254:0.0450925,((KBS0714_MOLHKGIG_00700:0,SA211_MHAAABBN_00437:0)n3:0,TT9_LFPAFLNI_00670:0)n2:0.0253625)n1:0.0984478)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001545_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001545_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e673d72d8198cb7b8513686de943a569e99c8622
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001545_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02132:0.279901,((KBS0714_MOLHKGIG_00691:0.069557,(TT9_LFPAFLNI_00661:0.001088,SA211_MHAAABBN_00428:0.003645)n3:0.004717)n2:0.116698,AS2_ACLBLIBL_02264:0.103865)n1:0.279901)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001549_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001549_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..36aeb6f9df880b229553b9be9f3109bcae38487b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001549_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02137:0,((TT9_LFPAFLNI_00657:0,(AS2_ACLBLIBL_02270:0,KBS0714_MOLHKGIG_00687:0)n3:0)n2:0,SA211_MHAAABBN_00424:0)n1:0)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001553_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001553_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4864164738767b17983ece94c4e419648990efb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001553_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02141:0.132888,(AS2_ACLBLIBL_02280:0.124945,(KBS0714_MOLHKGIG_00683:0,(SA211_MHAAABBN_00420:0,TT9_LFPAFLNI_00653:0)n3:0)n2:0.0963345)n1:0.132888)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001554_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001554_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ba741830a18600a599958e5e3adc5f8d2d9703c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001554_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02142:0.053103,(AS2_ACLBLIBL_02281:0.034995,(TT9_LFPAFLNI_00652:0,(KBS0714_MOLHKGIG_00682:0,SA211_MHAAABBN_00419:0)n3:0)n2:0.060085)n1:0.053103)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001555_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001555_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2293a4b7f8aeb2a0de9032b2f3ed44ae7409ae6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001555_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02143:0.11117,(AS2_ACLBLIBL_02282:0.0444507,((KBS0714_MOLHKGIG_00681:2.93947e-07,SA211_MHAAABBN_00418:0.00389725)n3:0.0007705,TT9_LFPAFLNI_00651:0.002365)n2:0.02044)n1:0.11117)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001556_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001556_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8beb3b1fd32aa5c936eb59353d27bbaa52e8a759
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001556_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02144:0.0452525,((TT9_LFPAFLNI_00650:0.0053195,(KBS0714_MOLHKGIG_00680:0,SA211_MHAAABBN_00417:0)n3:0.0001165)n2:0.026021,AS2_ACLBLIBL_02283:0.036081)n1:0.0452525)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001560_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001560_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b9db3d3fe9419ddecbb403397be9f6b55c72b85
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001560_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02149:0.157746,(((KBS0714_MOLHKGIG_00675:0,TT9_LFPAFLNI_00645:0)n3:0.0034355,SA211_MHAAABBN_00412:3.83476e-07)n2:0.0435183,AS2_ACLBLIBL_02287:0.0210865)n1:0.157746)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001563_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001563_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aad04702c8f9559b18112050d82f73ee8b425053
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001563_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02152:0.0224899,(AS2_ACLBLIBL_02290:0.0144301,((KBS0714_MOLHKGIG_00672:0.00152038,SA211_MHAAABBN_00409:8.37184e-08)n3:0.00019337,TT9_LFPAFLNI_00642:8.37184e-08)n2:0.0229814)n1:0.0224899)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001564_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001564_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b8050dff5d2881443214c833f9145b1a72a8641
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001564_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02153:0.110805,(((SA211_MHAAABBN_00408:0,TT9_LFPAFLNI_00641:0)n3:0,KBS0714_MOLHKGIG_00671:0)n2:0.0736365,AS2_ACLBLIBL_02291:0.0583345)n1:0.110805)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001566_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001566_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6865dff7682d67fea288241d48972c97b84deea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001566_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02155:0.0462305,((TT9_LFPAFLNI_00639:0.00281305,(SA211_MHAAABBN_00406:0.00034193,KBS0714_MOLHKGIG_00669:0.00628207)n3:0.00094866)n2:0.00907307,AS2_ACLBLIBL_02293:0.017438)n1:0.0462305)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001567_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001567_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..365d5b904d23cddf02eda240c488c1e20b588280
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001567_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02156:0.101169,(AS2_ACLBLIBL_02294:0.0321339,(TT9_LFPAFLNI_00638:0.00343313,(SA211_MHAAABBN_00405:0.00296362,KBS0714_MOLHKGIG_00668:0.00791838)n3:0.0130304)n2:0.0488994)n1:0.101169)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001569_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001569_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f453958a489d5d419b7a232b2aff9471a9df2466
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001569_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02158:0.098526,(AS2_ACLBLIBL_02302:0.085438,(TT9_LFPAFLNI_00631:3.67195e-07,(SA211_MHAAABBN_00398:0.006268,KBS0714_MOLHKGIG_00661:0.057345)n3:0.00094838)n2:0.0210995)n1:0.098526)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001570_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001570_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2a72e45e0d048db36c74266115fa4d4c23e5a72
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001570_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02159:0.199503,(((KBS0714_MOLHKGIG_00660:0.00188074,SA211_MHAAABBN_00397:0.00449426)n3:0.0257276,TT9_LFPAFLNI_00630:0.0230463)n2:0.0419303,AS2_ACLBLIBL_02303:0.088595)n1:0.199503)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001572_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001572_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5ec6813ec29a226331547e6c6d12e800a76023b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001572_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02161:0.187646,(AS2_ACLBLIBL_02305:0.0324973,((SA211_MHAAABBN_00395:0.00442052,KBS0714_MOLHKGIG_00658:0.00355648)n3:0.00269396,TT9_LFPAFLNI_00628:4.46452e-07)n2:0.0280557)n1:0.187646)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001574_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001574_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7906498eb816811f6185635b833cfedc04ce0016
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001574_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001576_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001576_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf963c6e87ebb5b19b19c635963af33702bbc727
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001576_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001577_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001577_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eec9464a87fae03179b915a5ce123ba3ab931075
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001577_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001578_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001578_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52e3c1f9bdebb62afa2569ce57a602b4e861135b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001578_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02169:0.261782,(AS2_ACLBLIBL_02312:0.324887,((SA211_MHAAABBN_00388:0.0204016,TT9_LFPAFLNI_00621:0.00998937)n3:0.0427966,KBS0714_MOLHKGIG_00651:0.0465206)n2:0.230785)n1:0.261782)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001579_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001579_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68c6c8921bf56e2310b1b51d4e3782f56d259d72
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001579_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02171:0.248864,(AS2_ACLBLIBL_02314:0.0698702,(SA211_MHAAABBN_00386:0.0130507,(KBS0714_MOLHKGIG_00649:0.022612,TT9_LFPAFLNI_00619:0.014851)n3:0.0146768)n2:0.0424093)n1:0.248864)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001580_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001580_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61f2936bbbcdd1f21b24caa7d5f1a5bac640a1c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001580_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02175:0.108866,((TT9_LFPAFLNI_00617:0.00575925,(KBS0714_MOLHKGIG_00647:0.0008285,SA211_MHAAABBN_00384:0.0016875)n3:0.00308475)n2:0.0425102,AS2_ACLBLIBL_02316:0.0234133)n1:0.108866)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001582_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001582_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14cb5c16d138da7e0509a1912413548546ee1b8e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001582_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02183:0.00300887,(((KBS0714_MOLHKGIG_00642:0.00606825,SA211_MHAAABBN_00379:0.00213475)n3:0.00371125,AS2_ACLBLIBL_02320:0.1387)n2:0.00540625,TT9_LFPAFLNI_00612:0.00630525)n1:0.00300887)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001583_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001583_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1dc55ace7de6451a7a1e5a7ad9052899ad4ebb93
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001583_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02184:0.0450413,(KBS0714_MOLHKGIG_00641:1.93337e-07,(AS2_ACLBLIBL_02321:0.0833345,(TT9_LFPAFLNI_00611:0.00974625,SA211_MHAAABBN_00378:1.93337e-07)n3:0.0032925)n2:0.00701417)n1:0.0450413)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001584_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001584_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5e8129ec8395d63701e2561632134bc47fdaee6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001584_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00676:0.7636,(((AS2_ACLBLIBL_02333:1.5524e-06,KBS0714_MOLHKGIG_00168:0.0159101)n3:0.00403637,SA211_MHAAABBN_00359:1.5524e-06)n2:0.00550088,TT9_LFPAFLNI_02011:0.00334887)n1:0.7636)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001585_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001585_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfef61c43adc3c65d809606ecf3a606a3292af57
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001585_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_02343:0.0459294,((KBS0714_MOLHKGIG_00612:0.0646493,(SA211_MHAAABBN_00328:0.00237333,SA211_MHAAABBN_01772:0.116068)n3:0.0128965)n2:0.0579648,TT9_LFPAFLNI_02009:3.4569e-07)n1:0.0459294)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001586_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001586_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88c3837cac2dc91818a86fc3b18ce61841d3a3b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001586_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02245:0.0422977,((AS2_ACLBLIBL_02350:0.894553,SA211_MHAAABBN_00317:0.0582007)n2:0.0157921,(TT9_LFPAFLNI_00585:0.0771442,KBS0714_MOLHKGIG_00584:0.0511798)n3:0.0537543)n1:0.0422977)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001587_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001587_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a35c7df85c2a03830d0a2bc75eab657b4fdafb12
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001587_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001589_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001589_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aadfd74ae96437d05ecb6b8f92ef92a209f11ecb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001589_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02248:0.156491,((KBS0714_MOLHKGIG_00579:0.062521,(SA211_MHAAABBN_00311:0.00804075,TT9_LFPAFLNI_00580:0.00502525)n3:0.0282065)n2:0.0563065,AS2_ACLBLIBL_02354:0.165375)n1:0.156491)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001590_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001590_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19b71637e78686196053cb7089c98bc64c00f603
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001590_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02249:0.0845322,(AS2_ACLBLIBL_02358:0.0273617,(TT9_LFPAFLNI_00576:0.0116649,(SA211_MHAAABBN_00307:0.00790951,KBS0714_MOLHKGIG_00575:0.00438749)n3:0.00312813)n2:0.0442956)n1:0.0845322)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001591_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001591_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2b4408f651ed2e630ac3fae123e89f7d55d960b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001591_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001593_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001593_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ded7e0c14ba5775fed8a375b82fe017752755053
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001593_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001597_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001597_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e5ff9c05def1c53b5ac45e148697c1161e0b890
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001597_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001601_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001601_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a7075b85aa6b2647a501634a8bce3f206b7cea3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001601_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001603_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001603_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76d6a74b0c08969aa63ae718c7df5187fba3e72b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001603_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001604_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001604_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c6421ef863e1abef02438ac39ecf222aa0d73e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001604_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001606_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001606_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..578985e2ba75971323db52bd3d7218a483b0c931
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001606_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001607_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001607_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8967ae0fc555ed5287536d69dea5f414955d43c6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001607_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001608_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001608_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2b2e1623648d85f1a05c5e6bd4f49b657dae366
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001608_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001609_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001609_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..098c29b0e2e9b5e6ce5ee4ef819d390f2c89c167
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001609_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001610_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001610_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ad6dd3d9630283163302ec34c89ce9c40424a89
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001610_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001612_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001612_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc3c88c44930d2571ce72e0ae5f05672b2e3afea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001612_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02284:0.0333465,(((KBS0714_MOLHKGIG_00546:5e-07,TT9_LFPAFLNI_00549:5e-07)n3:0.00020702,SA211_MHAAABBN_00271:0.00225248)n2:0.0165222,AS2_ACLBLIBL_02401:0.007146)n1:0.0333465)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001613_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001613_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8df4a552fb795c5e10927c822e42effbf0d1d141
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001613_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02285:0.345357,((SA211_MHAAABBN_00270:0.0127353,(KBS0714_MOLHKGIG_00545:0,TT9_LFPAFLNI_00548:0)n3:0.0278658)n2:0.288145,AS2_ACLBLIBL_02402:0.150096)n1:0.345357)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001614_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001614_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e937b9824874cc7d158943d21266af782696fa09
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001614_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02286:0.0522934,(AS2_ACLBLIBL_02403:0.0357152,(KBS0714_MOLHKGIG_00544:0.00577008,(SA211_MHAAABBN_00269:0.00628733,TT9_LFPAFLNI_00547:0.00800467)n3:0.00274442)n2:0.0322629)n1:0.0522934)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001616_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001616_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98bbbbd27b2354a8c9bb4e31eab1d3084894d2b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001616_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02290:0.0429266,(AS2_ACLBLIBL_02408:0.0660058,(SA211_MHAAABBN_00265:2.91273e-07,(KBS0714_MOLHKGIG_00541:0.0084945,TT9_LFPAFLNI_00544:0.0046675)n3:0.00140473)n2:0.124894)n1:0.0429266)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001617_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001617_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffc137d4b2e077b69dc9ef1ca99fd4eae55b71eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001617_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02291:0.0662529,((SA211_MHAAABBN_00264:0.00478432,(KBS0714_MOLHKGIG_00540:2.93176e-07,TT9_LFPAFLNI_00543:0.00431716)n3:0.00566584)n2:0.0740394,AS2_ACLBLIBL_02409:0.0722962)n1:0.0662529)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001618_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001618_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67d483d0a35ac9e710697138e82128c5f6bc76b3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001618_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02292:0.0673507,(((TT9_LFPAFLNI_00542:0,KBS0714_MOLHKGIG_00539:0)n3:0.00245733,SA211_MHAAABBN_00263:0.00314967)n2:0.0328146,AS2_ACLBLIBL_02410:0.0489167)n1:0.0673507)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001623_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001623_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d34a20623f0cfd1bb953b5a634e875f9ab112f97
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001623_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02301:0.201539,(AS2_ACLBLIBL_02419:0.212229,(KBS0714_MOLHKGIG_00533:0.0109608,(TT9_LFPAFLNI_00533:0.0175375,SA211_MHAAABBN_00254:0.0106035)n3:0.0181023)n2:0.159743)n1:0.201539)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001624_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001624_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db7781afbf73c84dc37cd9fd87cb7b0f06d38aac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001624_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02302:0.317443,((TT9_LFPAFLNI_00532:1.47427e-06,(SA211_MHAAABBN_00253:0.250394,KBS0714_MOLHKGIG_00532:1.47427e-06)n3:0.073815)n2:0.31187,AS2_ACLBLIBL_02420:0.272628)n1:0.317443)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001627_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001627_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c45dd59d73dad64c331b89e43f1595a8edb4cc2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001627_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02305:0.18949,(AS2_ACLBLIBL_02423:0.0696639,(TT9_LFPAFLNI_00529:0.0148666,(KBS0714_MOLHKGIG_00529:0.00463763,SA211_MHAAABBN_00250:0.00932437)n3:0.00227387)n2:0.0882364)n1:0.18949)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001628_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001628_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5bea207145ec11e6baa08da38c09a4f068637c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001628_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02307:0.0480948,(AS2_ACLBLIBL_02424:0.0285184,(TT9_LFPAFLNI_00527:0.00722562,(KBS0714_MOLHKGIG_00527:0.00555862,SA211_MHAAABBN_00248:0.00761638)n3:0.00472388)n2:0.00252887)n1:0.0480948)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001631_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001631_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e75562b325778e3cb88949fdce53e10b04715f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001631_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02316:0.154399,(TT9_LFPAFLNI_00516:0.152319,(AS2_ACLBLIBL_02432:0.508635,(SA211_MHAAABBN_00206:1.02833,SA211_MHAAABBN_00237:0.452652)n3:0.0502946)n2:0.460679)n1:0.154399)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001633_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001633_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06278ff5c5e63f3646401c38e5584b85842cfd5d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001633_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02321:0.0621586,(AS2_ACLBLIBL_02438:0.0773048,(TT9_LFPAFLNI_00512:0.0705583,(SA211_MHAAABBN_00233:0.0667038,KBS0714_MOLHKGIG_00513:0.0644943)n3:0.0443098)n2:0.0176318)n1:0.0621586)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001634_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001634_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d967d8b21278fd957acf31300a92867a7e671ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001634_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02322:0.0690876,(SA211_MHAAABBN_00232:0.0874709,(KBS0714_MOLHKGIG_00512:0.0167546,(AS2_ACLBLIBL_02439:0.0213296,TT9_LFPAFLNI_00511:0.0157914)n3:0.0109489)n2:0.174425)n1:0.0690876)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001636_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001636_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..266b38ef2439d22deea8bded227da34cec06a3a2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001636_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02326:0.0327491,(AS2_ACLBLIBL_02442:0.0385588,((KBS0714_MOLHKGIG_00508:0.00764675,TT9_LFPAFLNI_00507:0.00480925)n3:0.0015425,SA211_MHAAABBN_00228:0.008766)n2:0.0354945)n1:0.0327491)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001639_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001639_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..895dcd251bc056e22f2b3f2da06470ce3ebd68eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001639_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02329:0.0496352,((SA211_MHAAABBN_00225:0.00699963,(TT9_LFPAFLNI_00504:0.0109596,KBS0714_MOLHKGIG_00505:0.00177937)n3:0.00436237)n2:0.0652979,AS2_ACLBLIBL_02445:0.0726236)n1:0.0496352)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001641_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001641_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55440d1f1cfeff7e5315f77627949cfe12c055c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001641_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02331:0.215337,((SA211_MHAAABBN_00223:0.0169959,(TT9_LFPAFLNI_00502:0.0307961,KBS0714_MOLHKGIG_00503:0.0284189)n3:0.00728366)n2:0.186083,AS2_ACLBLIBL_02447:0.234868)n1:0.215337)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001643_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001643_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90c8e823ed385c1f35a2b2a7e0251f77e41b06d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001643_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02333:0.0172463,(SA211_MHAAABBN_00221:0.0084455,(AS2_ACLBLIBL_02449:0.021745,(KBS0714_MOLHKGIG_00500:0,TT9_LFPAFLNI_00499:0)n3:0.0112)n2:0.0139035)n1:0.0172463)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001644_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001644_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..138104374f2d73af93f448e5047b7bb93584741e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001644_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02334:0.0444648,(AS2_ACLBLIBL_02450:0.0412303,((KBS0714_MOLHKGIG_00497:0.00276577,TT9_LFPAFLNI_00496:0.00094923)n3:0.00246713,SA211_MHAAABBN_00218:0.0102738)n2:0.0506981)n1:0.0444648)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001645_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001645_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..575e9735f4ddeb532b69293c3dfd71f9cd3cfaf2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001645_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02337:0.0733342,(AS2_ACLBLIBL_02453:0.0248236,(KBS0714_MOLHKGIG_00494:0.00860662,(TT9_LFPAFLNI_00493:0.00534412,SA211_MHAAABBN_00215:0.00700988)n3:0.00097837)n2:0.0208639)n1:0.0733342)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001646_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001646_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd340d00be996ddd42fe7b2fed508ee6908ba778
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001646_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02338:0.106084,((KBS0714_MOLHKGIG_00493:0.0108453,(TT9_LFPAFLNI_00492:0,SA211_MHAAABBN_00214:0)n3:0.00453275)n2:0.0611162,AS2_ACLBLIBL_02454:0.0833403)n1:0.106084)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001647_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001647_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..112edca682831f0cf5b1b6dddb8941e699d60f10
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001647_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001649_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001649_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7f462d3757c3a39c95011286405bdc9a999d905
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001649_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001650_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001650_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..809a8f3770449d1bdc5ecb284824b666d4ee3a07
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001650_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02343:0.122995,((SA211_MHAAABBN_00207:0.0155685,(KBS0714_MOLHKGIG_00487:0.00270658,TT9_LFPAFLNI_00487:0.00027442)n3:0.0145102)n2:0.0328136,AS2_ACLBLIBL_02459:0.0491993)n1:0.122995)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001651_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001651_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0787e7e86b1adf9f810bc48735a797e1e5b55138
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001651_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02344:0.109375,((TT9_LFPAFLNI_00486:0.018715,(SA211_MHAAABBN_00205:0.00418075,KBS0714_MOLHKGIG_00486:0.00680325)n3:0.002946)n2:0.0424325,AS2_ACLBLIBL_02461:0.0431742)n1:0.109375)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001655_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001655_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02f10db644dd1e2540b4ab972c68da6e33c9c033
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001655_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02349:0.210928,(((KBS0714_MOLHKGIG_00482:0,TT9_LFPAFLNI_00482:0)n3:0,SA211_MHAAABBN_00200:0)n2:0.108573,AS2_ACLBLIBL_02465:0.22192)n1:0.210928)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001656_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001656_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e76f001037f45b2cc2ec5d65e43309bfdecf412f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001656_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02350:0.157286,(AS2_ACLBLIBL_02466:0.160274,((TT9_LFPAFLNI_00481:0.00013235,KBS0714_MOLHKGIG_00481:0.00414665)n3:0.00444935,SA211_MHAAABBN_00199:0.00692465)n2:0.194241)n1:0.157286)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001659_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001659_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc2839888f39c3e42493ec25007935dc2e0d618b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001659_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02353:0.100492,((SA211_MHAAABBN_00196:0.0135928,(KBS0714_MOLHKGIG_00478:0,TT9_LFPAFLNI_00478:0)n3:0.00739825)n2:0.0464103,AS2_ACLBLIBL_02469:0.0845863)n1:0.100492)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001663_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001663_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05c362e6492ca51d6a12800309d5d360274146ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001663_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02358:0.0222865,(((TT9_LFPAFLNI_00473:0.00400614,SA211_MHAAABBN_00191:0.00206386)n3:0.00229591,KBS0714_MOLHKGIG_00473:0.00132709)n2:0.01087,AS2_ACLBLIBL_02474:0.052972)n1:0.0222865)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001664_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001664_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69f03f283c1a9b4667d81c4e0b49d92990b360b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001664_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02359:0.227147,(AS2_ACLBLIBL_02475:0.167757,(TT9_LFPAFLNI_00472:0.00697889,(KBS0714_MOLHKGIG_00472:0,SA211_MHAAABBN_00190:0)n3:0.00949911)n2:0.0774993)n1:0.227147)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001665_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001665_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f69624362dc90372318ad0e21bccd0dbd0b9cf0c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001665_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02360:0.0428523,(AS2_ACLBLIBL_02476:0.130747,(SA211_MHAAABBN_00189:3.55551e-07,(KBS0714_MOLHKGIG_00471:3.55551e-07,TT9_LFPAFLNI_00471:0.002473)n3:0.000172)n2:0.136798)n1:0.0428523)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001666_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001666_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea2ab17a0f293ef375c1b4927efaef6be2ca4989
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001666_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02361:0.027012,(((TT9_LFPAFLNI_00470:0,KBS0714_MOLHKGIG_00470:0)n3:0,SA211_MHAAABBN_00188:0)n2:0.018379,AS2_ACLBLIBL_02477:0.019446)n1:0.027012)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001668_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001668_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1943ddd8ca1bd6ca85c7b44f89cfbf372385fd01
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001668_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02363:0.0758679,(AS2_ACLBLIBL_02479:0.104971,(SA211_MHAAABBN_00186:0.0017325,(KBS0714_MOLHKGIG_00468:0.00525325,TT9_LFPAFLNI_00468:0.00341875)n3:0.0015195)n2:0.078819)n1:0.0758679)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001671_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001671_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77cf1d9956ae14ccf005dbc20c3d66ac0e33371c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001671_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02366:0.106102,(AS2_ACLBLIBL_02482:0.0391461,(TT9_LFPAFLNI_00465:3.16865e-07,(KBS0714_MOLHKGIG_00465:0.00014263,SA211_MHAAABBN_00183:0.00313538)n3:0.0130349)n2:0.0501234)n1:0.106102)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001675_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001675_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4110ae39c6599fc012aa9add838d3691cacd471
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001675_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02371:0.25222,((KBS0714_MOLHKGIG_00460:0.0132406,(SA211_MHAAABBN_00178:0.016334,TT9_LFPAFLNI_00460:0.00579704)n3:0.0100174)n2:0.111683,AS2_ACLBLIBL_02487:0.122347)n1:0.25222)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001678_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001678_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3ecdc78011f0f5067491a9e511ccfb95d1696d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001678_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02374:0.1299,((KBS0714_MOLHKGIG_00457:3.05e-05,(TT9_LFPAFLNI_00457:0.003559,SA211_MHAAABBN_00175:0.001721)n3:0.01058)n2:0.103845,AS2_ACLBLIBL_02490:0.0643435)n1:0.1299)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001681_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001681_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ecd6d1162fc7346082c5dfda61b01962fa44c44
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001681_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02378:0.128632,(AS2_ACLBLIBL_02506:0.0315768,(KBS0714_MOLHKGIG_00450:0.0079366,(TT9_LFPAFLNI_00453:0.0049029,SA211_MHAAABBN_00171:0.0010431)n3:0.0070329)n2:0.00806603)n1:0.128632)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001682_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001682_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..679af727de3950fbb718655018e7ff022aca51a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001682_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02379:0.229582,(((TT9_LFPAFLNI_00452:0.0163414,SA211_MHAAABBN_00170:0.0396886)n3:0.0894269,KBS0714_MOLHKGIG_00449:0.0695816)n2:0.296862,AS2_ACLBLIBL_02507:0.143497)n1:0.229582)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001683_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001683_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cba58bfb8c5d52a97441f4a6915c380e85c33f2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001683_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02381:0.142219,(AS2_ACLBLIBL_02510:0.187729,(SA211_MHAAABBN_00168:0.0127942,(TT9_LFPAFLNI_00450:0.0227161,KBS0714_MOLHKGIG_00447:0.0043059)n3:0.00396382)n2:0.112584)n1:0.142219)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001685_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001685_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0baaa71842ecb87187f8a789ffc96fdbb2c998b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001685_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02383:0.178289,(AS2_ACLBLIBL_02512:0.104216,((SA211_MHAAABBN_00166:5.49593e-07,KBS0714_MOLHKGIG_00445:0.00440923)n3:0.0100353,TT9_LFPAFLNI_00448:0.00047596)n2:0.074646)n1:0.178289)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001686_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001686_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a21b3f52b6ca84a7069a9a7d50cf46ac5618ef14
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001686_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02384:0.0625284,(AS2_ACLBLIBL_02513:0.0280523,(SA211_MHAAABBN_00165:0.007227,(TT9_LFPAFLNI_00447:0.0057355,KBS0714_MOLHKGIG_00444:0.0029445)n3:0.001443)n2:0.0676555)n1:0.0625284)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001687_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001687_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4d953304823e0303fc9b3c04a1c307c78ec17b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001687_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02385:0.181689,(((KBS0714_MOLHKGIG_00443:0.00297712,SA211_MHAAABBN_00164:0.00572288)n3:0.00797562,TT9_LFPAFLNI_00446:0.00072038)n2:0.0628021,AS2_ACLBLIBL_02514:0.0971969)n1:0.181689)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001688_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001688_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a036885a7b3c28f92f84c0bc2cbaa6e201e302df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001688_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02386:0.0584066,(AS2_ACLBLIBL_02515:0.292908,((SA211_MHAAABBN_00163:0.00422388,TT9_LFPAFLNI_00445:0.00266513)n3:0.00075588,KBS0714_MOLHKGIG_00442:0.00426213)n2:0.106949)n1:0.0584066)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001689_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001689_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9eeeead74a966cadfaedc4a90a0c233f0fb49d5f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001689_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001690_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001690_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae49fc1189aa02ac97994ab39f2209ba095e2a08
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001690_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001696_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001696_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a43414d3793a2c4eba131f263a926e22cc42bb00
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001696_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02394:0.011071,((SA211_MHAAABBN_00155:0.00333059,(TT9_LFPAFLNI_00437:0,KBS0714_MOLHKGIG_00434:0)n3:0.00135141)n2:0.0065442,AS2_ACLBLIBL_02523:0.010163)n1:0.011071)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001698_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001698_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7919b2ecd9087a050517209bd1dd6d77e9b61ff7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001698_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02396:0.304856,(AS2_ACLBLIBL_02525:0.183714,(KBS0714_MOLHKGIG_00432:0.0299886,(SA211_MHAAABBN_00153:0.047883,TT9_LFPAFLNI_00435:0.0416871)n3:0.0256184)n2:0.317858)n1:0.304856)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001699_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001699_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2d1cd1614deb9d31067564b23ef5bb9b552e593
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001699_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02397:0.257031,(AS2_ACLBLIBL_02527:0.53734,((KBS0714_MOLHKGIG_00430:0.0202096,SA211_MHAAABBN_00151:0.0214073)n3:0.0233932,TT9_LFPAFLNI_00433:0.0900755)n2:0.310581)n1:0.257031)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001700_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001700_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..faa59304fba6caf19ea3b2c48c9f15e6f5b47a88
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001700_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02398:0.115861,((SA211_MHAAABBN_00150:0.00469725,(TT9_LFPAFLNI_00432:0.00113125,KBS0714_MOLHKGIG_00429:0.00275275)n3:0.00309825)n2:0.216688,AS2_ACLBLIBL_02528:0.139618)n1:0.115861)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001701_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001701_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60520fbaf176d058e09b5c41dfab65239afd5762
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001701_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02399:0.0730221,(AS2_ACLBLIBL_02529:0.120055,(KBS0714_MOLHKGIG_00428:0.00283525,(SA211_MHAAABBN_00149:0.0020195,TT9_LFPAFLNI_00431:0.0094805)n3:0.00241575)n2:0.0934848)n1:0.0730221)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001702_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001702_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..baa8f127a6fa72ccf4f595b815a47776935f1175
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001702_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02400:0.0107913,(AS2_ACLBLIBL_02530:0.0770295,((SA211_MHAAABBN_00148:0.00952007,TT9_LFPAFLNI_00430:0.00274793)n3:0.00231224,KBS0714_MOLHKGIG_00427:0.00096519)n2:0.00941132)n1:0.0107913)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001703_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001703_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..460554939cb2ec2f546dd3124ebce531e5395e9d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001703_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02401:0.0832678,(AS2_ACLBLIBL_02531:0.0360803,(SA211_MHAAABBN_00147:0.00371761,(TT9_LFPAFLNI_00429:0.00319585,KBS0714_MOLHKGIG_00426:2.52191e-07)n3:0.00026889)n2:0.0424082)n1:0.0832678)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001706_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001706_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5f67b3a39104b6f4381c27ca9fe78bd770450ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001706_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02406:0.0770928,(AS2_ACLBLIBL_02536:0.0470075,(TT9_LFPAFLNI_00425:0.0191817,(SA211_MHAAABBN_00143:9.567e-05,KBS0714_MOLHKGIG_00422:0.00613033)n3:0.00433535)n2:0.0376491)n1:0.0770928)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001707_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001707_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab3fd010c16320355d3a6bf341eec243288f04ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001707_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00761:0.00456713,(((KBS0714_MOLHKGIG_02019:0,SA211_MHAAABBN_01728:0)n3:0.55982,AS2_ACLBLIBL_02537:0.129484)n2:0.500254,TT9_LFPAFLNI_01956:0.0143508)n1:0.00456713)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001708_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001708_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6ed9f99e6485bea0f616f14da66e912e2f240b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001708_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02407:0.00948616,(TT9_LFPAFLNI_00424:0.0214167,(SA211_MHAAABBN_00142:0.0117663,(KBS0714_MOLHKGIG_00421:0.00325601,AS2_ACLBLIBL_02538:0.055771)n3:0.00096517)n2:0.00382878)n1:0.00948616)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001711_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001711_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d2736aba054339738a1b88b343e17034727b968
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001711_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02411:0.110681,(AS2_ACLBLIBL_02543:0.0485285,((KBS0714_MOLHKGIG_00417:0.00074325,TT9_LFPAFLNI_00420:0.00431475)n3:0.0138192,SA211_MHAAABBN_00138:0.00755325)n2:0.0292377)n1:0.110681)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001713_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001713_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5baa28667f37c4682d52b12a5475320276ea3dc1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001713_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02413:0.0533684,((KBS0714_MOLHKGIG_00414:2.593e-05,(SA211_MHAAABBN_00134:0,TT9_LFPAFLNI_00417:0)n3:0.00538407)n2:0.0238081,AS2_ACLBLIBL_02545:0.0180452)n1:0.0533684)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001716_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001716_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3452c6b7837e2907f81beec1e586e7a3c47a5d27
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001716_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001717_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001717_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f2417723bd200bd03871593838e146381f1c671
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001717_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001720_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001720_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3f3bb6afe39466fb0d58080ffe42f5d70a6af16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001720_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001721_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001721_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b12fd1196f9c0c1dca28155858d0fb64b461de4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001721_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02425:0.0459854,(AS2_ACLBLIBL_02556:0.0232203,(KBS0714_MOLHKGIG_00401:0.0229457,(SA211_MHAAABBN_00125:0.000805,TT9_LFPAFLNI_00407:0.003929)n3:0.012965)n2:0.0074205)n1:0.0459854)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001722_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001722_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d4484ce31906cd332318d15fa4c7327fb66b104
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001722_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001723_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001723_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a062e2eae37c35da1d1dc7eb06ac1902babb2361
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001723_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02429:0.0939669,((TT9_LFPAFLNI_00405:0.0002978,(KBS0714_MOLHKGIG_00399:0,SA211_MHAAABBN_00123:0)n3:0.0066592)n2:0.0169711,AS2_ACLBLIBL_02558:0.0228162)n1:0.0939669)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001726_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001726_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffc39aae4a02a65a0fd340b2ee2d3a80040e0993
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001726_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001727_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001727_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21b9519174749b0b2f59291cf11d84539a6c83f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001727_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001728_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001728_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e425e3a1db0aa1cffb1dacd2d0c55ec929fa5da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001728_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001730_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001730_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e3a42b0421ebda29b5132faa39ca051dab6c77a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001730_tree.txt
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001738_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001738_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e29a99d948bf46c694ee7149b461186605a5ef3d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001738_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02448:0.0558045,(AS2_ACLBLIBL_02576:0.003066,(SA211_MHAAABBN_00103:0.0203983,(TT9_LFPAFLNI_00385:0,KBS0714_MOLHKGIG_00379:0)n3:0.00466472)n2:0.001533)n1:0.0558045)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001739_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001739_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df9389a2cbe8acb0daba32bcf53f63c0eb7e0d8b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001739_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02449:0.0121925,(SA211_MHAAABBN_00088:0.009785,(AS2_ACLBLIBL_02590:0.0067315,(TT9_LFPAFLNI_00379:0.00127775,KBS0714_MOLHKGIG_00372:0.00217325)n3:0.002809)n2:0.0028365)n1:0.0121925)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001740_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001740_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f547367b7164bc38b1c7cf9d9f0a455bc2865ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001740_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02450:0.0369665,((TT9_LFPAFLNI_00378:0.0051895,(SA211_MHAAABBN_00087:0.00542,KBS0714_MOLHKGIG_00371:0.006892)n3:0.0023805)n2:0.007288,AS2_ACLBLIBL_02591:0.014124)n1:0.0369665)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001741_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001741_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cd4d816d225fe4d487b160876df0ec3519fb1f2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001741_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02451:0.0643773,(AS2_ACLBLIBL_02592:0.0466593,(KBS0714_MOLHKGIG_00370:0.0055805,(TT9_LFPAFLNI_00377:0.00214871,SA211_MHAAABBN_00086:0.00333529)n3:0.001453)n2:0.0342328)n1:0.0643773)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001742_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001742_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ca345248b69f451b0e83dade65c958f10ded52d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001742_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02452:0.118197,(AS2_ACLBLIBL_02593:0.156941,(KBS0714_MOLHKGIG_00368:0.0270364,(TT9_LFPAFLNI_00375:0,SA211_MHAAABBN_00084:0)n3:0.0209166)n2:0.164888)n1:0.118197)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001743_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001743_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9be37638051953b95cf94df3f020363a50f3d5d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001743_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02455:0.0732928,(AS2_ACLBLIBL_02596:0.0199535,((KBS0714_MOLHKGIG_00365:0,SA211_MHAAABBN_00081:0)n3:0,TT9_LFPAFLNI_00372:0)n2:0.0024145)n1:0.0732928)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001745_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001745_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e469a3b78a711329da69bda0decb21b0eef7533
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001745_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02457:0.0525911,(AS2_ACLBLIBL_02598:0.0354409,(KBS0714_MOLHKGIG_00363:0.00744838,(SA211_MHAAABBN_00079:0.00613463,TT9_LFPAFLNI_00370:0.00768237)n3:0.00153062)n2:0.0355881)n1:0.0525911)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001747_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001747_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..497c9c5badf02d3b2c9c2d5b1d774122f916135a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001747_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02459:0.0627842,(AS2_ACLBLIBL_02600:0.192976,(SA211_MHAAABBN_00077:3.60077e-07,(KBS0714_MOLHKGIG_00361:0.00813,TT9_LFPAFLNI_00368:0)n3:0.00011416)n2:0.0334021)n1:0.0627842)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001751_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001751_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01b845dc08e15e09189128be7700e18bbd191e2b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001751_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02464:0.169832,(AS2_ACLBLIBL_02605:0.0935545,(KBS0714_MOLHKGIG_00356:0.00741382,(SA211_MHAAABBN_00072:0.00253078,TT9_LFPAFLNI_00363:5.48631e-07)n3:0.00358168)n2:0.101886)n1:0.169832)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001753_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001753_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f46a72030092f0950d65e1347ad53171d4cce06c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001753_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02467:0.184582,((KBS0714_MOLHKGIG_00353:7.23379e-07,(TT9_LFPAFLNI_00360:0,SA211_MHAAABBN_00069:0)n3:0.0122939)n2:0.180745,AS2_ACLBLIBL_02608:0.162256)n1:0.184582)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001754_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001754_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c072fcb9f7a13efcabaff61087cdff813abb8259
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001754_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02468:0.0662591,(AS2_ACLBLIBL_02609:0.0598208,(SA211_MHAAABBN_00068:0.00721621,(KBS0714_MOLHKGIG_00352:0.0114567,TT9_LFPAFLNI_00359:0.00523535)n3:0.00173379)n2:0.0217672)n1:0.0662591)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001755_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001755_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ae76c81c1502b1902a2139a7d6688a1ec9512a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001755_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02469:0.252101,((TT9_LFPAFLNI_00358:0.017002,(KBS0714_MOLHKGIG_00351:7.20745e-07,SA211_MHAAABBN_00067:0.00310375)n3:0.0115325)n2:0.124636,AS2_ACLBLIBL_02610:0.0603588)n1:0.252101)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001756_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001756_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bba6e58f240094b236dd3b5ca3609f19bffdec5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001756_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02471:0.161428,(AS2_ACLBLIBL_02612:0.147443,(KBS0714_MOLHKGIG_00349:0.101074,(TT9_LFPAFLNI_00356:0.0226205,SA211_MHAAABBN_00065:0.0241295)n3:0.0983195)n2:0.0568455)n1:0.161428)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001758_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001758_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9381ff933e9595e9dfdc7fe02cfc48a52bd1f53
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001758_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02475:0.0655642,((KBS0714_MOLHKGIG_00346:0.00278826,(SA211_MHAAABBN_00062:0.00110802,TT9_LFPAFLNI_00353:0.00127598)n3:0.00278119)n2:0.0288798,AS2_ACLBLIBL_02623:0.0657287)n1:0.0655642)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001760_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001760_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f891f5c1366553108e161e6d599c1984ed45102
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001760_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02478:0.333446,(AS2_ACLBLIBL_02626:0.0942727,(KBS0714_MOLHKGIG_00343:0.00030465,(TT9_LFPAFLNI_00350:0.0077123,SA211_MHAAABBN_00059:0.0187267)n3:0.00736435)n2:0.115053)n1:0.333446)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001762_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001762_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4db1a9f5223cafd8ef02c9980f37a7ee35dad17
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001762_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02480:0.0429319,(AS2_ACLBLIBL_02628:0.0571612,((KBS0714_MOLHKGIG_00341:2.19278e-07,TT9_LFPAFLNI_00348:0.0103623)n3:0.00580749,SA211_MHAAABBN_00057:0.00626277)n2:0.0542451)n1:0.0429319)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001765_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001765_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78a922e9f960c31631c47b97b86dc2d04b2393b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001765_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02486:0.12021,(((KBS0714_MOLHKGIG_00338:0.00683914,TT9_LFPAFLNI_00345:0.00583886)n3:0.0179491,SA211_MHAAABBN_00054:0.00803715)n2:0.0749611,AS2_ACLBLIBL_02674:0.095589)n1:0.12021)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001767_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001767_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c62ec9ee2365b1b092c6b9386b58fac00af82907
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001767_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02492:0.587025,(((TT9_LFPAFLNI_00342:0.0157035,SA211_MHAAABBN_00051:1.77858e-06)n3:0.031274,KBS0714_MOLHKGIG_00335:0.0419465)n2:0.241291,AS2_ACLBLIBL_02680:0.27728)n1:0.587025)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001768_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001768_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35ad17a25dae8558f96b4b806d50566dca950df9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001768_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00735:0.0213473,KD337_16_NAFOICDF_00741:0.739382)n1:0.00415084,((TT9_LFPAFLNI_01979:0.0224352,SA211_MHAAABBN_01751:0.0111658)n3:0.00259225,KBS0714_MOLHKGIG_02045:0.010594)n2:0.00415084)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001769_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001769_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c400e89b98e615cc738fa5a4fd7902fdaf2dd9d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001769_tree.txt
@@ -0,0 +1 @@
+(SA211_MHAAABBN_01967:0,((SA211_MHAAABBN_00368:0,SA211_MHAAABBN_00329:0)n2:0,(SA211_MHAAABBN_02017:0,SA211_MHAAABBN_01110:0.27663)n3:0)n1:0)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001773_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001773_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..999e4e03cd75b97397283a15daa63268e2c6214d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001773_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00052:0.132396,((TT9_LFPAFLNI_00309:0.0293803,SA211_MHAAABBN_00010:0.0131208)n2:0.0343038,KBS0714_MOLHKGIG_00302:0.0658122)n1:0.132396)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001774_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001774_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd11fe6756d6e74814e1187eb99a0d729ffa8ca1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001774_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00068:0.0761758,(KBS0714_MOLHKGIG_00286:0.0220865,(SA211_MHAAABBN_02308:0.0013345,TT9_LFPAFLNI_00292:0.0175205)n2:0.0199445)n1:0.0761758)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001780_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001780_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebf9fe28ec51faff106f837d83d3ba0f07d2e96b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001780_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00127:0.017238,((TT9_LFPAFLNI_00243:0.00468175,SA211_MHAAABBN_02255:0.0100132)n2:0.0122162,KBS0714_MOLHKGIG_00243:0.064902)n1:0.017238)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001781_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001781_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea87d3303481f3c5031d03f9944a0a839f7c1fc0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001781_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00104:0.290916,(KBS0714_MOLHKGIG_02037:1.655,(AS2_ACLBLIBL_00142:0.339816,AS2_ACLBLIBL_00807:0.794409)n2:0.0882677)n1:0.0276913)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001782_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001782_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..469ba93d094ef9b5ba3cc979e068e0b4a4dafc06
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001782_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00161:0.072038,(TT9_LFPAFLNI_00220:0.012708,(SA211_MHAAABBN_02213:0.00140038,KBS0714_MOLHKGIG_00219:0.00834762)n2:0.0077375)n1:0.072038)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001784_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001784_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d72745cd3ffd06e2351ba6deb765d0542545fc4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001784_tree.txt
@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00145:0.182497,KD337_16_NAFOICDF_00125:1.96287)n1:0.0568291,(KBS0714_MOLHKGIG_00200:0.284494,AS2_ACLBLIBL_00189:0.267329)n2:0.0568291)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001791_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001791_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d56bedab4e3253787062745d542d03c56ecbd1db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001791_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00253:0.129333,(KBS0714_MOLHKGIG_00132:2.82409e-07,(SA211_MHAAABBN_02146:0,TT9_LFPAFLNI_00140:0)n2:0.029016)n1:0.129333)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001793_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001793_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7bdf3dfa6d9ad945c363e1564a38e15014c4fa1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001793_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00306:0.0631926,((TT9_LFPAFLNI_00080:0.013434,SA211_MHAAABBN_02098:0.005937)n2:0.0038225,KBS0714_MOLHKGIG_00085:0.00644884)n1:0.0631926)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001797_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001797_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb1b073789b35dffefa8a61d54baa9c75e9b2a22
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001797_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00352:0.079892,(KBS0714_MOLHKGIG_00051:0.0140149,(SA211_MHAAABBN_02064:0.00573125,TT9_LFPAFLNI_00046:0.00641575)n2:0.00512375)n1:0.079892)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001798_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001798_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..acee2fcf8e452202e38d9c2929b832fdc27b26b2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001798_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00384:0.111407,(SA211_MHAAABBN_02030:2.54687e-07,(TT9_LFPAFLNI_00012:0.031874,KBS0714_MOLHKGIG_00012:0)n2:0.0023955)n1:0.111407)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001799_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001799_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c99e08cdd617dc8ce7fd0cc194242c0c8f95fd2a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001799_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02201:2.31062e-08,(TT9_LFPAFLNI_00603:0.00618175,(AS2_ACLBLIBL_00400:0.0131365,KBS0714_MOLHKGIG_00628:0.0035765)n2:0.00023725)n1:2.31062e-08)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001800_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001800_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d80175dfaf5fc40fcc23ea62ae56a850eed3ab32
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001800_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02200:0.00347388,(TT9_LFPAFLNI_00602:2.38592e-08,(AS2_ACLBLIBL_00401:0.0144642,KBS0714_MOLHKGIG_00629:0.00323375)n2:0.00029725)n1:0.00347388)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001803_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001803_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60637f14eadff0d6918987a747a74c5cfa187f44
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001803_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00453:0.0159782,((KBS0714_MOLHKGIG_02284:0.00247075,SA211_MHAAABBN_01975:3.74892e-08)n2:0.00343625,TT9_LFPAFLNI_02223:3.74892e-08)n1:0.0159782)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001804_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001804_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eee819eb6ac27d147e45099de568a9ec966220d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001804_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00408:0.128521,((SA211_MHAAABBN_01965:0.0204525,AS2_ACLBLIBL_00459:0.0198915)n2:0.003966,KBS0714_MOLHKGIG_02273:0.0236524)n1:0.128521)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001807_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001807_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e82610d16a0c63a2ae531265fb754c9de472aeca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001807_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00516:0.218342,(KBS0714_MOLHKGIG_02221:0.0184335,(SA211_MHAAABBN_01937:0.008619,TT9_LFPAFLNI_02160:0.004762)n2:0.0040835)n1:0.218342)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001808_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001808_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6da68d6541ed37af6cd8a9f44ddd4adacd739d91
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001808_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00530:0.0824815,(SA211_MHAAABBN_01927:0.010892,(KBS0714_MOLHKGIG_02214:0.0108195,TT9_LFPAFLNI_02153:0.0108195)n2:0.0031345)n1:0.0824815)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001814_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001814_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70522cb87fa4bce6e2a9a9c954ca7ebc4e3480b5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001814_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00553:0.283229,(SA211_MHAAABBN_01906:0.053669,(TT9_LFPAFLNI_02137:0.0073419,KBS0714_MOLHKGIG_02193:0.0112431)n2:0.006162)n1:0.283229)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001815_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001815_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8535beab0bf06c2e5bde9f75ce2182266d5c125
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001815_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00561:0.111988,(KBS0714_MOLHKGIG_02188:0.234667,(TT9_LFPAFLNI_02133:0.00694225,SA211_MHAAABBN_01902:0.0250607)n2:0.0335847)n1:0.111988)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001816_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001816_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7b3bbcdb426a4e730ff346ea80b7c543ac7e02f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001816_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00562:0.186487,(KBS0714_MOLHKGIG_02187:0.0426602,(SA211_MHAAABBN_01901:0.0121588,TT9_LFPAFLNI_02132:0.00528318)n2:0.0122512)n1:0.186487)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001818_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001818_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edade5a45a425756957e92672307320252702c05
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001818_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00602:0.790033,(TT9_LFPAFLNI_02098:1.6456e-06,(SA211_MHAAABBN_01868:0.014686,KBS0714_MOLHKGIG_02155:0.041119)n2:0.0116435)n1:0.790033)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001820_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001820_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2702dd22f76dd63365d8639b37c420681d519f6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001820_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00539:0.0871293,((SA211_MHAAABBN_01859:0,TT9_LFPAFLNI_02089:0)n2:0.10526,AS2_ACLBLIBL_00615:0.410988)n1:0.0871293)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001824_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001824_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a853091fdc46fa89987efbe110256c6398941b73
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001824_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00670:0.0322769,(SA211_MHAAABBN_01815:9.46657e-08,(KBS0714_MOLHKGIG_02108:9.46657e-08,TT9_LFPAFLNI_02048:0.026609)n2:0.00393375)n1:0.0322769)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001825_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001825_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b79225b8195cc524d781c8bb66049456ceb526d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001825_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00678:0.215963,(TT9_LFPAFLNI_02041:0.013473,(KBS0714_MOLHKGIG_02101:0,SA211_MHAAABBN_01808:0)n2:0.010483)n1:0.215963)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001826_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001826_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33bcdbe5171224d9349a6bd6ac7689ce76f6cd5a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001826_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00679:0.259106,(TT9_LFPAFLNI_02040:0.000155,(SA211_MHAAABBN_01807:0,KBS0714_MOLHKGIG_02100:0)n2:0.007648)n1:0.259106)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001827_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001827_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49f010c24d7ab6a954002c23da0582b06e223317
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001827_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00682:0.112582,((SA211_MHAAABBN_01804:2.87936e-07,TT9_LFPAFLNI_02037:0.002303)n2:0.0195895,KBS0714_MOLHKGIG_02097:0.0413125)n1:0.112582)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001829_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001829_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6194a09ad2d61bdc5458dd69f3fea5dc9b4bef6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001829_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00604:0.00716525,(KBS0714_MOLHKGIG_02090:0.0052575,(SA211_MHAAABBN_01798:0.0052155,AS2_ACLBLIBL_00688:0.0160995)n2:0.015406)n1:0.00716525)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001834_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001834_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86a6082597274f512cbca8698271dfa560a4a4fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001834_tree.txt
@@ -0,0 +1 @@
+(KBS0714_MOLHKGIG_00625:0.039508,(AS2_ACLBLIBL_00734:4.33571e-07,(AS2_ACLBLIBL_00746:0.0140873,AS2_ACLBLIBL_00749:0.0757088)n2:0.272297)n1:0.039508)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001836_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001836_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4722147e34795f4f853d5fec2c0a98008aa39914
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001836_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00766:0.302257,((TT9_LFPAFLNI_01988:0.0371925,KBS0714_MOLHKGIG_02054:0.118074)n2:0.431497,SA211_MHAAABBN_01760:0.182534)n1:0.302257)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001838_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001838_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8dbcd861a199cb652c052b728f36bc185aebf36
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001838_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00788:0.00564212,(SA211_MHAAABBN_01739:0.00572475,(KBS0714_MOLHKGIG_02032:0.00646475,TT9_LFPAFLNI_01967:0.00901525)n2:0.00202325)n1:0.00564212)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001840_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001840_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28c1a506445e0270e6ea2f0a1d279648c349cd99
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001840_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00817:0.624667,((KBS0714_MOLHKGIG_01625:0.014645,SA211_MHAAABBN_01331:0.035188)n2:0.308236,TT9_LFPAFLNI_01554:0.160308)n1:0.624667)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001843_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001843_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccd03eb848143285a6ad9c0e37297fd2ffab580d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001843_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00779:0.0401647,(AS2_ACLBLIBL_00846:0.132966,(SA211_MHAAABBN_01706:3.11019e-07,TT9_LFPAFLNI_01934:0.010962)n2:0.0887675)n1:0.0401647)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001844_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001844_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ada19e79149b35f557b0de982081a8ff205d6db7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001844_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00785:0.105321,((SA211_MHAAABBN_01703:7.40972e-07,TT9_LFPAFLNI_01931:0.004495)n2:0.202065,AS2_ACLBLIBL_00848:0.325456)n1:0.105321)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001846_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001846_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a55ce89e4fc626704b9c15b682a0960467f72f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001846_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00787:0.0362073,(AS2_ACLBLIBL_00850:0.0264575,(TT9_LFPAFLNI_01929:1.42786e-07,SA211_MHAAABBN_01701:0.00524986)n2:0.038836)n1:0.0362073)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001847_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001847_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0fd4ab49a6de21a0120be88b3f0e91da49aab29
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001847_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00788:0.064764,(AS2_ACLBLIBL_00851:0.019725,(SA211_MHAAABBN_01700:0,TT9_LFPAFLNI_01928:0)n2:0.014444)n1:0.064764)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001848_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001848_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d56733fa3b004c4c903aa3856df80fffaf059e99
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001848_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00790:1.91435e-06,((SA211_MHAAABBN_01698:0.0651198,AS2_ACLBLIBL_00853:0.0428682)n2:0.742349,TT9_LFPAFLNI_00737:1.31294)n1:1.91435e-06)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001849_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001849_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfb0b139c0338fcfaee461485bae71a26b194844
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001849_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00791:0.231623,((TT9_LFPAFLNI_00736:1.42231,AS2_ACLBLIBL_00854:2.06428e-06)n2:0.343581,SA211_MHAAABBN_01697:0.147418)n1:0.231623)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001851_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001851_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a065404b858065e3d61e2fe1403d3a500c9a28f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001851_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00870:0.0032545,(SA211_MHAAABBN_01681:0,(TT9_LFPAFLNI_01913:0,KBS0714_MOLHKGIG_01987:0)n2:0)n1:0.0032545)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001852_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001852_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4b3448411b16552634137ca6c438ebecd4bf046
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001852_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00881:0.0929955,(KBS0714_MOLHKGIG_01977:2.46735e-07,(TT9_LFPAFLNI_01902:2.46735e-07,SA211_MHAAABBN_01670:0.0150045)n2:0.0524395)n1:0.0929955)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001855_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001855_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe447411ce68dadeb833cc65057095457ed4e481
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001855_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00841:0.00553325,((SA211_MHAAABBN_01646:0.011731,TT9_LFPAFLNI_01876:0.012315)n2:0.002863,AS2_ACLBLIBL_00902:0.0245105)n1:0.00553325)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001856_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001856_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f79ca215c5b7e4f46a58fa1ce048df7f286e303e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001856_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00842:0,(AS2_ACLBLIBL_00903:0,(SA211_MHAAABBN_01645:0.003244,TT9_LFPAFLNI_01875:0.006748)n2:0.068121)n1:0)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001859_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001859_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fba55f97468374f2ce0700d5e36441d90e2fd5b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001859_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00848:0.00288437,(TT9_LFPAFLNI_01865:4.68089e-07,(KBS0714_MOLHKGIG_01946:4.68089e-07,AS2_ACLBLIBL_00916:0.463723)n2:0.00140275)n1:0.00288437)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001862_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001862_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b8af757b0e96ba1490e8d7cbf5fcba2aafdde09
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001862_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00945:0.244708,(SA211_MHAAABBN_01991:7.05275e-07,(KBS0714_MOLHKGIG_02298:0.010851,TT9_LFPAFLNI_02239:0.176745)n2:0.048741)n1:0.244708)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001863_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001863_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b4434e44369aa32d6ba8fc2bb2636d2fbd5e95d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001863_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00961:0.228138,(TT9_LFPAFLNI_01818:0.00425692,(KBS0714_MOLHKGIG_01898:0.012204,SA211_MHAAABBN_01594:0.00451)n2:0.0044885)n1:0.228138)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001865_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001865_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87b7af8273191a0fafaa735b671ffb4edcad0a48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001865_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00966:0.282807,(SA211_MHAAABBN_01588:0.01356,(KBS0714_MOLHKGIG_01892:0.00940438,TT9_LFPAFLNI_01812:0.00677862)n2:0.0053755)n1:0.282807)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001866_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001866_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efadbfdef54720798b2b072ec56873221195cb56
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001866_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00980:0.173187,(TT9_LFPAFLNI_01799:0.011841,(KBS0714_MOLHKGIG_01879:0,SA211_MHAAABBN_01575:0)n2:0.057617)n1:0.173187)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001872_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001872_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fa4455aec0fa36ac4589d6078f84e6274c9b160
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001872_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01195:0.189369,(KBS0714_MOLHKGIG_01683:0.0087099,(TT9_LFPAFLNI_01612:0.013696,SA211_MHAAABBN_01387:0.021746)n2:0.000638)n1:0.189369)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001873_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001873_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..242bb40422281bdd98a5f2044b08ebaddab05627
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001873_tree.txt
@@ -0,0 +1 @@
+((AS2_ACLBLIBL_01199:0.270961,KBS0714_MOLHKGIG_01679:0.270009)n1:0.425413,(KD337_16_NAFOICDF_01217:1.49068,KD337_16_NAFOICDF_02117:1.31849)n2:0.425413)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001876_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001876_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7251ae910fcfce7c5ac11f7d75c759a839d71916
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001876_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01189:0.00627,(AS2_ACLBLIBL_01285:0.009714,(SA211_MHAAABBN_01324:0.00411813,KBS0714_MOLHKGIG_01614:0.00414687)n2:0.004159)n1:0.00627)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001878_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001878_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0879de80d94f3cc0ece573660cb612ded061a3a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001878_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01334:0.0110697,((KBS0714_MOLHKGIG_01588:0,TT9_LFPAFLNI_01515:0)n2:0.0011095,SA211_MHAAABBN_01299:0.0005395)n1:0.0110697)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001879_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001879_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57dd440fc126e80a71f1d099eae05453a64467f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001879_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01336:0.006579,((SA211_MHAAABBN_01297:0,KBS0714_MOLHKGIG_01586:0)n2:0,TT9_LFPAFLNI_01513:0)n1:0.006579)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001885_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001885_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95f92f5fef20a800f690919c9aa51f496abf3cdd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001885_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01665:0.0564549,(KBS0714_MOLHKGIG_01223:0.00331014,(TT9_LFPAFLNI_01181:0.00376525,SA211_MHAAABBN_00942:0.00821075)n2:0.00622075)n1:0.0564549)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001886_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001886_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf51a4c1951089c0737e68c239bba43845b74423
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001886_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01734:0.532262,((KBS0714_MOLHKGIG_01155:0,TT9_LFPAFLNI_01105:0)n2:0,SA211_MHAAABBN_00874:0)n1:0.532262)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001887_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001887_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d3c1f8f7a2fd48a4ed6337f5fbcce4d554402ea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001887_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01781:0.0350683,(SA211_MHAAABBN_00831:0.0011405,(TT9_LFPAFLNI_01062:0.002253,KBS0714_MOLHKGIG_01112:8.1261e-08)n2:0.00809)n1:0.0350683)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001888_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001888_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9271aa37b916318417b29c5104d232af7f86a73e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001888_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01872:0.00424047,(TT9_LFPAFLNI_00960:0.00223706,(KBS0714_MOLHKGIG_01016:0.00394925,SA211_MHAAABBN_00730:0.00224575)n2:7.75e-06)n1:0.00424047)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001890_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001890_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d1e41a088f5329becdbf95f237f3e130ac57932
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001890_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_01879:0.015521,(TT9_LFPAFLNI_00953:0.019751,(SA211_MHAAABBN_00724:0,KBS0714_MOLHKGIG_01010:0)n2:0.047685)n1:0.015521)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001894_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001894_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62e6e30de0ea4e655fdc16571234df4bca1a82c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001894_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_02191:0.278153,(KBS0714_MOLHKGIG_00739:0.0302364,(TT9_LFPAFLNI_00703:0.051701,SA211_MHAAABBN_00470:0.035598)n2:0.0116385)n1:0.278153)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001895_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001895_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfcad8bfdf9caca5ddc84790b4d5fffdc8c0fc55
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001895_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_02247:0.0968189,(KD337_16_NAFOICDF_02120:0.234041,(KD337_16_NAFOICDF_00715:1.26156,KD337_16_NAFOICDF_00402:1.05135)n2:1.20744)n1:0.0968189)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001904_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001904_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb014f81fdf7fe3e81d25168c7dcdaa86a578376
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001904_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_02323:0.18375,((TT9_LFPAFLNI_01026:0,KBS0714_MOLHKGIG_01077:0)n2:0,SA211_MHAAABBN_00796:0)n1:0.18375)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001905_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001905_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96a7102a1cc512b3704092916440e55e89519bdb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001905_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_02342:0,(AS2_ACLBLIBL_02640:0,(AS2_ACLBLIBL_02651:0,AS2_ACLBLIBL_02337:0)n2:0)n1:0)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001906_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001906_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d21435c4b7486120dc67525f19458791b8a4e10b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001906_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_02352:0.28078,((KBS0714_MOLHKGIG_00581:0.288873,SA211_MHAAABBN_00314:0.0430277)n2:0.175372,TT9_LFPAFLNI_00582:0.0932419)n1:0.28078)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001912_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001912_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90906e3d346f4feb4138b00a280766fe8fb197ba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001912_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02298:0.196519,(AS2_ACLBLIBL_02416:0.155535,(TT9_LFPAFLNI_00536:0.00641214,SA211_MHAAABBN_00257:0.00331986)n2:0.141905)n1:0.196519)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001915_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001915_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02d2062369edd92263dac13cbd39f4d9dbd22f9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001915_tree.txt
@@ -0,0 +1 @@
+(AS2_ACLBLIBL_02526:0.170354,(KBS0714_MOLHKGIG_00431:0.0224978,(TT9_LFPAFLNI_00434:0.0100007,SA211_MHAAABBN_00152:0.00445325)n2:0.00488375)n1:0.170354)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001921_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001921_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5421d7877a39818909023117dd001f4c1fa60051
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001921_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00200:0.145972,(KBS0714_MOLHKGIG_00118:0.0166565,(SA211_MHAAABBN_02131:0,TT9_LFPAFLNI_00123:0)n2:0.0106235)n1:0.145972)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001922_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001922_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5aabd72b4dafa2fe6c1ff7090e5fbbb48b08b66
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001922_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01469:0.488434,((KBS0714_MOLHKGIG_00155:0.364817,TT9_LFPAFLNI_00168:0.306391)n2:0.2137,SA211_MHAAABBN_02169:1.62571e-06)n1:0.488434)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001925_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001925_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1fda70a4863a6291f69664ea3c88cdd6a2ca86f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001925_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00048:0.189877,(TT9_LFPAFLNI_00291:0.0111728,(SA211_MHAAABBN_02307:0.00934425,KBS0714_MOLHKGIG_00285:0.0255728)n2:0.00676325)n1:0.189877)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001926_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001926_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4efcb9fdb020e1368e09ce6219968d15058b613e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001926_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02441:0.00842475,(KBS0714_MOLHKGIG_00387:0.0124685,(TT9_LFPAFLNI_00393:0.0291575,SA211_MHAAABBN_00111:0.0454005)n2:0.005502)n1:0.00842475)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001927_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001927_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e260eb641c40a08189c5691c9d7ccfc29c69d037
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001927_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02433:0.179869,((SA211_MHAAABBN_00119:3.70908e-07,KBS0714_MOLHKGIG_00395:0.004598)n2:0.004235,TT9_LFPAFLNI_00401:0.003286)n1:0.179869)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001931_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001931_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..420b527059b4c35ba5c0d02eda68a0a3da5d0e67
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001931_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02259:0.115709,(KBS0714_MOLHKGIG_00569:0.075382,(SA211_MHAAABBN_00293:0.0338904,TT9_LFPAFLNI_00571:0.0385486)n2:0.021649)n1:0.115709)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001936_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001936_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10760f541bd637b1350dafbb9578a0e9c83b9b68
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001936_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01971:0.129221,(SA211_MHAAABBN_00580:0.0100573,(TT9_LFPAFLNI_00817:0.00274725,KBS0714_MOLHKGIG_00858:0.00471675)n2:0.00682175)n1:0.129221)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001937_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001937_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a22c335fa49ea94ba938570fd67a8938626917b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001937_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01881:0.223678,(TT9_LFPAFLNI_00904:0.0141567,(SA211_MHAAABBN_00671:0.00385347,KBS0714_MOLHKGIG_00958:0.00298453)n2:0.00167725)n1:0.223678)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001940_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001940_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1dde881ea9cb395420d4b718587fd7725e6fa2b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001940_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02229:0.0414845,(SA211_MHAAABBN_00786:0.001791,(KBS0714_MOLHKGIG_01067:0.0155645,TT9_LFPAFLNI_01014:1.1219e-07)n2:0.012907)n1:0.0414845)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001941_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001941_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44b0ec2b0b03997899f7506c8d49275c231b3bbb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001941_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01674:0.148188,((KBS0714_MOLHKGIG_01111:0.00413725,SA211_MHAAABBN_00830:0.00711975)n2:0.178211,TT9_LFPAFLNI_01061:0.0657219)n1:0.148188)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001943_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001943_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..076377bdbb984313fcb900476639d35b471baa95
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001943_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01627:0.440908,(KBS0714_MOLHKGIG_01160:0.00349,(SA211_MHAAABBN_00879:0,TT9_LFPAFLNI_01110:0)n2:0.004541)n1:0.440908)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001944_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001944_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..890448b63bc83f78bbeaf4781cc49db357685d57
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001944_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01573:0.099632,(SA211_MHAAABBN_00931:0.006754,(KBS0714_MOLHKGIG_01212:0.01303,TT9_LFPAFLNI_01169:0.00316705)n2:0.003209)n1:0.099632)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001945_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001945_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40e77bffd01189c9eb2cc83da5800db78c5620b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001945_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00710:0.109406,(TT9_LFPAFLNI_01248:0.003917,(KBS0714_MOLHKGIG_01290:0,SA211_MHAAABBN_01009:0)n2:0.00994)n1:0.109406)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001946_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001946_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..214b586bb1a6c7cb0e04448f1d88242674bc6379
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001946_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01482:0.45154,(TT9_LFPAFLNI_01264:0.012041,(SA211_MHAAABBN_01029:5e-07,KBS0714_MOLHKGIG_01306:5e-07)n2:0.0152625)n1:0.45154)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001947_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001947_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1d2b2411e0253676699c132a3cc0cb5fdf0e957
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001947_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01431:0.085167,(SA211_MHAAABBN_01077:0.004552,(KBS0714_MOLHKGIG_01357:0,TT9_LFPAFLNI_01312:0)n2:0.004422)n1:0.085167)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001949_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001949_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b039c03473f80d05c37376fe0e5195681e0166c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001949_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01402:0.130426,((SA211_MHAAABBN_01135:0,TT9_LFPAFLNI_01355:0)n2:0.0037735,KBS0714_MOLHKGIG_01405:0.0007925)n1:0.130426)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001950_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001950_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b5d039b1b28e8aa91994a83be01c0c4ed685799
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001950_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01397:0.0792801,(TT9_LFPAFLNI_01359:0.00272875,(KBS0714_MOLHKGIG_01409:0.0134161,SA211_MHAAABBN_01139:0.00372492)n2:0.00153525)n1:0.0792801)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001952_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001952_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c575800f05924af05f5b970f61e0fc9c25f46a07
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001952_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01395:0.196183,(SA211_MHAAABBN_01141:0.215283,(TT9_LFPAFLNI_01361:0.00175313,KBS0714_MOLHKGIG_01411:0.00394987)n2:0.06504)n1:0.196183)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001955_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001955_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..821c4083f646cb0146065d822dd430fd7ba180c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001955_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01332:0.192562,(SA211_MHAAABBN_01202:0.0400447,(KBS0714_MOLHKGIG_01470:0.0235067,TT9_LFPAFLNI_01420:0.0206253)n2:0.0235013)n1:0.192562)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001956_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001956_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee83290978ee9c85970f6792413982269a360aa1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001956_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01326:0.004976,((SA211_MHAAABBN_01208:0,KBS0714_MOLHKGIG_01476:0)n2:0,TT9_LFPAFLNI_01426:0)n1:0.004976)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001957_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001957_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..343da5707ed5aa2765b5b218d333fb0f06924b8d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001957_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01325:0.00871075,(TT9_LFPAFLNI_01427:5e-07,(SA211_MHAAABBN_01209:5e-07,KBS0714_MOLHKGIG_01477:5e-07)n2:0)n1:0.00871075)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001962_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001962_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..167f4d4d3390595dda9501a94b9ddd2b6273966a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001962_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01004:0.0998831,(KBS0714_MOLHKGIG_01805:0.0230137,(SA211_MHAAABBN_01502:0.0307257,TT9_LFPAFLNI_01726:0.00326825)n2:0.0135552)n1:0.0998831)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001967_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001967_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ffaa628dc8eaf92c988c02ba32e880884a19d70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001967_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00879:0.180096,(TT9_LFPAFLNI_01836:0.0102048,(KBS0714_MOLHKGIG_01916:0.0080407,SA211_MHAAABBN_01612:0.0014513)n2:0.00621675)n1:0.180096)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001969_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001969_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca7715a643f2c46cf1752bbf8c2ea1eaa519db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001969_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00797:0.161649,((SA211_MHAAABBN_01690:0,KBS0714_MOLHKGIG_01996:0)n2:0.008576,TT9_LFPAFLNI_01922:0.013997)n1:0.161649)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001973_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001973_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..349fa14f880dedd2d3a08b32f5fd7a47d59f5db5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001973_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00731:0.0971653,((TT9_LFPAFLNI_01983:0.00095475,KBS0714_MOLHKGIG_02049:0.00290425)n2:0.00420825,SA211_MHAAABBN_01755:0.00499932)n1:0.0971653)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001974_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001974_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f45539a4226a5b9084acf593073318c61c7ebd0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001974_tree.txt
@@ -0,0 +1 @@
+(KBS0714_MOLHKGIG_02062:3.99043e-06,(KD337_16_NAFOICDF_02222:0.0256893,(KD337_16_NAFOICDF_02440:2.50428,KD337_16_NAFOICDF_02426:0.790823)n2:0.688168)n1:3.99043e-06)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001975_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001975_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..374baf983fce334a250ed002edb83e329b34f8f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001975_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00573:0.0115495,(KBS0714_MOLHKGIG_02124:5.4403e-08,(TT9_LFPAFLNI_02062:0.0083745,SA211_MHAAABBN_01832:0.0047595)n2:0.018374)n1:0.0115495)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001976_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001976_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df33dd8c5f9fd93b3a5fac6fe321295fc61dc50e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001976_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00507:0.690589,((KBS0714_MOLHKGIG_02171:0.00331875,TT9_LFPAFLNI_02116:0.00426025)n2:0.108224,SA211_MHAAABBN_01885:0.0386336)n1:0.690589)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001981_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001981_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6849e6d7c6f92f2c4c6ef701e127a41212c803cf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001981_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00389:0.103606,((SA211_MHAAABBN_01993:0,TT9_LFPAFLNI_02241:0)n2:0,KBS0714_MOLHKGIG_02300:0)n1:0.103606)n0;
\ No newline at end of file
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001984_tree.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001984_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f1c43580b9789a11cee01376b4d3ef80584d1bb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Resolved_Gene_Trees/OG0001984_tree.txt
@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00698:0.00551468,((KD337_16_NAFOICDF_01398:2.33821,KD337_16_NAFOICDF_00661:0.0815815)n2:0.163786,KD337_16_NAFOICDF_00722:0.0249686)n1:0.00551468)n0;
\ No newline at end of file