diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000002_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000002_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..963c09a875518fb505f486152e5e9756f10ecfd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000002_tree.txt
@@ -0,0 +1 @@
+((((GCF_005280335_1_GCF_005280335.1_02630:0,GCF_005280335_1_GCF_005280335.1_02348:0)n3:0.0265228,(GCF_003691675_1_GCF_003691675.1_01117:0.00997735,(GCF_003691675_1_GCF_003691675.1_02266:2.17225e-07,(GCF_003691675_1_GCF_003691675.1_01328:2.17225e-07,GCF_003691675_1_GCF_003691675.1_00320:2.17225e-07)n6:2.17225e-07)n5:2.17225e-07)n4:2.17225e-07)n2:1.277e-05,(GCF_002008305_4_GCF_002008305.4_01387:2.17225e-07,(GCF_003691675_1_GCF_003691675.1_00787:0.00123687,((GCF_003691675_1_GCF_003691675.1_01659:0.00804765,((GCF_023573625_1_GCF_023573625.1_00113:0,GCF_023573625_1_GCF_023573625.1_01883:0)n12:0.00507023,(GCF_020097155_1_GCF_020097155.1_00316:0.0496737,(GCF_020097155_1_GCF_020097155.1_00621:0,GCF_020097155_1_GCF_020097155.1_00626:0)n14:0.00225519)n13:0.000250577)n11:0.00882327)n10:0.00487737,((GCF_003691675_1_GCF_003691675.1_00332:0,GCF_020097155_1_GCF_020097155.1_02231:0)n16:0.00696494,GCF_023573625_1_GCF_023573625.1_01019:0.00622306)n15:0.0154368)n9:0.00526825)n8:0.00195477)n7:0.000217197)n1:0.00186499,(((GCF_005280335_1_GCF_005280335.1_01313:0,GCF_005280335_1_GCF_005280335.1_01318:0)n19:0.00353253,GCF_005280335_1_GCF_005280335.1_01280:0.00212247)n18:0.026897,((GCF_023573625_1_GCF_023573625.1_01540:0.00040598,(GCF_002008305_4_GCF_002008305.4_01069:0.020798,(GCF_005280335_1_GCF_005280335.1_02332:2.17225e-07,(GCF_005280335_1_GCF_005280335.1_00757:2.17225e-07,GCF_005280335_1_GCF_005280335.1_01303:2.17225e-07)n24:2.17225e-07)n23:2.17225e-07)n22:2.603e-05)n21:0.00161499,((GCF_020097155_1_GCF_020097155.1_01795:0,GCF_020097155_1_GCF_020097155.1_01837:0)n26:0,GCF_020097155_1_GCF_020097155.1_02208:0)n25:0.0040327)n20:0.00138189)n17:0.00186499)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000004_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000004_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ad220c12e25166bba212ed062925dbb67bfd366
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000004_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00116:2.54473e-06,((((GCF_005280335_1_GCF_005280335.1_00895:0,GCF_005280335_1_GCF_005280335.1_00228:0)n5:0.261294,GCF_003691675_1_GCF_003691675.1_01012:0.0329093)n4:0.0941234,(GCF_005280335_1_GCF_005280335.1_02100:0.00437312,GCF_003691675_1_GCF_003691675.1_00355:2.54473e-06)n6:2.54473e-06)n3:9.74e-06,(GCF_002008305_4_GCF_002008305.4_01393:2.54473e-06,GCF_002008305_4_GCF_002008305.4_00376:2.54473e-06)n7:2.54473e-06)n2:9.74e-06)n1:4.87e-06,(((GCF_023573625_1_GCF_023573625.1_01880:0,(GCF_023573625_1_GCF_023573625.1_01547:0,GCF_023573625_1_GCF_023573625.1_01549:0)n11:0)n10:0.00038011,(GCF_005280335_1_GCF_005280335.1_01506:2.54473e-06,(GCF_002008305_4_GCF_002008305.4_02277:2.54473e-06,(GCF_003691675_1_GCF_003691675.1_01746:2.54473e-06,(GCF_003691675_1_GCF_003691675.1_01125:2.54473e-06,(GCF_003691675_1_GCF_003691675.1_02016:2.54473e-06,(GCF_005280335_1_GCF_005280335.1_00643:2.54473e-06,((GCF_005280335_1_GCF_005280335.1_00899:0.586123,GCF_020097155_1_GCF_020097155.1_01829:0.607318)n19:0.356428,(GCF_005280335_1_GCF_005280335.1_00229:2.54473e-06,(GCF_003691675_1_GCF_003691675.1_01015:0.0885647,GCF_002008305_4_GCF_002008305.4_02069:0.00598831)n21:0.118524)n20:0.351008)n18:0.0540488)n17:9.3951e-05)n16:9.3951e-06)n15:9.3951e-07)n14:9.3951e-08)n13:1.0439e-08)n12:0.00319271)n9:0.00074121,((GCF_003691675_1_GCF_003691675.1_01819:2.54473e-06,GCF_023573625_1_GCF_023573625.1_01974:2.54473e-06)n23:2.54473e-06,GCF_002008305_4_GCF_002008305.4_02112:2.54473e-06)n22:2.54473e-06)n8:4.87e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000005_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000005_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..244ede5f3984cc70093e79f50913563a64474dbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000005_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01778:0.481639,(GCF_020097155_1_GCF_020097155.1_00678:1.30712,(GCF_020097155_1_GCF_020097155.1_00227:0.484699,((GCF_005280335_1_GCF_005280335.1_02274:0.0197706,((GCF_020097155_1_GCF_020097155.1_00448:0.024019,GCF_020097155_1_GCF_020097155.1_02206:0.045165)n6:0.0519192,(((((GCF_020097155_1_GCF_020097155.1_00751:0,GCF_020097155_1_GCF_020097155.1_01794:0)n11:0.00010659,(GCF_020097155_1_GCF_020097155.1_00631:0,GCF_020097155_1_GCF_020097155.1_02162:0)n12:0.00285841)n10:0.00068751,GCF_020097155_1_GCF_020097155.1_00627:0.00079899)n9:0.00179948,(((GCF_020097155_1_GCF_020097155.1_00226:8.503e-05,GCF_020097155_1_GCF_020097155.1_01835:0.00216597)n15:0.00412963,GCF_020097155_1_GCF_020097155.1_00312:0.00488987)n14:0.00407,GCF_020097155_1_GCF_020097155.1_01890:0.00760725)n13:0.00215033)n8:0.00719922,(GCF_020097155_1_GCF_020097155.1_00315:0,GCF_020097155_1_GCF_020097155.1_00645:0)n16:0.0276021)n7:0.000678897)n5:7.5433e-05)n4:0.042145,(GCF_005280335_1_GCF_005280335.1_01282:0.0551577,((GCF_020097155_1_GCF_020097155.1_00641:0.0523848,(GCF_020097155_1_GCF_020097155.1_01361:0.0470863,GCF_020097155_1_GCF_020097155.1_01832:0.172567)n20:0.0189387)n19:0.0548108,(GCF_020097155_1_GCF_020097155.1_00652:0.0381747,GCF_020097155_1_GCF_020097155.1_01820:0.0480273)n21:0.00871096)n18:0.000967885)n17:0.0461351)n3:0.364143)n2:0.895467)n1:0.481639)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000009_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000009_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92225bed1204864d9e9ea9d45e1a3d38969d661c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000009_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01157:3.37914e-07,((GCF_002008305_4_GCF_002008305.4_02228:0.118103,GCF_002008305_4_GCF_002008305.4_01400:3.37914e-07)n3:5.49e-06,(GCF_003691675_1_GCF_003691675.1_01393:3.37914e-07,GCF_003691675_1_GCF_003691675.1_00091:3.37914e-07)n4:3.37914e-07)n2:5.49e-06)n1:2.745e-06,(GCF_003691675_1_GCF_003691675.1_00344:3.37914e-07,(GCF_023573625_1_GCF_023573625.1_02163:3.37914e-07,((GCF_003691675_1_GCF_003691675.1_02283:3.37914e-07,((GCF_002008305_4_GCF_002008305.4_01503:0.219835,GCF_023573625_1_GCF_023573625.1_01350:3.37914e-07)n10:5.49e-06,(GCF_002008305_4_GCF_002008305.4_00712:3.37914e-07,GCF_023573625_1_GCF_023573625.1_00607:3.37914e-07)n11:3.37914e-07)n9:5.49e-06)n8:5.49e-06,(GCF_023573625_1_GCF_023573625.1_01017:3.37914e-07,GCF_003691675_1_GCF_003691675.1_01014:3.37914e-07)n12:3.37914e-07)n7:4.941e-06)n6:5.49e-07)n5:5.49e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000011_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000011_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96c30cb7bc8fe81ade54e4d8748c220e6e68d39d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000011_tree.txt
@@ -0,0 +1 @@
+((((GCF_023573625_1_GCF_023573625.1_02005:0.716908,(GCF_003691675_1_GCF_003691675.1_01769:0.0296533,(GCF_003691675_1_GCF_003691675.1_00789:0.011358,GCF_003691675_1_GCF_003691675.1_00350:0.00684395)n5:0.563744)n4:0.0626382)n3:0.0292449,GCF_002008305_4_GCF_002008305.4_00609:0.0183647)n2:0.0386524,(GCF_005280335_1_GCF_005280335.1_00727:0.0449685,GCF_005280335_1_GCF_005280335.1_02366:0.0709745)n6:0.0331058)n1:0.0312093,((GCF_023573625_1_GCF_023573625.1_02002:0.0440971,(((GCF_003691675_1_GCF_003691675.1_00339:0,GCF_003691675_1_GCF_003691675.1_01779:0)n11:0,GCF_002008305_4_GCF_002008305.4_00616:0)n10:0.0106229,GCF_002008305_4_GCF_002008305.4_02074:0.0162467)n9:0.00180519)n8:0.132574,GCF_005280335_1_GCF_005280335.1_00719:0.0109301)n7:0.0312093)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000013_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000013_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f45820dc12f0318c86d7c7159fb40a4cecccc4bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000013_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02496:0.295843,GCF_005280335_1_GCF_005280335.1_00706:0.475675)n2:0.36602,(GCF_003691675_1_GCF_003691675.1_00341:0.125681,(GCF_020097155_1_GCF_020097155.1_01887:0.0313903,(GCF_023573625_1_GCF_023573625.1_01544:0.310013,GCF_023573625_1_GCF_023573625.1_00898:0.0181851)n5:0.00202057)n4:0.115146)n3:0.0525349)n1:0.0442475,((GCF_005280335_1_GCF_005280335.1_02276:2.1735e-06,((GCF_005280335_1_GCF_005280335.1_02495:0.160142,GCF_005280335_1_GCF_005280335.1_02636:0.0164108)n9:0.0877972,GCF_005280335_1_GCF_005280335.1_02615:2.1735e-06)n8:0.0316281)n7:0.0419219,GCF_003691675_1_GCF_003691675.1_01765:0.00214371)n6:0.0442475)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000016_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000016_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc20cb0555af3162591c877c27b9f1dca9fc48b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000016_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_01897:0.0339341,((GCF_002008305_4_GCF_002008305.4_00992:0.0125064,GCF_020097155_1_GCF_020097155.1_01844:0.0118856)n3:0.00231212,(GCF_023573625_1_GCF_023573625.1_00935:0.00377569,GCF_003691675_1_GCF_003691675.1_00706:0.00465431)n4:0.00501738)n2:0.00301887)n1:0.00535712,(((GCF_003691675_1_GCF_003691675.1_01478:0,GCF_002008305_4_GCF_002008305.4_01771:0)n7:0.00351475,GCF_023573625_1_GCF_023573625.1_01700:0.00446625)n6:0.0128569,(GCF_005280335_1_GCF_005280335.1_01106:0.0304285,GCF_020097155_1_GCF_020097155.1_01032:0.0938865)n8:0.00598188)n5:0.00535712)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000018_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000018_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a926f277ab340f388d928b2de66be1f09a62081c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000018_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01559:0.014803,(GCF_003691675_1_GCF_003691675.1_01269:0.0153261,GCF_023573625_1_GCF_023573625.1_01486:0.00921789)n2:0.00776337)n1:0.181754,(((GCF_020097155_1_GCF_020097155.1_01147:0.53626,GCF_005280335_1_GCF_005280335.1_01236:0.222989)n5:0.27643,(GCF_002008305_4_GCF_002008305.4_01658:0.00021408,GCF_002008305_4_GCF_002008305.4_01845:0.581811)n6:0.0646457)n4:0.141314,(GCF_023573625_1_GCF_023573625.1_01588:0.0062415,GCF_003691675_1_GCF_003691675.1_01363:2.24875e-06)n7:0.00986642)n3:0.181754)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000019_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000019_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74ca22a69d264b7237803703d8fdc11823760862
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000019_tree.txt
@@ -0,0 +1 @@
+(((((GCF_005280335_1_GCF_005280335.1_02275:0.00604717,GCF_005280335_1_GCF_005280335.1_02634:8.83441e-07)n4:0.0115305,(GCF_005280335_1_GCF_005280335.1_02616:0,GCF_005280335_1_GCF_005280335.1_02497:0)n5:0.0024707)n3:0.017677,GCF_003691675_1_GCF_003691675.1_01766:0.049677)n2:0.140935,(GCF_023573625_1_GCF_023573625.1_00899:0.0680276,GCF_020097155_1_GCF_020097155.1_01886:0.0102924)n6:0.187902)n1:0.0237485,(GCF_003691675_1_GCF_003691675.1_00342:0.126053,GCF_023573625_1_GCF_023573625.1_01543:0.216031)n7:0.0237485)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000021_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000021_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ce532b641d280e40535c320b256a259824addf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000021_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00572:2.09768e-06,((GCF_002008305_4_GCF_002008305.4_00571:0.0101993,GCF_003691675_1_GCF_003691675.1_00295:0.00689172)n3:0.130018,(GCF_002008305_4_GCF_002008305.4_00570:0.0291583,GCF_003691675_1_GCF_003691675.1_00294:0.00112167)n4:0.251294)n2:0.0279216)n1:0.135402,(GCF_020097155_1_GCF_020097155.1_02254:0.433067,(GCF_005280335_1_GCF_005280335.1_02374:0.538221,GCF_005280335_1_GCF_005280335.1_02375:0.298736)n6:0.0331928)n5:0.216609)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000022_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000022_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..050f76ed913501b5db5517c89231b5f67983d421
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000022_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01247:0.00251147,(GCF_003691675_1_GCF_003691675.1_01008:0,GCF_002008305_4_GCF_002008305.4_01289:0)n2:0.00094753)n1:0.0416592,(((GCF_020097155_1_GCF_020097155.1_02196:0.00219647,GCF_005280335_1_GCF_005280335.1_00405:0.00492553)n5:0.0102903,GCF_023573625_1_GCF_023573625.1_00598:0.00369116)n4:0.00751134,(GCF_002008305_4_GCF_002008305.4_00633:0.0137077,GCF_020097155_1_GCF_020097155.1_00711:0.0675873)n6:0.0075097)n3:0.0416592)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000023_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000023_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f52ec01e3502f5f16f5274e1beaeb14e4c9112b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000023_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00513:0.112772,GCF_003691675_1_GCF_003691675.1_01940:0.0217247)n1:0.00921548,((GCF_023573625_1_GCF_023573625.1_02170:3.2581e-06,(((GCF_020097155_1_GCF_020097155.1_00440:0.814397,GCF_020097155_1_GCF_020097155.1_00650:1.16394)n6:0.371866,GCF_020097155_1_GCF_020097155.1_01865:0.374875)n5:0.318328,GCF_020097155_1_GCF_020097155.1_00454:0.0314157)n4:0.0277241)n3:0.00991827,GCF_002008305_4_GCF_002008305.4_02238:3.2581e-06)n2:0.00921548)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000030_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000030_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72719c65a659676f7835d9f14878a0b445853714
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000030_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00360:3.70302e-06,((GCF_005280335_1_GCF_005280335.1_02334:0.00266569,GCF_002008305_4_GCF_002008305.4_00169:0.00704631)n3:0.00381069,((GCF_005280335_1_GCF_005280335.1_02217:0.857785,GCF_005280335_1_GCF_005280335.1_00191:1.29451)n5:0.312949,GCF_005280335_1_GCF_005280335.1_00171:0.525499)n4:0.626918)n2:0.0696576)n1:0.00056303,GCF_023573625_1_GCF_023573625.1_02010:0.00188381)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000032_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000032_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18de9de6e0714179b870a3bb788c2583e3d8a388
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000032_tree.txt
@@ -0,0 +1 @@
+(((GCF_023573625_1_GCF_023573625.1_00245:0.0145651,GCF_005280335_1_GCF_005280335.1_00124:0.0115879)n2:0.0115397,(((GCF_003691675_1_GCF_003691675.1_00096:0.64215,GCF_003691675_1_GCF_003691675.1_00100:0.960251)n5:0.334581,GCF_020097155_1_GCF_020097155.1_00093:0.184839)n4:0.173129,GCF_003691675_1_GCF_003691675.1_02257:0.00139753)n3:0.000155281)n1:0.00070703,GCF_002008305_4_GCF_002008305.4_00245:0.00111569)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000035_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000035_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f25b7f4b04d30cbe071a4b37edd1c02d2b74a981
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000035_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00604:0,GCF_003691675_1_GCF_003691675.1_00372:0)n1:0.00058057,((GCF_002008305_4_GCF_002008305.4_00627:0.00758284,GCF_020097155_1_GCF_020097155.1_02189:0.0463392)n3:0.00165752,((GCF_005280335_1_GCF_005280335.1_00389:0.0009096,GCF_005280335_1_GCF_005280335.1_00393:0.0420804)n5:0.0170603,GCF_005280335_1_GCF_005280335.1_00410:0.00046546)n4:0.00100654)n2:0.00058057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000036_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000036_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7f9595575e086eed5b002e74b13368712e0749c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000036_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_00631:0,(GCF_023573625_1_GCF_023573625.1_00600:0,((GCF_005280335_1_GCF_005280335.1_00403:0.014339,GCF_020097155_1_GCF_020097155.1_02198:0.012672)n3:0.0128564,((GCF_005280335_1_GCF_005280335.1_01253:0.943844,GCF_005280335_1_GCF_005280335.1_01330:1.37119)n5:0.145467,GCF_020097155_1_GCF_020097155.1_00451:1.31048)n4:0.869025)n2:0.0258181)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000038_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000038_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67541380f9223e77dc89adf97dd3f3ca6d96ce0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000038_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01485:0.00726013,((GCF_020097155_1_GCF_020097155.1_01023:0.0598848,(GCF_002008305_4_GCF_002008305.4_00836:0.444817,GCF_002008305_4_GCF_002008305.4_00837:0.131953)n4:0.665023)n3:0.00863038,(GCF_002008305_4_GCF_002008305.4_01778:0.00569369,GCF_023573625_1_GCF_023573625.1_01707:0.00439331)n5:0.00159828)n2:0.000177587)n1:0.0301199,GCF_005280335_1_GCF_005280335.1_01099:0.0790576)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000039_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000039_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f0f21159f4f2dbe19c76dbd773f3efaaf7f5027
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000039_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_02045:1.0626,((GCF_002008305_4_GCF_002008305.4_00894:0.0261265,GCF_003691675_1_GCF_003691675.1_00616:0.0431745)n3:0.694971,(GCF_002008305_4_GCF_002008305.4_00884:0.0113939,GCF_003691675_1_GCF_003691675.1_00606:0.00290412)n4:0.678113)n2:0.0753458)n1:0.17617,(GCF_023573625_1_GCF_023573625.1_00845:0.860434,GCF_020097155_1_GCF_020097155.1_01944:0.589537)n5:0.477201)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000053_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000053_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..650cffad7cf7a3aff032312e419325b3f0d09b61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000053_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01948:0.0118519,(((GCF_002008305_4_GCF_002008305.4_02261:0.0358708,GCF_020097155_1_GCF_020097155.1_00418:0.0461942)n3:0.00460275,(GCF_023573625_1_GCF_023573625.1_02192:0.0110168,GCF_020097155_1_GCF_020097155.1_00422:1.48026)n4:0.164473)n2:0.0991336,(GCF_023573625_1_GCF_023573625.1_02178:0.00688531,GCF_002008305_4_GCF_002008305.4_02246:1.8616e-06)n5:0.00177087)n1:0.000196763)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000055_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000055_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d9dffa32114e2d3c0fd7de76f6bcd62bdeabde2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000055_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01696:0.100453,((GCF_023573625_1_GCF_023573625.1_00735:0.264599,(GCF_005280335_1_GCF_005280335.1_01010:0.884884,(GCF_020097155_1_GCF_020097155.1_00870:0.790182,GCF_020097155_1_GCF_020097155.1_00943:0.512508)n4:0.0569454)n3:0.0265043)n2:0.169595,(GCF_020097155_1_GCF_020097155.1_00792:0.125211,GCF_005280335_1_GCF_005280335.1_00855:0.0607083)n5:0.00674537)n1:0.100453)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000056_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000056_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93c0fc50e81bc1aad788ba019320b35b7c871170
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000056_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00025:0.0109923,(GCF_005280335_1_GCF_005280335.1_00371:0.4045,(GCF_003691675_1_GCF_003691675.1_02043:0.0188413,(GCF_020097155_1_GCF_020097155.1_00353:0.436862,GCF_005280335_1_GCF_005280335.1_00370:0.240568)n4:0.0856916)n3:0.00660142)n2:0.000733491)n1:0.00869274,GCF_002008305_4_GCF_002008305.4_00025:0.00328129)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000059_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000059_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3e70532cd356eb599788d29c899af9eb8f095b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000059_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00048:0.0131357,GCF_002008305_4_GCF_002008305.4_00053:0.0130953)n1:0.0243654,(GCF_003691675_1_GCF_003691675.1_02066:0.0100957,(GCF_005280335_1_GCF_005280335.1_00346:0.0188688,(GCF_020097155_1_GCF_020097155.1_00293:0.183162,GCF_020097155_1_GCF_020097155.1_00284:0.0417863)n4:0.00464292)n3:0.1045)n2:0.0243654)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000061_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000061_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4463eac796fe178697dbaf45c26c40700639a1ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000061_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02081:0.00378656,GCF_002008305_4_GCF_002008305.4_00068:0.00132244)n1:0.00920197,(GCF_023573625_1_GCF_023573625.1_00062:0.0156086,(GCF_005280335_1_GCF_005280335.1_00326:0.0562451,(GCF_020097155_1_GCF_020097155.1_00266:0.0438693,GCF_020097155_1_GCF_020097155.1_00684:0.716861)n4:0.0272474)n3:0.0187114)n2:0.00920197)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000062_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000062_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9010184773f535894f66488fd3b4f35d63cfd2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000062_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00070:0,GCF_002008305_4_GCF_002008305.4_00076:0)n1:0.00120586,(GCF_003691675_1_GCF_003691675.1_02089:0.00795127,(GCF_020097155_1_GCF_020097155.1_00258:0.141675,(GCF_005280335_1_GCF_005280335.1_00317:0.018845,GCF_005280335_1_GCF_005280335.1_02338:1.21423)n4:0.134914)n3:0.257748)n2:0.00120586)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000064_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000064_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89b2dc84dd9173b622b8a321b80f311aa34b6869
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000064_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00119:0.357038,(GCF_005280335_1_GCF_005280335.1_00265:0.0607186,(GCF_005280335_1_GCF_005280335.1_00088:0.624841,GCF_020097155_1_GCF_020097155.1_00137:0.440565)n3:0.340575)n2:0.0378417)n1:0.0101917,(GCF_023573625_1_GCF_023573625.1_00127:0,GCF_003691675_1_GCF_003691675.1_02135:0)n4:0.0235994)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000068_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000068_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2796d9226b0dc675e9341fae7ed46bb5d8112fa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000068_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00216:0,GCF_003691675_1_GCF_003691675.1_02209:0)n1:0,(GCF_002008305_4_GCF_002008305.4_00216:0,(GCF_020097155_1_GCF_020097155.1_00321:0.725649,(GCF_005280335_1_GCF_005280335.1_00167:0.0474076,GCF_005280335_1_GCF_005280335.1_02206:0.473855)n4:0.0526506)n3:0.601676)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000070_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000070_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd13c79bd43bf351c9dda2f804c2a1f9c7ea3398
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000070_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02236:0,GCF_002008305_4_GCF_002008305.4_00223:0)n1:0.00215106,(GCF_023573625_1_GCF_023573625.1_00224:0.00279487,(GCF_020097155_1_GCF_020097155.1_00115:0.196804,(GCF_005280335_1_GCF_005280335.1_00157:0.11808,GCF_005280335_1_GCF_005280335.1_00588:1.2504)n4:0.138933)n3:0.0479959)n2:0.00215106)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000071_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000071_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..208e31ab521b8a22d85db29a5c1779f7e482ade3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000071_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00236:0.00582243,((GCF_020097155_1_GCF_020097155.1_00100:0.150016,GCF_003691675_1_GCF_003691675.1_00102:0.41198)n3:0.0803618,(GCF_003691675_1_GCF_003691675.1_02249:0.00185525,GCF_023573625_1_GCF_023573625.1_00237:0.00135175)n4:0.00497574)n2:0.00055286)n1:0.0240957,GCF_005280335_1_GCF_005280335.1_00135:0.028429)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000073_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000073_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6a579c172e7e5b8b8aa417360fd76aa66452567
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000073_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00258:0.00275811,GCF_023573625_1_GCF_023573625.1_00257:1.20469e-06)n1:0.00625153,(((GCF_020097155_1_GCF_020097155.1_00526:0.780972,GCF_020097155_1_GCF_020097155.1_00079:0.143595)n4:0.052061,GCF_005280335_1_GCF_005280335.1_00111:0.144119)n3:0.0595365,GCF_003691675_1_GCF_003691675.1_02272:0.00953305)n2:0.00625153)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000075_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000075_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9c5078ac01e54f00dfacdf9b92fc9eb7be92d06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000075_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00281:0.00455281,GCF_002008305_4_GCF_002008305.4_00282:0.00810519)n1:0.00100184,(((GCF_020097155_1_GCF_020097155.1_00057:0.167643,GCF_020097155_1_GCF_020097155.1_00450:2.04508)n4:0.101533,GCF_005280335_1_GCF_005280335.1_00071:0.0693888)n3:0.0977394,GCF_003691675_1_GCF_003691675.1_02297:0.00368381)n2:0.00100184)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000079_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000079_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..396157301f6cf9e71369c158dc3cc39c0d7713f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000079_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00019:0.0517623,(GCF_020097155_1_GCF_020097155.1_00687:0.973311,GCF_020097155_1_GCF_020097155.1_00015:0.0556756)n3:0.042543)n2:0.0196211,GCF_023573625_1_GCF_023573625.1_00325:0.00310519)n1:0.000707155,(GCF_003691675_1_GCF_003691675.1_00033:0.00143222,GCF_002008305_4_GCF_002008305.4_00318:0.00358678)n4:0.000707155)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000085_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000085_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47f83efd6e66308d1da4d168e56b21a6f4f06b02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000085_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00144:1.07609e-06,((GCF_002008305_4_GCF_002008305.4_00423:1.07609e-06,(GCF_005280335_1_GCF_005280335.1_02535:0.426985,GCF_020097155_1_GCF_020097155.1_02405:0.0545607)n4:0.112307)n3:0.0500062,GCF_005280335_1_GCF_005280335.1_02534:0.408798)n2:0.045422)n1:0.0181123,GCF_023573625_1_GCF_023573625.1_00426:1.07609e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000086_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000086_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c565d8bb33aa64a92e41eff64e6957651b2c649
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000086_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00448:9.89524e-07,GCF_003691675_1_GCF_003691675.1_00169:0.00144544)n1:0.00012172,(GCF_023573625_1_GCF_023573625.1_00451:0.00279306,(GCF_005280335_1_GCF_005280335.1_02509:0.0405486,(GCF_020097155_1_GCF_020097155.1_00683:0.879254,GCF_020097155_1_GCF_020097155.1_02380:0.044158)n4:0.00490644)n3:0.0164049)n2:0.00012172)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000093_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000093_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bec3e7a131b9dcaeff146e4ba18dd1f5b334fad0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000093_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00578:0.083449,((GCF_023573625_1_GCF_023573625.1_02119:5e-07,GCF_002008305_4_GCF_002008305.4_02174:5e-07)n3:0,(GCF_020097155_1_GCF_020097155.1_00505:0.0795175,GCF_002008305_4_GCF_002008305.4_00604:1.63863)n4:0.0581179)n2:0.00645755)n1:0.0638863,GCF_003691675_1_GCF_003691675.1_01888:5e-07)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000095_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000095_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..595c7df3028f9898f9209c76f6cbc10dd66a011e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000095_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00611:0.138852,((GCF_003691675_1_GCF_003691675.1_00327:0,GCF_023573625_1_GCF_023573625.1_02008:0)n3:0.110276,(GCF_020097155_1_GCF_020097155.1_01190:1.83429,GCF_003691675_1_GCF_003691675.1_01771:0.2065)n4:0.0520686)n2:0.0057854)n1:0.0162313,GCF_005280335_1_GCF_005280335.1_02344:0.186836)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000096_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000096_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4169475a9ff4a81d8987cc1bf71c7134ed1e3793
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000096_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00544:0.233251,GCF_020097155_1_GCF_020097155.1_00702:0.216236)n2:0.0796547,(GCF_003691675_1_GCF_003691675.1_00326:0.0188012,(GCF_003691675_1_GCF_003691675.1_01774:0.0629467,GCF_002008305_4_GCF_002008305.4_00614:0.0369522)n4:0.165104)n3:0.0183449)n1:0.143923,GCF_023573625_1_GCF_023573625.1_02007:0.0229808)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000101_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000101_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b777e62ffc2507074a0fed23e9b8ceb8e93b23a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000101_tree.txt
@@ -0,0 +1 @@
+(((GCF_003691675_1_GCF_003691675.1_00387:0.00714744,GCF_023573625_1_GCF_023573625.1_00620:0.00460756)n2:0.0232114,((GCF_020097155_1_GCF_020097155.1_02170:0.0998882,GCF_002008305_4_GCF_002008305.4_00841:2.72111)n4:0.166145,GCF_002008305_4_GCF_002008305.4_00650:0.0268802)n3:0.00298669)n1:0.0241048,GCF_005280335_1_GCF_005280335.1_02313:0.0815279)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000102_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000102_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31ebcc8186b212f040a21e7d4908500659f6c643
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000102_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00626:0.00215956,GCF_002008305_4_GCF_002008305.4_00656:1.76115e-06)n1:0.000439155,(GCF_003691675_1_GCF_003691675.1_00393:1.76115e-06,(GCF_020097155_1_GCF_020097155.1_02164:0.1325,(GCF_005280335_1_GCF_005280335.1_02307:0.0793687,GCF_005280335_1_GCF_005280335.1_00162:1.35017)n4:0.150019)n3:0.0467118)n2:0.000439155)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000103_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000103_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7fe542b58bec3ab7717cd9bb86dc0c6d345a6e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000103_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00662:0.0145909,(GCF_020097155_1_GCF_020097155.1_02443:0.882809,(GCF_005280335_1_GCF_005280335.1_02262:0.241719,GCF_005280335_1_GCF_005280335.1_02263:0.102872)n3:0.0114302)n2:0.613258)n1:0.0082523,(GCF_002008305_4_GCF_002008305.4_00692:8.77e-06,GCF_003691675_1_GCF_003691675.1_00429:0.00258823)n4:0.0082523)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000121_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000121_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ca499fa73da6c8ac65956c23507fb1a0b345af1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000121_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01147:0.00354933,(GCF_020097155_1_GCF_020097155.1_01639:0.0945169,(GCF_005280335_1_GCF_005280335.1_01745:0.018807,GCF_005280335_1_GCF_005280335.1_00771:1.29056)n3:0.143396)n2:0.0146736)n1:0.00258283,(GCF_003691675_1_GCF_003691675.1_00866:0,GCF_023573625_1_GCF_023573625.1_01097:0)n4:0.00258283)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000122_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000122_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d995d73750989f510645d5fce2d692ff2d9cc6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000122_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01152:0.006064,(GCF_005280335_1_GCF_005280335.1_01740:0.0136365,(GCF_020097155_1_GCF_020097155.1_01634:0.133546,GCF_020097155_1_GCF_020097155.1_00545:1.72434)n3:0.191594)n2:0.0490223)n1:0.0054025,(GCF_023573625_1_GCF_023573625.1_01102:0,GCF_003691675_1_GCF_003691675.1_00871:0)n4:0.0054025)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000125_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000125_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8a72e68edb1bc6673a7fcdee26e7c88ba3ee7a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000125_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01334:0,GCF_023573625_1_GCF_023573625.1_01290:0)n1:0.0009345,(GCF_003691675_1_GCF_003691675.1_01055:0.001254,(GCF_005280335_1_GCF_005280335.1_01557:0.0230717,(GCF_020097155_1_GCF_020097155.1_00131:1.74033,GCF_020097155_1_GCF_020097155.1_01453:0.080809)n4:0.155963)n3:0.0602017)n2:0.0009345)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000126_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000126_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad27cc1203380ed506ab9fa3c9421bd647464bf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000126_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01296:0,GCF_003691675_1_GCF_003691675.1_01061:0)n1:0.001687,(GCF_002008305_4_GCF_002008305.4_01341:0.009796,(GCF_005280335_1_GCF_005280335.1_01551:0.0524475,(GCF_020097155_1_GCF_020097155.1_01415:2.21555,GCF_020097155_1_GCF_020097155.1_01447:0.0115707)n4:0.240493)n3:0.0441125)n2:0.001687)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000127_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000127_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1b80731079f786197568d3a2536aee820deda6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000127_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01089:0.0279526,((GCF_002008305_4_GCF_002008305.4_01953:2.62665,GCF_005280335_1_GCF_005280335.1_01524:0.149712)n3:0.147465,(GCF_002008305_4_GCF_002008305.4_01369:0.0206304,GCF_023573625_1_GCF_023573625.1_01324:0.0139016)n4:0.00471415)n2:0.000523794)n1:0.123173,GCF_020097155_1_GCF_020097155.1_01419:0.355848)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000129_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000129_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2062b82a9cd8fcc43e552247792cf48ec104c204
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000129_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01182:0.0783039,((GCF_020097155_1_GCF_020097155.1_01775:2.07476,GCF_020097155_1_GCF_020097155.1_01353:0.118945)n3:0.0679801,GCF_005280335_1_GCF_005280335.1_01449:0.0893554)n2:0.0175669)n1:0.0219283,(GCF_023573625_1_GCF_023573625.1_01400:0.0126206,GCF_002008305_4_GCF_002008305.4_01450:0.0209564)n4:0.0219283)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000133_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000133_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30bb1387b62c3b2c7780d2f860b35d4fa697ffce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000133_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01569:0.00075565,GCF_003691675_1_GCF_003691675.1_01279:0.00286035)n1:0.00214667,(GCF_023573625_1_GCF_023573625.1_01496:0.011983,(GCF_020097155_1_GCF_020097155.1_01248:0.116296,(GCF_005280335_1_GCF_005280335.1_01355:0.0971153,GCF_005280335_1_GCF_005280335.1_02577:0.253778)n4:0.0281976)n3:0.0438714)n2:0.00214667)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000137_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000137_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10332b046cac4d4bf59612535f8464c734abd692
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000137_tree.txt
@@ -0,0 +1 @@
+(((GCF_003691675_1_GCF_003691675.1_01296:0.0107404,GCF_023573625_1_GCF_023573625.1_01512:0.00705462)n2:0.004935,((GCF_002008305_4_GCF_002008305.4_02251:0.0624845,GCF_020097155_1_GCF_020097155.1_00456:0.143819)n4:0.743811,GCF_002008305_4_GCF_002008305.4_01585:0.0049464)n3:0.0005496)n1:0.002995,GCF_005280335_1_GCF_005280335.1_01337:0.012057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000140_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000140_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46096cb3fb88de6b61332b2354faad97dd7a8a65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000140_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01624:0.00159981,GCF_003691675_1_GCF_003691675.1_01330:0.00262219)n1:0.00496603,(GCF_023573625_1_GCF_023573625.1_01551:0.0129489,(GCF_005280335_1_GCF_005280335.1_01273:0.00074256,(GCF_020097155_1_GCF_020097155.1_01182:2.97924e-06,GCF_020097155_1_GCF_020097155.1_00781:2.65218)n4:0.294686)n3:0.00535781)n2:0.00496603)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000147_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000147_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b88d3b02f8ed04aa326b8f02d509230d23dea53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000147_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01730:0.0181789,(GCF_020097155_1_GCF_020097155.1_01000:0.112101,(GCF_005280335_1_GCF_005280335.1_01065:0.0541836,GCF_005280335_1_GCF_005280335.1_02644:0.750796)n3:0.0834218)n2:0.0335367)n1:0.00407606,(GCF_003691675_1_GCF_003691675.1_01506:0,GCF_002008305_4_GCF_002008305.4_01809:0)n4:0.00407606)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000153_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000153_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56bbc7c93202db5cddeaca5f7bf370c97fe45769
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000153_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00882:0.10563,GCF_003691675_1_GCF_003691675.1_01669:0.00015482)n1:0.00342676,(GCF_023573625_1_GCF_023573625.1_01901:0.00436273,(GCF_020097155_1_GCF_020097155.1_00817:0.0844846,(GCF_002008305_4_GCF_002008305.4_01976:0.0780945,GCF_002008305_4_GCF_002008305.4_01975:0.088041)n4:0.00978234)n3:0.445738)n2:0.00342676)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000154_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000154_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fd120e73cd07ec56e9cbb5fd00fa01696296652
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000154_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01677:0.0042535,(GCF_005280335_1_GCF_005280335.1_00875:0.100395,(GCF_020097155_1_GCF_020097155.1_00810:0.017556,GCF_020097155_1_GCF_020097155.1_00823:0.142689)n3:0.0158543)n2:0.224434)n1:0.00059125,(GCF_002008305_4_GCF_002008305.4_01983:0,GCF_023573625_1_GCF_023573625.1_01909:0)n4:0.00059125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000158_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000158_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b67e5d50c56e0b05912c06b4cddaa15e9bdc149f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000158_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00789:0.344869,GCF_023573625_1_GCF_023573625.1_01966:1.39692e-06)n2:0.12469,((GCF_002008305_4_GCF_002008305.4_02031:0.201987,GCF_003691675_1_GCF_003691675.1_01738:1.39692e-06)n4:0.0859973,GCF_002008305_4_GCF_002008305.4_02029:0.300184)n3:0.0333538)n1:0.0362852,GCF_020097155_1_GCF_020097155.1_00750:0.298897)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000164_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000164_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..698bf5fed80b5e24599a8e4e475209d45026cc17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000164_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02122:0.0118992,GCF_023573625_1_GCF_023573625.1_02060:0.00899377)n1:0.00105476,(GCF_003691675_1_GCF_003691675.1_01830:0.0109383,(GCF_005280335_1_GCF_005280335.1_00658:0.188184,(GCF_020097155_1_GCF_020097155.1_00575:0.0308103,GCF_020097155_1_GCF_020097155.1_00718:0.569135)n4:0.0632372)n3:0.127671)n2:0.00105476)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000167_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000167_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a81cb45f0231a08ed99f37c41e584c83bf3eefa9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000167_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01898:0.0137146,(GCF_023573625_1_GCF_023573625.1_02129:0.00420819,((GCF_020097155_1_GCF_020097155.1_00491:0.134548,GCF_023573625_1_GCF_023573625.1_00166:2.39922)n4:0.0920547,GCF_005280335_1_GCF_005280335.1_00566:0.0584983)n3:0.0566995)n2:0.00629994)n1:0.00501097,GCF_002008305_4_GCF_002008305.4_02184:0.00185681)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000172_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000172_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b31c2a565491a9735d9dd1173d664838d68ac5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000172_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_02019:0.697218,((GCF_005280335_1_GCF_005280335.1_01501:0.616067,((GCF_020097155_1_GCF_020097155.1_00694:0.309231,GCF_020097155_1_GCF_020097155.1_00347:0.207293)n4:1.00149,GCF_020097155_1_GCF_020097155.1_00288:0.496316)n3:0.0551463)n2:0.531048,GCF_023573625_1_GCF_023573625.1_00111:4.21885e-06)n1:0.697218)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000174_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000174_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4a3dbb4a148afe0847c03019967ea38b9678715
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000174_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00376:0.123165,GCF_005280335_1_GCF_005280335.1_00423:0.046814)n2:0.0261023,GCF_023573625_1_GCF_023573625.1_00001:0.0169327)n1:0.00394762,(GCF_003691675_1_GCF_003691675.1_02006:0.0140412,GCF_002008305_4_GCF_002008305.4_00001:0.00670375)n3:0.00394762)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000175_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000175_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87b194384e87a59964e20d997903996637cac0cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000175_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00002:0,GCF_023573625_1_GCF_023573625.1_00002:0)n1:0,(GCF_003691675_1_GCF_003691675.1_02007:0,(GCF_020097155_1_GCF_020097155.1_00375:0.0955265,GCF_005280335_1_GCF_005280335.1_00422:0.0531075)n3:0.0214555)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000179_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000179_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e951f68ac90ed787ddc26455769adfb069198a1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000179_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02011:0.00117137,GCF_023573625_1_GCF_023573625.1_00006:0.00028863)n1:0.00108431,(GCF_002008305_4_GCF_002008305.4_00006:0.00543937,(GCF_020097155_1_GCF_020097155.1_00370:0.0978781,GCF_005280335_1_GCF_005280335.1_00418:0.0437689)n3:0.0306456)n2:0.00108431)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000182_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000182_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01508623a78a0cdd7352c38f211ba62413861371
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000182_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02029:0.0139413,GCF_002008305_4_GCF_002008305.4_00011:0.00520267)n1:0.000822285,(GCF_023573625_1_GCF_023573625.1_00011:0.00024798,(GCF_020097155_1_GCF_020097155.1_02181:0.28413,GCF_005280335_1_GCF_005280335.1_00386:0.0743763)n3:0.0717949)n2:0.000822285)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000183_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000183_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea863a3cf15e78fff6e1fb616abab113cfb6f530
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000183_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00364:0.764763,GCF_005280335_1_GCF_005280335.1_00383:0.140139)n2:0.229514,GCF_003691675_1_GCF_003691675.1_02032:0.0454325)n1:0.00834649,(GCF_002008305_4_GCF_002008305.4_00014:0.00406444,GCF_023573625_1_GCF_023573625.1_00014:0.00237656)n3:0.00834649)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000190_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000190_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa666b57b8ea7bded7ebdf999f92c70d312efa88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000190_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00021:0.00017867,GCF_003691675_1_GCF_003691675.1_02039:3.88946e-07)n1:0.00391625,(GCF_023573625_1_GCF_023573625.1_00021:0.0094685,(GCF_005280335_1_GCF_005280335.1_00375:0.0190076,GCF_020097155_1_GCF_020097155.1_00357:0.350104)n3:0.0025335)n2:0.00391625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000194_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000194_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48873f7640b3aa0dffadca3e69f9208d9108f1bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000194_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00031:0.00236134,GCF_003691675_1_GCF_003691675.1_02049:0.00397766)n1:0.00121645,((GCF_020097155_1_GCF_020097155.1_00304:0.137803,GCF_005280335_1_GCF_005280335.1_00366:0.0167207)n3:0.00964019,GCF_002008305_4_GCF_002008305.4_00032:0.00015293)n2:0.00121645)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000196_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000196_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..172645815c0458ffcf840d3297ad165763b70a8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000196_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00034:0.00537062,GCF_003691675_1_GCF_003691675.1_02051:0.00163337)n1:0.00287806,(GCF_023573625_1_GCF_023573625.1_00033:0.00409888,(GCF_005280335_1_GCF_005280335.1_00362:0.0698459,GCF_020097155_1_GCF_020097155.1_00303:0.0697571)n3:0.0414646)n2:0.00287806)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000197_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000197_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe89ca3ca66581e81abe54c71d858a8aeb2a5436
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000197_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00209:0.0173781,GCF_023573625_1_GCF_023573625.1_00190:0.0112119)n1:0.0583316,(GCF_003691675_1_GCF_003691675.1_02020:2.28121,(GCF_002008305_4_GCF_002008305.4_00190:0.0810099,GCF_002008305_4_GCF_002008305.4_00035:1.11263)n3:0.123626)n2:1.23235)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000198_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000198_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca42dac7230f31acaab43303c71c613576a283dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000198_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00039:1.87355e-07,GCF_003691675_1_GCF_003691675.1_02052:0.0054225)n1:0.0006135,(GCF_023573625_1_GCF_023573625.1_00034:0.006956,(GCF_005280335_1_GCF_005280335.1_00361:0.0770592,GCF_020097155_1_GCF_020097155.1_00302:0.0596908)n3:0.037334)n2:0.0006135)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000200_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000200_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1538e92d01d432ffb46016236741a3836795c8d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000200_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00042:0.00829239,(GCF_005280335_1_GCF_005280335.1_00358:0.0316395,GCF_020097155_1_GCF_020097155.1_00300:0.105368)n2:0.044158)n1:0.00266755,(GCF_023573625_1_GCF_023573625.1_00037:0.00140726,GCF_003691675_1_GCF_003691675.1_02055:1.95994e-07)n3:0.00266755)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000203_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000203_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f03e6f5d2a0670f53a08e549144326377fcadd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000203_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00355:0.137567,GCF_020097155_1_GCF_020097155.1_00297:0.241853)n2:0.157886,GCF_002008305_4_GCF_002008305.4_00045:0.0173742)n1:0.00396942,(GCF_023573625_1_GCF_023573625.1_00040:0,GCF_003691675_1_GCF_003691675.1_02058:0)n3:0.00396942)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000205_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000205_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a23f8d2477904528c48f78d87eaaff0dddb3462f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000205_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00042:0.0394335,GCF_003691675_1_GCF_003691675.1_02060:0.0031415)n1:0.00779875,(GCF_002008305_4_GCF_002008305.4_00047:0.0074735,(GCF_005280335_1_GCF_005280335.1_00348:0.177708,GCF_020097155_1_GCF_020097155.1_00295:0.531933)n3:0.205707)n2:0.00779875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000210_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000210_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afcae9aaf7ad8f95992be52a91eebd6113303cf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000210_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00057:0.00348725,GCF_023573625_1_GCF_023573625.1_00052:0.00294775)n1:0.00043375,((GCF_020097155_1_GCF_020097155.1_00278:0.377439,GCF_005280335_1_GCF_005280335.1_00338:0.134075)n3:0.07292,GCF_003691675_1_GCF_003691675.1_02070:0.0059605)n2:0.00043375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000211_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000211_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b0600337ee212ab03dddf6a57ed9736c17458a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000211_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00053:0.002865,GCF_003691675_1_GCF_003691675.1_02071:0.005806)n1:0.0011615,((GCF_005280335_1_GCF_005280335.1_00337:0.0715117,GCF_020097155_1_GCF_020097155.1_00277:0.40234)n3:0.089566,GCF_002008305_4_GCF_002008305.4_00058:0.009443)n2:0.0011615)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000213_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000213_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e60184b3d2f210cf56d0fc5d7987feb6abb41f02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000213_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00061:0,GCF_023573625_1_GCF_023573625.1_00056:0)n1:0.000338825,((GCF_020097155_1_GCF_020097155.1_00275:0.0568432,GCF_005280335_1_GCF_005280335.1_00334:0.0182718)n3:0.0155126,GCF_003691675_1_GCF_003691675.1_02074:0.00841335)n2:0.000338825)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000216_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000216_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9afd7f249e882dc2a58edff66a1c349a51fef9bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000216_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00060:0.00792154,GCF_002008305_4_GCF_002008305.4_00066:2.73844e-07)n1:0.00361186,(GCF_003691675_1_GCF_003691675.1_02079:0.00359182,(GCF_005280335_1_GCF_005280335.1_00329:0.112464,GCF_020097155_1_GCF_020097155.1_00268:0.0778048)n3:0.0650224)n2:0.00361186)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000217_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000217_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad6fba25a8e66215819dea6285386c5b71d1513e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000217_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02080:0,GCF_002008305_4_GCF_002008305.4_00067:0)n1:0.00200578,((GCF_005280335_1_GCF_005280335.1_00327:0.148028,GCF_020097155_1_GCF_020097155.1_00267:0.152254)n3:0.0450878,GCF_023573625_1_GCF_023573625.1_00061:0.00241945)n2:0.00200578)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000223_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000223_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8cd188b3c68be94e04d9d4f1184a8b9441792980
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000223_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00075:0,GCF_003691675_1_GCF_003691675.1_02088:0)n1:0.00124225,(GCF_023573625_1_GCF_023573625.1_00069:0.0024175,(GCF_005280335_1_GCF_005280335.1_00318:0.085422,GCF_020097155_1_GCF_020097155.1_00259:0.12497)n3:0.0359915)n2:0.00124225)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000224_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000224_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..029759b1dce8fdd128a7d3c435208d3dad6c2455
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000224_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02090:0.0105849,GCF_023573625_1_GCF_023573625.1_00071:0.00990812)n1:0.00231581,(GCF_002008305_4_GCF_002008305.4_00077:0.00353188,(GCF_020097155_1_GCF_020097155.1_00257:0.215258,GCF_005280335_1_GCF_005280335.1_00316:0.0298874)n3:0.0182241)n2:0.00231581)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000225_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000225_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28919d66a3f236f92a8672eb0e67b437f32e791d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000225_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00072:0,GCF_003691675_1_GCF_003691675.1_02091:0)n1:0.00821124,(GCF_002008305_4_GCF_002008305.4_00078:0.0208165,(GCF_005280335_1_GCF_005280335.1_00315:0.156983,GCF_020097155_1_GCF_020097155.1_00256:0.387495)n3:0.0702702)n2:0.00821124)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000226_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000226_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b74885fd9b70981843035ab6a52ddcff16469131
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000226_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00314:0.0874433,GCF_020097155_1_GCF_020097155.1_00255:0.460412)n2:0.0942182,GCF_002008305_4_GCF_002008305.4_00079:0.0165716)n1:0.0180137,(GCF_003691675_1_GCF_003691675.1_02092:0,GCF_023573625_1_GCF_023573625.1_00073:0)n3:0.0180137)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000230_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000230_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffb503510540b12183f871f9711b8fea8f4930cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000230_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00079:0,GCF_003691675_1_GCF_003691675.1_02097:0)n1:0.0101487,(GCF_002008305_4_GCF_002008305.4_00084:0.0132625,(GCF_005280335_1_GCF_005280335.1_00307:0.120451,GCF_020097155_1_GCF_020097155.1_00251:0.486689)n3:0.053005)n2:0.0101487)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000232_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000232_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e300afbd00eec4e59d925ffc72b9a7b97f4b7147
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000232_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00082:0.00057775,GCF_003691675_1_GCF_003691675.1_02100:0.00357425)n1:0.0217294,(GCF_020097155_1_GCF_020097155.1_00249:0.700708,(GCF_005280335_1_GCF_005280335.1_00304:0.061099,GCF_002008305_4_GCF_002008305.4_00087:0.031628)n3:0.0563492)n2:0.0217294)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000233_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000233_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ba6ed9dd70c32998f5124b2cb539408cfdf06ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000233_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02101:5e-07,GCF_023573625_1_GCF_023573625.1_00083:5e-07)n1:0.0123974,(GCF_002008305_4_GCF_002008305.4_00088:0.00586964,(GCF_005280335_1_GCF_005280335.1_00303:0.121483,GCF_020097155_1_GCF_020097155.1_00248:0.324907)n3:0.0988576)n2:0.0123974)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000234_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000234_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d021e84a36f1c7f1e8eb17cdd7c2bdf7930014ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000234_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00302:0.0869264,GCF_020097155_1_GCF_020097155.1_00247:0.300545)n2:0.0756449,GCF_023573625_1_GCF_023573625.1_00084:0.0270961)n1:0.00902719,(GCF_002008305_4_GCF_002008305.4_00089:0.0244666,GCF_003691675_1_GCF_003691675.1_02102:0.00659638)n3:0.00902719)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000236_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000236_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cd94cd8cd31e16764ada2948942b225dda1c5dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000236_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00091:0,GCF_023573625_1_GCF_023573625.1_00086:0)n1:0.00264961,(GCF_003691675_1_GCF_003691675.1_02104:0.00471879,(GCF_005280335_1_GCF_005280335.1_00300:0.00766933,GCF_020097155_1_GCF_020097155.1_00245:0.00921367)n3:0.0299746)n2:0.00264961)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000237_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000237_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9384bfed04f2da3687cdc1eed71d5beb03ceb9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000237_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00092:0,GCF_023573625_1_GCF_023573625.1_00087:0)n1:0.00777038,(GCF_005280335_1_GCF_005280335.1_00299:0.0171442,(GCF_003691675_1_GCF_003691675.1_02105:0.0100617,GCF_020097155_1_GCF_020097155.1_00244:0.00534725)n3:0.00388525)n2:0.00777038)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000241_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000241_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e47b0aae061edb209826896034fd3b86ccb5c78c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000241_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00091:0.00398725,GCF_003691675_1_GCF_003691675.1_02109:0.00083575)n1:0.00345013,((GCF_020097155_1_GCF_020097155.1_00240:0.102351,GCF_005280335_1_GCF_005280335.1_00295:0.100721)n3:0.0669068,GCF_002008305_4_GCF_002008305.4_00096:0.00605025)n2:0.00345013)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000242_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000242_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..598b4e654cad24752bb85eaa2a840465e7eff48d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000242_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00092:0.00360812,GCF_002008305_4_GCF_002008305.4_00097:0.00098188)n1:0.00107057,(GCF_003691675_1_GCF_003691675.1_02110:0.00372637,(GCF_005280335_1_GCF_005280335.1_00294:0.0309364,GCF_020097155_1_GCF_020097155.1_00239:0.0905666)n3:0.0134831)n2:0.00107057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000243_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000243_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a56c286f9a62939352becb7777590fa68d9a566e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000243_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00238:0.171802,GCF_005280335_1_GCF_005280335.1_00293:0.171404)n2:0.170815,GCF_003691675_1_GCF_003691675.1_02111:0.0162697)n1:0.000348625,(GCF_002008305_4_GCF_002008305.4_00098:0,GCF_023573625_1_GCF_023573625.1_00093:0)n3:0.000348625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000244_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000244_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..893847e5522eceaaad808554a4a3bb649b65d1e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000244_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00100:0.00153069,GCF_023573625_1_GCF_023573625.1_00095:1.831e-05)n1:0.00035386,(GCF_003691675_1_GCF_003691675.1_02113:0.00175347,(GCF_020097155_1_GCF_020097155.1_00237:0.0674523,GCF_005280335_1_GCF_005280335.1_00291:0.0145157)n3:0.00993389)n2:0.00035386)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000245_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000245_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8c0788b3468e70c088d6b6a561c567739b157ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000245_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00289:0.105492,GCF_023573625_1_GCF_023573625.1_00096:0.0609512)n2:0.0701897,GCF_020097155_1_GCF_020097155.1_00235:0.497697)n1:0.0168749,(GCF_003691675_1_GCF_003691675.1_02114:0,GCF_002008305_4_GCF_002008305.4_00101:0)n3:0.0168749)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000250_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000250_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c66ffa91aa4f5f677d195d723d47cd32ad65e02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000250_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00283:0.0917203,GCF_020097155_1_GCF_020097155.1_00224:0.341852)n2:0.130457,GCF_023573625_1_GCF_023573625.1_00102:0.0362025)n1:0.00840725,(GCF_002008305_4_GCF_002008305.4_00107:0.0001,GCF_003691675_1_GCF_003691675.1_02120:0.002221)n3:0.00840725)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000251_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000251_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b9f5afa9ee8383fff0b4930b9120ba22e6c068b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000251_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00103:2.9666e-07,(GCF_005280335_1_GCF_005280335.1_00282:0.0891228,GCF_020097155_1_GCF_020097155.1_00223:0.0587973)n2:0.147899)n1:0.000521125,(GCF_003691675_1_GCF_003691675.1_02121:0,GCF_002008305_4_GCF_002008305.4_00108:0)n3:0.000521125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000252_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000252_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8aa4c2c8fbde469c2691563c688772632870744
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000252_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00109:0,GCF_023573625_1_GCF_023573625.1_00104:0)n1:0,((GCF_005280335_1_GCF_005280335.1_00281:0.166242,GCF_020097155_1_GCF_020097155.1_00222:0.0914245)n3:0.236177,GCF_003691675_1_GCF_003691675.1_02122:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000256_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000256_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d832338ccf0f3c9e681156c7ff44182c9314249
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000256_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00113:5e-07,GCF_003691675_1_GCF_003691675.1_02126:5e-07)n1:0,(GCF_023573625_1_GCF_023573625.1_00108:5e-07,(GCF_005280335_1_GCF_005280335.1_00277:0.043781,GCF_020097155_1_GCF_020097155.1_00218:0.138303)n3:0.0851395)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000257_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000257_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..920bd10085a3637fd1340ca6f4d1b8e34d04131b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000257_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00115:0,GCF_003691675_1_GCF_003691675.1_02128:0)n1:0.00147987,((GCF_005280335_1_GCF_005280335.1_00272:0.0829247,GCF_020097155_1_GCF_020097155.1_00204:0.142208)n3:0.0740511,GCF_023573625_1_GCF_023573625.1_00120:0.00519526)n2:0.00147987)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000258_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000258_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e32ac4a8d322642afa691308431c62409143b76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000258_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00121:0.0179034,GCF_002008305_4_GCF_002008305.4_00116:0.0179786)n1:0.00686247,((GCF_005280335_1_GCF_005280335.1_00271:0.121443,GCF_020097155_1_GCF_020097155.1_00203:0.384719)n3:0.0958559,GCF_003691675_1_GCF_003691675.1_02129:0.0175398)n2:0.00686247)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000264_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000264_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e2864ce2dbf51578a62998cab1221243fdbee45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000264_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02140:0.00283038,GCF_023573625_1_GCF_023573625.1_00134:3.93911e-07)n1:0.00798931,(GCF_002008305_4_GCF_002008305.4_00126:0.00729887,(GCF_005280335_1_GCF_005280335.1_00259:0.10669,GCF_020097155_1_GCF_020097155.1_00193:0.208182)n3:0.0533061)n2:0.00798931)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000267_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000267_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcba1bf2b567ff5fad269fd793c7883a08ccaf8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000267_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00141:0.019744,(GCF_005280335_1_GCF_005280335.1_00252:0.0834142,GCF_020097155_1_GCF_020097155.1_00188:0.121183)n2:0.0844822)n1:0.00840923,(GCF_003691675_1_GCF_003691675.1_02147:0.00425296,GCF_002008305_4_GCF_002008305.4_00133:0.00545404)n3:0.00840923)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000269_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000269_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..427cca3e0b9c7f2094831e2457ce07a34c8eeba8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000269_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02150:0.00949525,GCF_023573625_1_GCF_023573625.1_00144:5.67653e-07)n1:0.00656325,((GCF_020097155_1_GCF_020097155.1_00182:0.335167,GCF_005280335_1_GCF_005280335.1_00248:0.119881)n3:0.0834665,GCF_002008305_4_GCF_002008305.4_00136:0.0076375)n2:0.00656325)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000270_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000270_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51822e288facab2e22d2c38baaaffe5161574602
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000270_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00247:0.0549907,GCF_002008305_4_GCF_002008305.4_00137:0.00568625)n1:0.00164212,(GCF_020097155_1_GCF_020097155.1_00181:0.0100117,(GCF_023573625_1_GCF_023573625.1_00145:0.0031775,GCF_003691675_1_GCF_003691675.1_02151:0.0002945)n3:0.00089775)n2:0.00164212)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000274_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000274_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e08594d46b8a183ef92b6d6891085c5b006fc23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000274_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02155:0,GCF_023573625_1_GCF_023573625.1_00149:0)n1:0.00074397,((GCF_005280335_1_GCF_005280335.1_00243:0.408477,GCF_020097155_1_GCF_020097155.1_00177:0.323771)n3:0.0612097,GCF_002008305_4_GCF_002008305.4_00141:0.00278206)n2:0.00074397)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000275_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000275_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a592e8edbe623ef7d0aad73ae3d392c73bebaa10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000275_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00142:3.5312e-07,GCF_003691675_1_GCF_003691675.1_02156:0.0198869)n1:0.000173435,((GCF_020097155_1_GCF_020097155.1_00176:0.23583,GCF_005280335_1_GCF_005280335.1_00242:0.0481546)n3:0.0495954,GCF_023573625_1_GCF_023573625.1_00150:3.5312e-07)n2:0.000173435)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000276_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000276_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a78bd562934de07a6c044ff803e16d51b09680f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000276_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02157:0.0149732,GCF_002008305_4_GCF_002008305.4_00143:0.0742338)n1:0.0367265,(GCF_023573625_1_GCF_023573625.1_00151:0.0233685,(GCF_005280335_1_GCF_005280335.1_00241:0.0898309,GCF_020097155_1_GCF_020097155.1_00175:0.0861191)n3:0.0369245)n2:0.0367265)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000278_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000278_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f2cfcc699e65780cb9830b6015976a5d924c1e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000278_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00154:0.0047995,GCF_003691675_1_GCF_003691675.1_02160:0.0012845)n1:0.00138562,((GCF_020097155_1_GCF_020097155.1_00173:0.0312775,GCF_005280335_1_GCF_005280335.1_00238:0.0271285)n3:0.0299078,GCF_002008305_4_GCF_002008305.4_00146:0.00947775)n2:0.00138562)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000280_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000280_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b07ae0ecf4edc2a9b8cf75620bcc1bd8ec14d9db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000280_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00148:0,(GCF_020097155_1_GCF_020097155.1_00820:0.113554,GCF_005280335_1_GCF_005280335.1_00235:0.0130175)n2:0.0033165)n1:0,(GCF_023573625_1_GCF_023573625.1_00156:0,GCF_003691675_1_GCF_003691675.1_02162:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000281_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000281_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..916da1242d8ec131beafb7c43ec5745aa7288fb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000281_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02163:0.00098251,GCF_023573625_1_GCF_023573625.1_00157:0.00029049)n1:0.00112255,(GCF_002008305_4_GCF_002008305.4_00149:0.00119554,(GCF_020097155_1_GCF_020097155.1_00819:0.332875,GCF_005280335_1_GCF_005280335.1_00234:0.0907178)n3:0.0635741)n2:0.00112255)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000282_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000282_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8a8763a104a4814258998becf604b358fe7f92a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000282_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00150:0,GCF_023573625_1_GCF_023573625.1_00158:0)n1:0,((GCF_005280335_1_GCF_005280335.1_00233:0.0831285,GCF_020097155_1_GCF_020097155.1_00172:0.424499)n3:0.0889695,GCF_003691675_1_GCF_003691675.1_02164:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000284_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000284_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b32fe77fce3b66ace96154f95feb9f5e1a66acad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000284_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00170:0.113673,GCF_005280335_1_GCF_005280335.1_00231:0.028986)n2:0.026646,GCF_003691675_1_GCF_003691675.1_02166:0)n1:0,(GCF_023573625_1_GCF_023573625.1_00160:0,GCF_002008305_4_GCF_002008305.4_00152:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000286_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000286_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..439b96c3060f01a0ac88f1d3b88b65fb5e36c504
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000286_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_02333:1.5524e-06,GCF_002008305_4_GCF_002008305.4_00168:0.0159101)n1:0.00201819,((GCF_020097155_1_GCF_020097155.1_00676:1.5272,GCF_023573625_1_GCF_023573625.1_02011:0.00334887)n3:0.00550087,GCF_003691675_1_GCF_003691675.1_00359:1.5524e-06)n2:0.00201819)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000289_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000289_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9dff21f424ab5c3d96d513a26c0c34ace984f8b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000289_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00177:0.0038965,(GCF_005280335_1_GCF_005280335.1_00221:0.027053,GCF_020097155_1_GCF_020097155.1_00166:0.100765)n2:0.0135535)n1:0.00026325,(GCF_003691675_1_GCF_003691675.1_02176:0.0031475,GCF_002008305_4_GCF_002008305.4_00180:0.0019415)n3:0.00026325)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000294_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000294_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9c7214cf136352de58a06651fbebdcaf8ab2e46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000294_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02181:0.00996683,GCF_023573625_1_GCF_023573625.1_00182:0.00797417)n1:0.00471563,(GCF_002008305_4_GCF_002008305.4_00185:0.0118123,(GCF_020097155_1_GCF_020097155.1_00161:0.107839,GCF_005280335_1_GCF_005280335.1_00216:0.0198214)n3:0.00480471)n2:0.00471563)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000295_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000295_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf152b95006525f76cf4dde5a9647b2aeb7187b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000295_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00186:0.00191583,GCF_003691675_1_GCF_003691675.1_02182:0.00262517)n1:0.00559582,(GCF_020097155_1_GCF_020097155.1_00160:0.0544935,(GCF_005280335_1_GCF_005280335.1_00215:0.00641973,GCF_023573625_1_GCF_023573625.1_00183:0.0118673)n3:0.00269354)n2:0.00559582)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000298_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000298_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f88674b62e6996249f873a7aba13bae4312810e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000298_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00154:3.2086e-08,GCF_005280335_1_GCF_005280335.1_00207:0.0224635)n2:0.00228,GCF_002008305_4_GCF_002008305.4_00193:0.0066685)n1:0.00036675,(GCF_003691675_1_GCF_003691675.1_02189:0,GCF_023573625_1_GCF_023573625.1_00193:0)n3:0.00036675)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000299_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000299_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8ca60194c0577f4067c4fa991996083762004ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000299_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02190:0.00386,GCF_002008305_4_GCF_002008305.4_00194:0.0068)n1:0.0136569,(GCF_023573625_1_GCF_023573625.1_00194:0.00601868,(GCF_005280335_1_GCF_005280335.1_00206:0.0485681,GCF_020097155_1_GCF_020097155.1_00153:0.00256985)n3:0.00447032)n2:0.0136569)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000300_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000300_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd8a70f87e2dcb6de2eda29f5e3239d49a3d5f8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000300_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02191:0,GCF_002008305_4_GCF_002008305.4_00195:0)n1:0.00987806,(GCF_023573625_1_GCF_023573625.1_00195:0.256679,(GCF_020097155_1_GCF_020097155.1_00152:0.00344067,GCF_005280335_1_GCF_005280335.1_00204:0.535484)n3:0.013849)n2:0.00987806)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000301_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000301_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a365270161e2474771f6c12c19b88ed5162bee5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000301_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02192:0,GCF_023573625_1_GCF_023573625.1_00196:0)n1:0.017402,(GCF_002008305_4_GCF_002008305.4_00196:0.026949,(GCF_005280335_1_GCF_005280335.1_00203:0.150037,GCF_020097155_1_GCF_020097155.1_00151:0.0228675)n3:0.0118065)n2:0.017402)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000303_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000303_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6de606cda4cf2b5227102ee7c5f4da2dd466036
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000303_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00202:0.00337213,GCF_023573625_1_GCF_023573625.1_00204:0.00538387)n1:0.00471331,(GCF_020097155_1_GCF_020097155.1_00144:0.0214154,(GCF_005280335_1_GCF_005280335.1_00190:0.231385,GCF_003691675_1_GCF_003691675.1_02197:0.0139604)n3:0.00943712)n2:0.00471331)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000305_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000305_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..342497a7f280f01954de54f955402e90eb8ed531
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000305_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_00140:0.00662625,GCF_002008305_4_GCF_002008305.4_00204:0.00691375)n1:0.0309054,(GCF_005280335_1_GCF_005280335.1_00198:0.19755,(GCF_023573625_1_GCF_023573625.1_00206:0,GCF_003691675_1_GCF_003691675.1_02199:0)n3:0.00535925)n2:0.0309054)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000312_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000312_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f93703784e5e4ce07335a685c3d98a335e9c35e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000312_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02207:0.0295485,GCF_023573625_1_GCF_023573625.1_00214:0.0258265)n1:0.00277725,((GCF_020097155_1_GCF_020097155.1_00120:0.244116,GCF_005280335_1_GCF_005280335.1_00169:0.261873)n3:0.265166,GCF_002008305_4_GCF_002008305.4_00214:0.025921)n2:0.00277725)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000313_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000313_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adb210aefa8033f3193c2e8a6b06ed8a7e33ac58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000313_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00215:1.27052e-06,(GCF_020097155_1_GCF_020097155.1_00119:0.846728,GCF_005280335_1_GCF_005280335.1_00166:0.228703)n2:0.170898)n1:0.00417294,(GCF_023573625_1_GCF_023573625.1_00215:0.0325369,GCF_003691675_1_GCF_003691675.1_02208:1.27052e-06)n3:0.00417294)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000314_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000314_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67f9b8f3ecaa2c23863d03e5562777acd1c018cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000314_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01604:0.263741,GCF_020097155_1_GCF_020097155.1_00616:1.07248)n2:0.327215,GCF_002008305_4_GCF_002008305.4_00218:0.0128632)n1:0.00896592,(GCF_003691675_1_GCF_003691675.1_02212:0,GCF_023573625_1_GCF_023573625.1_00219:0)n3:0.00896592)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000316_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000316_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac85ca2c161d14817f210ba23922ecd7a16429bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000316_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00158:0.0091505,GCF_020097155_1_GCF_020097155.1_00116:0.107388)n2:0.0199933,GCF_023573625_1_GCF_023573625.1_00223:0.00027925)n1:0.00140663,(GCF_002008305_4_GCF_002008305.4_00222:5e-07,GCF_003691675_1_GCF_003691675.1_02235:5e-07)n3:0.00140663)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000321_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000321_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc84a208b8bdb3dff34b0ecb05ad0aceaed946dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000321_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02243:0.00069437,GCF_002008305_4_GCF_002008305.4_00230:0.00185763)n1:0.00232744,((GCF_020097155_1_GCF_020097155.1_00108:0.0619449,GCF_005280335_1_GCF_005280335.1_00151:0.124915)n3:0.0631744,GCF_023573625_1_GCF_023573625.1_00231:0.00458412)n2:0.00232744)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000323_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000323_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4aa1a596acde913c2f9e56721f66cbb021b3c18f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000323_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00232:0.001516,GCF_003691675_1_GCF_003691675.1_02245:0.007762)n1:0.00768438,(GCF_023573625_1_GCF_023573625.1_00233:0.00759775,(GCF_020097155_1_GCF_020097155.1_00105:0.094414,GCF_005280335_1_GCF_005280335.1_00147:0.099015)n3:0.130152)n2:0.00768438)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000326_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000326_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22b62b3049ed441ccdece6a8e24bcff67b56fc86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000326_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00235:0.0104153,(GCF_020097155_1_GCF_020097155.1_00101:0.196317,GCF_005280335_1_GCF_005280335.1_00136:0.0640627)n2:0.0718564)n1:0.00920833,(GCF_023573625_1_GCF_023573625.1_00236:0.00663182,GCF_003691675_1_GCF_003691675.1_02248:0.00181918)n3:0.00920833)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000329_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000329_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c97cc5301f2ec8921d3425fc96b4a7df32209591
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000329_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00097:0.482273,GCF_005280335_1_GCF_005280335.1_00132:0.0503878)n2:0.0559528,GCF_002008305_4_GCF_002008305.4_00239:0.00539179)n1:0.00133961,(GCF_023573625_1_GCF_023573625.1_00240:0,GCF_003691675_1_GCF_003691675.1_02252:0)n3:0.00133961)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000330_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000330_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8eaa92716836a43b6dd6873579942f02fbd41e96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000330_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00131:0.230069,GCF_020097155_1_GCF_020097155.1_00096:0.578811)n2:0.181465,GCF_002008305_4_GCF_002008305.4_00240:0.0383175)n1:0.0108755,(GCF_023573625_1_GCF_023573625.1_00241:0.00516825,GCF_003691675_1_GCF_003691675.1_02253:0.0253818)n3:0.0108755)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000331_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000331_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11ab4abb4045011af0c8ed1eac305fcf590f6930
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000331_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02254:0.0164058,GCF_023573625_1_GCF_023573625.1_00242:0.00908116)n1:0.00576373,((GCF_020097155_1_GCF_020097155.1_00095:0.781331,GCF_005280335_1_GCF_005280335.1_00128:0.15731)n3:0.0789046,GCF_002008305_4_GCF_002008305.4_00241:0.0120704)n2:0.00576373)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000333_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000333_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..715b2f7dfec8e49fd89b0390166d37da559bfcc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000333_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00246:0.00235987,GCF_003691675_1_GCF_003691675.1_02258:0.00026613)n1:0.00218068,(GCF_023573625_1_GCF_023573625.1_00246:0.00147058,(GCF_005280335_1_GCF_005280335.1_00123:0.396281,GCF_020097155_1_GCF_020097155.1_00092:0.352065)n3:0.0232548)n2:0.00218068)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000337_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000337_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62e808cc647a6e6323522d5e4333e1929dc92bad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000337_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00254:0.00255982,GCF_002008305_4_GCF_002008305.4_00255:0.00164818)n1:0.0005571,(GCF_003691675_1_GCF_003691675.1_02269:0.0001284,(GCF_020097155_1_GCF_020097155.1_00082:0.164614,GCF_005280335_1_GCF_005280335.1_00114:0.00198767)n3:0.00368633)n2:0.0005571)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000343_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000343_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87e69e6ea4f59ec412948fb2fc6e5de14312b0f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000343_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00264:0,GCF_003691675_1_GCF_003691675.1_02277:0)n1:0.00508075,(GCF_023573625_1_GCF_023573625.1_00262:0.0188155,(GCF_020097155_1_GCF_020097155.1_00070:0.495992,GCF_005280335_1_GCF_005280335.1_00099:8.46146e-07)n3:0.337909)n2:0.00508075)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000346_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000346_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bbd07e243534ec5e8ccd650e2f2d148777f368ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000346_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00267:0,GCF_003691675_1_GCF_003691675.1_02280:0)n1:0,(GCF_023573625_1_GCF_023573625.1_00265:0,(GCF_020097155_1_GCF_020097155.1_00067:0.330646,GCF_005280335_1_GCF_005280335.1_00096:0.070796)n3:0.042428)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000347_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000347_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f60b7fc460c183823b530fd3439256ee0719d2aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000347_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00066:0.277455,GCF_005280335_1_GCF_005280335.1_00095:0.018418)n2:0.0268919,GCF_002008305_4_GCF_002008305.4_00268:0.00065183)n1:0.000956085,(GCF_023573625_1_GCF_023573625.1_00266:0,GCF_003691675_1_GCF_003691675.1_02281:0)n3:0.000956085)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000348_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000348_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c08b1927c9ce67c98e735f582ba7ac68797a310b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000348_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02282:0.0130814,GCF_023573625_1_GCF_023573625.1_00267:1.98649e-06)n1:8.319e-05,(GCF_002008305_4_GCF_002008305.4_00269:1.98649e-06,(GCF_020097155_1_GCF_020097155.1_00397:0.597888,GCF_005280335_1_GCF_005280335.1_00444:0.690885)n3:0.6848)n2:8.319e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000349_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000349_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20cf7e97cbd55214417491d48a198e2ffd3c3756
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000349_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00268:0,GCF_003691675_1_GCF_003691675.1_02285:0)n1:0.00192475,((GCF_020097155_1_GCF_020097155.1_00064:0.096921,GCF_005280335_1_GCF_005280335.1_00087:0.037145)n3:0.0199855,GCF_002008305_4_GCF_002008305.4_00270:0.0089415)n2:0.00192475)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000351_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000351_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9d779e6820fd4705f185a9146c00eb95eb9c81e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000351_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02292:0.0010207,GCF_002008305_4_GCF_002008305.4_00277:0.0060403)n1:0.00161423,(GCF_023573625_1_GCF_023573625.1_00276:0.00058695,(GCF_020097155_1_GCF_020097155.1_00061:0.12151,GCF_005280335_1_GCF_005280335.1_00076:0.0441028)n3:0.0364983)n2:0.00161423)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000353_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000353_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e92a2048d9a858c86668087b4eeeae68f2e6b95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000353_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00280:0.00261544,GCF_003691675_1_GCF_003691675.1_02295:0.00714056)n1:0.00420964,((GCF_023573625_1_GCF_023573625.1_00279:0.0306765,GCF_005280335_1_GCF_005280335.1_00073:0.0062285)n3:0.00648511,GCF_020097155_1_GCF_020097155.1_00059:0.202047)n2:0.00420964)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000361_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000361_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..779f8eb0b4b172cf51e7075b1b256c8885a09c0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000361_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00300:5e-07,GCF_002008305_4_GCF_002008305.4_00293:5e-07)n1:0,(GCF_003691675_1_GCF_003691675.1_00001:5e-07,(GCF_020097155_1_GCF_020097155.1_00040:0.11057,GCF_005280335_1_GCF_005280335.1_00061:0.0261035)n3:0.013596)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000362_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000362_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d40d76c1aa2aeb5b10bc161c08e2fb430721da6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000362_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00060:0.0203972,GCF_020097155_1_GCF_020097155.1_00039:0.19501)n2:0.0173465,GCF_002008305_4_GCF_002008305.4_00294:2.4461e-07)n1:0.00390575,(GCF_023573625_1_GCF_023573625.1_00301:0.0052005,GCF_003691675_1_GCF_003691675.1_00002:0.0003625)n3:0.00390575)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000363_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000363_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ee8586f99a3d37b55f90c42cf161d935386c457
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000363_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00036:0.0289839,GCF_005280335_1_GCF_005280335.1_00058:0.0431371)n2:0.00611387,GCF_002008305_4_GCF_002008305.4_00296:0.00577812)n1:0.00192644,(GCF_003691675_1_GCF_003691675.1_00004:0.00196638,GCF_023573625_1_GCF_023573625.1_00303:2.963e-05)n3:0.00192644)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000364_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000364_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c32a61babc089e92cfa91703efaad6176df3369e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000364_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00006:0.0282457,GCF_023573625_1_GCF_023573625.1_00305:0.0142393)n1:0.0370575,(GCF_005280335_1_GCF_005280335.1_00056:0.149221,(GCF_002008305_4_GCF_002008305.4_00298:0.165129,GCF_020097155_1_GCF_020097155.1_00034:0.309799)n3:0.0593177)n2:0.0370575)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000366_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000366_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed1725f3fc73d14e7398567e4b8d04eb104c34c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000366_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00054:0.0355087,GCF_020097155_1_GCF_020097155.1_00032:0.153057)n2:0.0332795,GCF_003691675_1_GCF_003691675.1_00008:0.00096938)n1:0.00139506,(GCF_002008305_4_GCF_002008305.4_00300:8.39e-06,GCF_023573625_1_GCF_023573625.1_00307:0.00588161)n3:0.00139506)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000376_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000376_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d33176bd88c876da67140fcdf725d6d25ccb5f8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000376_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00030:0.0085985,GCF_023573625_1_GCF_023573625.1_00322:0.0025315)n1:0.00409262,((GCF_020097155_1_GCF_020097155.1_00018:0.301091,GCF_005280335_1_GCF_005280335.1_00022:0.0865873)n3:0.0817652,GCF_002008305_4_GCF_002008305.4_00315:0.0137088)n2:0.00409262)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000378_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000378_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..065602283eea468ae87925bde25a2f388977292c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000378_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00317:0.0196806,(GCF_005280335_1_GCF_005280335.1_00020:0.0447267,GCF_020097155_1_GCF_020097155.1_00016:0.25704)n2:0.0593385)n1:0.00186996,(GCF_023573625_1_GCF_023573625.1_00324:0.00028415,GCF_003691675_1_GCF_003691675.1_00032:0.0104499)n3:0.00186996)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000385_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000385_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9faa9d2b6d20af7cbfb54aa055032c094679afa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000385_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00008:0.11532,GCF_005280335_1_GCF_005280335.1_00012:0.022531)n2:0.0296332,GCF_023573625_1_GCF_023573625.1_00332:0.00554275)n1:0.00246413,(GCF_003691675_1_GCF_003691675.1_00040:0.00386125,GCF_002008305_4_GCF_002008305.4_00325:0.00187475)n3:0.00246413)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000387_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000387_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1150dc5d7eeb2acb2a97ee11ea604728b388d3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000387_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00005:0.0750158,GCF_020097155_1_GCF_020097155.1_00006:0.174003)n2:0.0464608,GCF_003691675_1_GCF_003691675.1_00046:0.00379275)n1:0.000159375,(GCF_002008305_4_GCF_002008305.4_00330:0.00209225,GCF_023573625_1_GCF_023573625.1_00337:0.00902075)n3:0.000159375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000388_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000388_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a418b613add9864c5dc0a36683aecdc5527eeef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000388_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00047:0.00630288,GCF_023573625_1_GCF_023573625.1_00338:0.00573612)n1:0.000608185,(GCF_002008305_4_GCF_002008305.4_00331:0.0114766,(GCF_005280335_1_GCF_005280335.1_00004:0.0948421,GCF_020097155_1_GCF_020097155.1_00005:0.154093)n3:0.0320009)n2:0.000608185)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000391_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000391_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb2a9e7de73e2883f5823321fd32631aad1cb670
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000391_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00345:0.00583886,GCF_002008305_4_GCF_002008305.4_00338:0.00683914)n1:0.00897454,((GCF_005280335_1_GCF_005280335.1_02674:0.095589,GCF_020097155_1_GCF_020097155.1_02486:0.240421)n3:0.0749611,GCF_003691675_1_GCF_003691675.1_00054:0.00803715)n2:0.00897454)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000394_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000394_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3546685e62834bb2788eb6097cc0b3381c7fe913
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000394_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02480:0.0858638,GCF_005280335_1_GCF_005280335.1_02628:0.0571612)n2:0.0546238,GCF_003691675_1_GCF_003691675.1_00057:0.00588401)n1:0.00290375,(GCF_002008305_4_GCF_002008305.4_00341:2.19278e-07,GCF_023573625_1_GCF_023573625.1_00348:0.0100305)n3:0.00290375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000395_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000395_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84a92d1f800e2c8147cf52dd04889ea356983046
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000395_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00058:0.00466412,GCF_002008305_4_GCF_002008305.4_00342:0.0178789)n1:0.00460669,(GCF_023573625_1_GCF_023573625.1_00349:0.00815963,(GCF_020097155_1_GCF_020097155.1_02479:0.353535,GCF_005280335_1_GCF_005280335.1_02627:0.10013)n3:0.140118)n2:0.00460669)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000396_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000396_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d5fe2d9d7eebb1d8086dbc5ece56e87f3227b6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000396_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02478:0.666892,GCF_005280335_1_GCF_005280335.1_02626:0.0942727)n2:0.115053,GCF_002008305_4_GCF_002008305.4_00343:0.00030465)n1:0.00368218,(GCF_023573625_1_GCF_023573625.1_00350:0.0077123,GCF_003691675_1_GCF_003691675.1_00059:0.0187267)n3:0.00368218)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000397_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000397_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e867c902c818678009a61067a81ff68bb46ce9f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000397_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00344:0.00695689,GCF_003691675_1_GCF_003691675.1_00060:0.00705111)n1:0.00360195,(GCF_023573625_1_GCF_023573625.1_00351:0.015324,(GCF_020097155_1_GCF_020097155.1_02477:0.273928,GCF_005280335_1_GCF_005280335.1_02625:0.0765307)n3:0.0663408)n2:0.00360195)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000398_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000398_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..029077b4eeed081cd388d757d4fdf4267fe4b3d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000398_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00346:0.00288781,(GCF_005280335_1_GCF_005280335.1_02623:0.0657287,GCF_020097155_1_GCF_020097155.1_02475:0.131128)n2:0.0287803)n1:0.00139059,(GCF_023573625_1_GCF_023573625.1_00353:0.00258084,GCF_003691675_1_GCF_003691675.1_00062:2.3369e-07)n3:0.00139059)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000400_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000400_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..486d579402d20239e5ebac3fb4545300daa62602
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000400_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02471:0.322857,GCF_005280335_1_GCF_005280335.1_02612:0.147443)n2:0.0568455,GCF_002008305_4_GCF_002008305.4_00349:0.101074)n1:0.0491598,(GCF_023573625_1_GCF_023573625.1_00356:0.0226205,GCF_003691675_1_GCF_003691675.1_00065:0.0241295)n3:0.0491598)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000401_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000401_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..331b01ac4f4b0dede654c9ce007b0a140f72fec1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000401_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00067:0.00310375,GCF_002008305_4_GCF_002008305.4_00351:7.20746e-07)n1:0.00576625,((GCF_005280335_1_GCF_005280335.1_02610:0.0603588,GCF_020097155_1_GCF_020097155.1_02469:0.504201)n3:0.124636,GCF_023573625_1_GCF_023573625.1_00358:0.017002)n2:0.00576625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000402_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000402_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..044b2bfe7e39fc6d92d320b5c96647e0ccb6a001
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000402_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00068:0.00721621,(GCF_020097155_1_GCF_020097155.1_02468:0.132518,GCF_005280335_1_GCF_005280335.1_02609:0.0598208)n2:0.0217672)n1:0.000866895,(GCF_023573625_1_GCF_023573625.1_00359:0.00523535,GCF_002008305_4_GCF_002008305.4_00352:0.0114567)n3:0.000866895)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000406_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000406_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df249767bfdf5e403fc5c8ee4e061b04f46e1bbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000406_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00073:0,GCF_023573625_1_GCF_023573625.1_00364:0)n1:0,(GCF_002008305_4_GCF_002008305.4_00357:0,(GCF_020097155_1_GCF_020097155.1_02463:0.121856,GCF_005280335_1_GCF_005280335.1_02604:0.055601)n3:0.016789)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000407_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000407_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54215234ebbd5a3d41a499c1ad623a02fd35cdf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000407_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00365:0.00085225,GCF_003691675_1_GCF_003691675.1_00074:0.00550975)n1:0.00968162,(GCF_002008305_4_GCF_002008305.4_00358:0.0163492,(GCF_020097155_1_GCF_020097155.1_02462:0.298735,GCF_005280335_1_GCF_005280335.1_02603:0.14417)n3:0.0682583)n2:0.00968162)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000408_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000408_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d76ff2753b17c14f2182f3e8adfef5b576476b84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000408_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02601:0.147182,GCF_020097155_1_GCF_020097155.1_02460:0.618555)n2:0.296444,GCF_002008305_4_GCF_002008305.4_00360:0.0072455)n1:0.0646328,(GCF_023573625_1_GCF_023573625.1_00367:0,GCF_003691675_1_GCF_003691675.1_00076:0)n3:0.0646328)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000409_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000409_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b40e4abb807ae59311fae0e2b417a6c656b83320
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000409_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00077:3.60077e-07,(GCF_020097155_1_GCF_020097155.1_02459:0.125568,GCF_005280335_1_GCF_005280335.1_02600:0.192976)n2:0.0334021)n1:5.708e-05,(GCF_023573625_1_GCF_023573625.1_00368:0,GCF_002008305_4_GCF_002008305.4_00361:0.00813)n3:5.708e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000411_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000411_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5eb5f87fa267742eb7293fa77bdc189bd068de9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000411_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00363:0.00744838,(GCF_020097155_1_GCF_020097155.1_02457:0.105182,GCF_005280335_1_GCF_005280335.1_02598:0.0354409)n2:0.0355881)n1:0.00076531,(GCF_003691675_1_GCF_003691675.1_00079:0.00613463,GCF_023573625_1_GCF_023573625.1_00370:0.00768237)n3:0.00076531)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000415_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000415_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b373346cf3acb59e78354b0237ca6c3b8c2716f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000415_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00370:0.0055805,(GCF_005280335_1_GCF_005280335.1_02592:0.0466593,GCF_020097155_1_GCF_020097155.1_02451:0.128755)n2:0.0342328)n1:0.0007265,(GCF_023573625_1_GCF_023573625.1_00377:0.00214871,GCF_003691675_1_GCF_003691675.1_00086:0.00333529)n3:0.0007265)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000417_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000417_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a1475a75f985aabf005eae81c824c8977d4a117
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000417_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00088:0.009785,GCF_020097155_1_GCF_020097155.1_02449:0.024385)n1:0.00141825,(GCF_005280335_1_GCF_005280335.1_02590:0.0067315,(GCF_002008305_4_GCF_002008305.4_00372:0.00217325,GCF_023573625_1_GCF_023573625.1_00379:0.00127775)n3:0.002809)n2:0.00141825)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000419_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000419_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..478565ba9837b8bafca2bf7744c88b4f67041658
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000419_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_00374:0,(GCF_023573625_1_GCF_023573625.1_00381:0,(GCF_020097155_1_GCF_020097155.1_01178:1.21972,(GCF_005280335_1_GCF_005280335.1_02588:0.011386,GCF_005280335_1_GCF_005280335.1_01001:1.04095)n3:0.115661)n2:0.891269)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000420_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000420_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd4a43c1d7554f4dc33b4b67c3bc7f34c5e60a18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000420_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_00377:0,(GCF_023573625_1_GCF_023573625.1_00383:0,(GCF_020097155_1_GCF_020097155.1_01180:0.769663,(GCF_005280335_1_GCF_005280335.1_02586:0.0047035,GCF_005280335_1_GCF_005280335.1_00011:1.20996)n3:0.13444)n2:0.462107)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000421_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000421_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13a055e12b457db088b20581e51333c7c9327c4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000421_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00103:0.0203983,(GCF_020097155_1_GCF_020097155.1_02448:0.111609,GCF_005280335_1_GCF_005280335.1_02576:0.003066)n2:0.001533)n1:0.00233236,(GCF_002008305_4_GCF_002008305.4_00379:0,GCF_023573625_1_GCF_023573625.1_00385:0)n3:0.00233236)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000422_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000422_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0265bce0f03488039de94daf13627f78d35cc9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000422_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00380:0,GCF_023573625_1_GCF_023573625.1_00386:0)n1:0.00605663,(GCF_003691675_1_GCF_003691675.1_00104:5.50157e-08,(GCF_005280335_1_GCF_005280335.1_02575:0.0170933,GCF_020097155_1_GCF_020097155.1_02447:5.50157e-08)n3:0.0273157)n2:0.00605663)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000424_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000424_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c39720d2bd2c462b18ed5afda2e8527993f39fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000424_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00382:0.00904121,GCF_003691675_1_GCF_003691675.1_00106:0.00863579)n1:0.00057469,(GCF_023573625_1_GCF_023573625.1_00388:0.00453833,(GCF_005280335_1_GCF_005280335.1_02573:0.0259072,GCF_020097155_1_GCF_020097155.1_02445:0.00317683)n3:0.0202423)n2:0.00057469)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000425_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000425_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62aea50b71b9c30ca7172ae888ab6238350efcb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000425_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_02572:2.45182e-06,((GCF_003691675_1_GCF_003691675.1_00107:0.0138052,GCF_023573625_1_GCF_023573625.1_00389:0.0616577)n3:0.0067495,GCF_003691675_1_GCF_003691675.1_00098:2.12554)n2:0.236171)n1:0.00587875,GCF_002008305_4_GCF_002008305.4_00383:0.004315)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000426_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000426_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2c410979a81b575fbbf1f13850c808657ba129e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000426_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00390:0,GCF_002008305_4_GCF_002008305.4_00384:0)n1:0.00256012,(GCF_003691675_1_GCF_003691675.1_00108:4.30005e-07,(GCF_020097155_1_GCF_020097155.1_01754:0.401812,GCF_005280335_1_GCF_005280335.1_02571:0.0151258)n3:0.00898625)n2:0.00256012)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000428_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000428_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdcc29befff4ad6d9a2c249e94bef627097da3ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000428_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00394:0,GCF_002008305_4_GCF_002008305.4_00388:0)n1:0.00886425,((GCF_005280335_1_GCF_005280335.1_02568:0.0069325,GCF_020097155_1_GCF_020097155.1_02439:0.349481)n3:0.0225845,GCF_003691675_1_GCF_003691675.1_00112:3.94588e-07)n2:0.00886425)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000429_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000429_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad6bd94287ff98aec3580c832787d60b7de86b7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000429_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00395:0.00999337,(GCF_020097155_1_GCF_020097155.1_02438:0.511366,GCF_005280335_1_GCF_005280335.1_02567:0.0812429)n2:0.0851051)n1:0.00248107,(GCF_003691675_1_GCF_003691675.1_00113:0.00364562,GCF_002008305_4_GCF_002008305.4_00389:0.00332038)n3:0.00248107)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000435_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000435_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a81ee402716caab432f54825b8a5db37bb0a6731
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000435_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02431:0.388558,GCF_005280335_1_GCF_005280335.1_02560:0.171572)n2:0.105125,GCF_023573625_1_GCF_023573625.1_00403:0.00737923)n1:0.00189539,(GCF_003691675_1_GCF_003691675.1_00121:0.0115754,GCF_002008305_4_GCF_002008305.4_00397:0.00958762)n3:0.00189539)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000439_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000439_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46a5daa0b656e8d003a9d675e0d057ed84e53460
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000439_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00125:0.000805,GCF_023573625_1_GCF_023573625.1_00407:0.003929)n1:0.00648251,((GCF_020097155_1_GCF_020097155.1_02425:0.0919707,GCF_005280335_1_GCF_005280335.1_02556:0.0232203)n3:0.0074205,GCF_002008305_4_GCF_002008305.4_00401:0.0229457)n2:0.00648251)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000443_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000443_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad979710f3f7df1bb3771c6de756a3d00986f2cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000443_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00406:0.00251325,GCF_023573625_1_GCF_023573625.1_00412:0.00558375)n1:0.00082125,(GCF_003691675_1_GCF_003691675.1_00129:0.003464,(GCF_005280335_1_GCF_005280335.1_02550:0.00703525,GCF_020097155_1_GCF_020097155.1_02418:0.410177)n3:0.005961)n2:0.00082125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000445_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000445_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..094e079103a9df3d12cb044010d8d93292d64ed2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000445_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00411:0,GCF_003691675_1_GCF_003691675.1_00131:0)n1:0.00351012,(GCF_005280335_1_GCF_005280335.1_02548:0.0140337,(GCF_020097155_1_GCF_020097155.1_02416:0.0132228,GCF_023573625_1_GCF_023573625.1_00414:0.0115532)n3:0.0128158)n2:0.00351012)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000448_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000448_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..583f87fb6357136fdd2c028cf4157c5824a3fb8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000448_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00419:0.014288,GCF_003691675_1_GCF_003691675.1_00136:3.61996e-07)n1:0.0005215,((GCF_005280335_1_GCF_005280335.1_02544:0.036661,GCF_020097155_1_GCF_020097155.1_02412:0.270972)n3:0.041118,GCF_002008305_4_GCF_002008305.4_00416:3.61996e-07)n2:0.0005215)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000452_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000452_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..487ebf875d30e59d7e4e42ba78b5c4c226114a80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000452_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00421:0.00329475,GCF_005280335_1_GCF_005280335.1_02538:0.0557322)n1:0.000482585,(GCF_003691675_1_GCF_003691675.1_00142:0.0113504,(GCF_023573625_1_GCF_023573625.1_00424:0.0214167,GCF_020097155_1_GCF_020097155.1_02407:0.0189723)n3:0.00424476)n2:0.000482585)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000458_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000458_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2500fab2667d30537262d1c2dafde9bcc32ca58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000458_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00431:0.0094805,GCF_003691675_1_GCF_003691675.1_00149:0.0020195)n1:0.00120787,((GCF_005280335_1_GCF_005280335.1_02529:0.120055,GCF_020097155_1_GCF_020097155.1_02399:0.146044)n3:0.0934848,GCF_002008305_4_GCF_002008305.4_00428:0.00283525)n2:0.00120787)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000459_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000459_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69f20b438fd61c667fdae9c77387f9f05a147754
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000459_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02398:0.231722,GCF_005280335_1_GCF_005280335.1_02528:0.139618)n2:0.216688,GCF_003691675_1_GCF_003691675.1_00150:0.00469725)n1:0.00154912,(GCF_023573625_1_GCF_023573625.1_00432:0.00113125,GCF_002008305_4_GCF_002008305.4_00429:0.00275275)n3:0.00154912)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000460_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000460_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adb832c14d229d10e2050d4d9e180f7af190ff03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000460_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00430:0.0202096,GCF_003691675_1_GCF_003691675.1_00151:0.0214073)n1:0.0116966,(GCF_023573625_1_GCF_023573625.1_00433:0.0900755,(GCF_020097155_1_GCF_020097155.1_02397:0.514062,GCF_005280335_1_GCF_005280335.1_02527:0.53734)n3:0.310581)n2:0.0116966)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000462_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000462_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9831114dcfdef875b3e276d3941ea44890dd0a6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000462_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00436:0,GCF_003691675_1_GCF_003691675.1_00154:0)n1:0.000317375,((GCF_005280335_1_GCF_005280335.1_02524:0.0155617,GCF_020097155_1_GCF_020097155.1_02395:0.0612173)n3:0.0261982,GCF_002008305_4_GCF_002008305.4_00433:0.00307625)n2:0.000317375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000463_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000463_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4584f65998ab2fec05919f68fe32f34da4339bfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000463_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00437:0,GCF_002008305_4_GCF_002008305.4_00434:0)n1:0.000675705,((GCF_005280335_1_GCF_005280335.1_02523:0.010163,GCF_020097155_1_GCF_020097155.1_02394:0.022142)n3:0.0065442,GCF_003691675_1_GCF_003691675.1_00155:0.00333059)n2:0.000675705)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000465_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000465_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e4b61d931d5a3bd7a3384204765671f446cf8e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000465_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00157:0,GCF_002008305_4_GCF_002008305.4_00436:0)n1:0,(GCF_023573625_1_GCF_023573625.1_00439:0,(GCF_020097155_1_GCF_020097155.1_02392:0.0642015,GCF_005280335_1_GCF_005280335.1_02521:0.0152365)n3:0.0311105)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000467_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000467_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5452f51ee903455a40f0911d83c59164caa1e042
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000467_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00159:0,GCF_023573625_1_GCF_023573625.1_00441:0)n1:0.000743875,(GCF_002008305_4_GCF_002008305.4_00438:0.00156125,(GCF_005280335_1_GCF_005280335.1_02519:0.0575398,GCF_020097155_1_GCF_020097155.1_02390:0.119746)n3:0.0436952)n2:0.000743875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000472_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000472_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4204569571a4438a2cce60d094b6933266ee723
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000472_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00164:0.00572288,GCF_002008305_4_GCF_002008305.4_00443:0.00297712)n1:0.00398781,((GCF_020097155_1_GCF_020097155.1_02385:0.363377,GCF_005280335_1_GCF_005280335.1_02514:0.0971969)n3:0.0628021,GCF_023573625_1_GCF_023573625.1_00446:0.00072038)n2:0.00398781)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000475_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000475_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2b98dc20b1697965b9606079b5d7f199af32bbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000475_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00449:0.00203879,GCF_003691675_1_GCF_003691675.1_00167:0.00646521)n1:0.00036263,(GCF_002008305_4_GCF_002008305.4_00446:0.0110813,(GCF_020097155_1_GCF_020097155.1_02382:0.14091,GCF_005280335_1_GCF_005280335.1_02511:0.0267843)n3:0.0217924)n2:0.00036263)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000477_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000477_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f4ffd243ff9d184b9e3d6ff2da8f9c68c0b6fc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000477_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00452:0.0163414,GCF_003691675_1_GCF_003691675.1_00170:0.0396886)n1:0.0447134,(GCF_002008305_4_GCF_002008305.4_00449:0.0695816,(GCF_005280335_1_GCF_005280335.1_02507:0.143497,GCF_020097155_1_GCF_020097155.1_02379:0.459165)n3:0.296862)n2:0.0447134)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000479_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000479_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f68513120fbfe4af06e92c82e3f417c8b29d3b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000479_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00451:0.0272926,GCF_005280335_1_GCF_005280335.1_02505:0.0383604)n1:0.0308624,(GCF_020097155_1_GCF_020097155.1_02377:0.109494,(GCF_023573625_1_GCF_023573625.1_00454:0.00248713,GCF_003691675_1_GCF_003691675.1_00172:0.00076487)n3:0.0944959)n2:0.0308624)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000480_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000480_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..810ae408e4140c8d21016c01137ca6a453908a5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000480_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_02375:0.261543,GCF_002008305_4_GCF_002008305.4_00456:0.0096105)n1:0.0147315,(GCF_005280335_1_GCF_005280335.1_02491:0.005451,(GCF_003691675_1_GCF_003691675.1_00174:0,GCF_023573625_1_GCF_023573625.1_00456:0)n3:0.001021)n2:0.0147315)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000486_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000486_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c3a7082e6e2fd80e2bdb3ea2a3800dca0f0daf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000486_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00462:9.56692e-07,GCF_023573625_1_GCF_023573625.1_00462:0.00775494)n1:0.00051047,((GCF_005280335_1_GCF_005280335.1_02485:0.103052,GCF_020097155_1_GCF_020097155.1_02369:0.754648)n3:0.0912373,GCF_003691675_1_GCF_003691675.1_00180:0)n2:0.00051047)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000491_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000491_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f76f3906745a7637e1f7151441d38ae1e1a55a57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000491_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00468:0.00341875,GCF_002008305_4_GCF_002008305.4_00468:0.00525325)n1:0.00075975,(GCF_003691675_1_GCF_003691675.1_00186:0.0017325,(GCF_020097155_1_GCF_020097155.1_02363:0.151736,GCF_005280335_1_GCF_005280335.1_02479:0.104971)n3:0.078819)n2:0.00075975)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000492_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000492_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65de604d9e344dfb0d1054374a5d4bb9570cc555
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000492_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00469:0.009566,(GCF_005280335_1_GCF_005280335.1_02478:0.154772,GCF_020097155_1_GCF_020097155.1_02362:0.398684)n2:0.120115)n1:0.011524,(GCF_023573625_1_GCF_023573625.1_00469:0,GCF_003691675_1_GCF_003691675.1_00187:0)n3:0.011524)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000495_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000495_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09d02f1c84c7733dbea6ce4e7d10697693ccef15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000495_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00472:0.00697889,(GCF_020097155_1_GCF_020097155.1_02359:0.454294,GCF_005280335_1_GCF_005280335.1_02475:0.167757)n2:0.0774993)n1:0.00474955,(GCF_003691675_1_GCF_003691675.1_00190:0,GCF_002008305_4_GCF_002008305.4_00472:0)n3:0.00474955)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000496_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000496_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7d1e38ef6bf8e89bf468f78ff40f6be7ceeb6d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000496_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00473:0.00186909,(GCF_005280335_1_GCF_005280335.1_02474:0.052972,GCF_020097155_1_GCF_020097155.1_02358:0.044573)n2:0.010328)n1:0.00114795,(GCF_023573625_1_GCF_023573625.1_00473:0.00552606,GCF_003691675_1_GCF_003691675.1_00191:0.00054394)n3:0.00114795)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000497_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000497_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69c757a4a448dff8de22bd0e9f524afd481a287
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000497_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00474:5.96433e-07,GCF_002008305_4_GCF_002008305.4_00474:0.00138377)n1:0.0023478,(GCF_003691675_1_GCF_003691675.1_00192:0.00685818,(GCF_020097155_1_GCF_020097155.1_02357:0.45201,GCF_005280335_1_GCF_005280335.1_02473:0.0903662)n3:0.0412385)n2:0.0023478)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000499_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000499_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cec6a5f14c5ad3a270cc29e86a4b61f92dfc34a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000499_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02354:0.154453,GCF_005280335_1_GCF_005280335.1_02470:0.221355)n2:0.0573485,GCF_003691675_1_GCF_003691675.1_00195:0.0052575)n1:0.0014695,(GCF_002008305_4_GCF_002008305.4_00477:5e-07,GCF_023573625_1_GCF_023573625.1_00477:5e-07)n3:0.0014695)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000501_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000501_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1383eaa3adebefc722c4797bf618db3a7a8acfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000501_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00479:5e-07,GCF_002008305_4_GCF_002008305.4_00479:5e-07)n1:0.00205318,(GCF_003691675_1_GCF_003691675.1_00197:0.00869714,(GCF_005280335_1_GCF_005280335.1_02468:0.146077,GCF_020097155_1_GCF_020097155.1_02352:0.491515)n3:0.139361)n2:0.00205318)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000502_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000502_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d960287a1eff2d02bcfd3fa44752506baaf2547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000502_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02467:0.0627658,GCF_020097155_1_GCF_020097155.1_02351:0.370019)n2:0.101708,GCF_023573625_1_GCF_023573625.1_00480:0.0190754)n1:0.00653778,(GCF_003691675_1_GCF_003691675.1_00198:0.00705752,GCF_002008305_4_GCF_002008305.4_00480:0.0161655)n3:0.00653778)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000504_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000504_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d18a4bc50a16fbd47666b3fd85cdf857cd25e58e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000504_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00200:0,GCF_023573625_1_GCF_023573625.1_00482:0)n1:0,((GCF_005280335_1_GCF_005280335.1_02465:0.22192,GCF_020097155_1_GCF_020097155.1_02349:0.421856)n3:0.108573,GCF_002008305_4_GCF_002008305.4_00482:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000508_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000508_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..324ba3eb0f2b329cabf5ac02074276ce8a641b98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000508_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00205:0.00418075,GCF_002008305_4_GCF_002008305.4_00486:0.00680325)n1:0.001473,(GCF_023573625_1_GCF_023573625.1_00486:0.018715,(GCF_020097155_1_GCF_020097155.1_02344:0.218751,GCF_005280335_1_GCF_005280335.1_02461:0.0431742)n3:0.0424325)n2:0.001473)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000510_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000510_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2623b12414e655471c57318543ff86b838c0b8da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000510_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00211:0.0146121,GCF_002008305_4_GCF_002008305.4_00490:0.00375393)n1:0.00165367,(GCF_020097155_1_GCF_020097155.1_02341:0.180404,(GCF_023573625_1_GCF_023573625.1_00489:0.00038867,GCF_005280335_1_GCF_005280335.1_02457:0.00684233)n3:0.00581348)n2:0.00165367)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000511_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000511_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c2adddd4b8f8e46b8481b351a0f7deff5cb8228
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000511_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00491:0.00179825,GCF_023573625_1_GCF_023573625.1_00490:0.00359975)n1:0.00127925,(GCF_003691675_1_GCF_003691675.1_00212:0.0048905,(GCF_005280335_1_GCF_005280335.1_02456:0.0287158,GCF_020097155_1_GCF_020097155.1_02340:0.133666)n3:0.0332285)n2:0.00127925)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000514_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000514_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33a28379039dbce2981a775e3f8f6c786b1ce6b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000514_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00493:0.00534412,GCF_003691675_1_GCF_003691675.1_00215:0.00700988)n1:0.00048919,(GCF_002008305_4_GCF_002008305.4_00494:0.00860662,(GCF_020097155_1_GCF_020097155.1_02337:0.146668,GCF_005280335_1_GCF_005280335.1_02453:0.0248236)n3:0.0208639)n2:0.00048919)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000515_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000515_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86fc8149e71e4e6fdea3afa4900129c3ba9fbb43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000515_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02450:0.0412303,GCF_020097155_1_GCF_020097155.1_02334:0.0889297)n2:0.0503535,GCF_003691675_1_GCF_003691675.1_00218:0.0106184)n1:0.00123357,(GCF_023573625_1_GCF_023573625.1_00496:0.00041239,GCF_002008305_4_GCF_002008305.4_00497:0.00330261)n3:0.00123357)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000517_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000517_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb581add705e9a6e6a8698747a08687f45c7788a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000517_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00501:0.00293413,GCF_003691675_1_GCF_003691675.1_00222:0.00499487)n1:0.00431136,(GCF_023573625_1_GCF_023573625.1_00500:0.0126722,(GCF_020097155_1_GCF_020097155.1_02332:0.336984,GCF_005280335_1_GCF_005280335.1_02448:0.066944)n3:0.0863845)n2:0.00431136)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000522_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000522_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e366025b1590e8c19eb5b45a021f843def91865f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000522_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00227:0.0129649,GCF_023573625_1_GCF_023573625.1_00506:0.00753309)n1:0.00211797,((GCF_020097155_1_GCF_020097155.1_02327:0.0941865,GCF_005280335_1_GCF_005280335.1_02443:0.0696755)n3:0.111751,GCF_002008305_4_GCF_002008305.4_00507:0.0223439)n2:0.00211797)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000524_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000524_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69b6d43e22cb8beaaf071f43f42dfb48a45888d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000524_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00231:0.0345389,GCF_023573625_1_GCF_023573625.1_00510:0.0355691)n1:0.00359324,(GCF_020097155_1_GCF_020097155.1_02323:0.580493,(GCF_005280335_1_GCF_005280335.1_02440:0.0266115,GCF_002008305_4_GCF_002008305.4_00511:0.0153935)n3:0.0195146)n2:0.00359324)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000535_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000535_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7becb0b075f792f5e86fb63a4cb618cf834de25f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000535_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02301:0.403077,GCF_005280335_1_GCF_005280335.1_02419:0.212229)n2:0.159743,GCF_002008305_4_GCF_002008305.4_00533:0.0109608)n1:0.00905113,(GCF_003691675_1_GCF_003691675.1_00254:0.0106035,GCF_023573625_1_GCF_023573625.1_00533:0.0175375)n3:0.00905113)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000536_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000536_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c26edcbb36b6756e6a1fcdf29e008cd5be3b83bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000536_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00537:0.0406699,GCF_003691675_1_GCF_003691675.1_00258:0.0209481)n1:0.0127519,(GCF_002008305_4_GCF_002008305.4_00534:0.0332791,(GCF_020097155_1_GCF_020097155.1_02297:0.884894,GCF_005280335_1_GCF_005280335.1_02415:0.318586)n3:0.162248)n2:0.0127519)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000537_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000537_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5485abfe4f6507c9a5371ce74b4c57d6eb441a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000537_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00535:5.14898e-07,GCF_003691675_1_GCF_003691675.1_00259:0.0170025)n1:0.00648875,(GCF_023573625_1_GCF_023573625.1_00538:0.012047,(GCF_020097155_1_GCF_020097155.1_02296:0.329316,GCF_005280335_1_GCF_005280335.1_02414:0.051533)n3:0.0950005)n2:0.00648875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000541_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000541_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2aa00791fc5760bb757b322b3fd4aa0f80a09b73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000541_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00543:0.00431716,GCF_002008305_4_GCF_002008305.4_00540:2.93176e-07)n1:0.00283292,((GCF_005280335_1_GCF_005280335.1_02409:0.0722962,GCF_020097155_1_GCF_020097155.1_02291:0.132506)n3:0.0740394,GCF_003691675_1_GCF_003691675.1_00264:0.00478432)n2:0.00283292)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000543_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000543_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cec4843add170be05de2f3664dac80ba1752ae69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000543_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00268:0.00569396,GCF_023573625_1_GCF_023573625.1_00546:0.016034)n1:0.00680387,(GCF_002008305_4_GCF_002008305.4_00543:0.0168884,(GCF_005280335_1_GCF_005280335.1_02404:0.14325,GCF_020097155_1_GCF_020097155.1_02287:0.361768)n3:0.209749)n2:0.00680387)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000547_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000547_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7053f0602c3864b9c8b918c24dfc74ac29a0e562
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000547_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00548:0.00297812,GCF_023573625_1_GCF_023573625.1_00551:0.00148687)n1:0.00781519,(GCF_003691675_1_GCF_003691675.1_00273:0.00386763,(GCF_020097155_1_GCF_020097155.1_02282:0.426226,GCF_005280335_1_GCF_005280335.1_02398:0.0840836)n3:0.126231)n2:0.00781519)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000551_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000551_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75b90068602076dfa7779ac8b7cbe3534974c6e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000551_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00278:0,GCF_002008305_4_GCF_002008305.4_00553:0)n1:0.00374137,(GCF_023573625_1_GCF_023573625.1_00556:0.0200752,(GCF_020097155_1_GCF_020097155.1_02277:0.149805,GCF_005280335_1_GCF_005280335.1_02392:0.141148)n3:0.498513)n2:0.00374137)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000552_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000552_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adc4bba2aaacdd6bc74b04bbe6de186cf3c1d817
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000552_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02273:0.103145,GCF_005280335_1_GCF_005280335.1_02390:0.117992)n2:0.0286323,GCF_003691675_1_GCF_003691675.1_00280:0.00543675)n1:0.00120312,(GCF_002008305_4_GCF_002008305.4_00555:0,GCF_023573625_1_GCF_023573625.1_00558:0)n3:0.00120312)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000553_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000553_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8efa6a1e333afef55087678aa85ceecde9c641da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000553_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00281:0.0015893,GCF_002008305_4_GCF_002008305.4_00556:0.0063037)n1:0.00163605,(GCF_023573625_1_GCF_023573625.1_00559:0.00667015,(GCF_005280335_1_GCF_005280335.1_02389:0.0313912,GCF_020097155_1_GCF_020097155.1_02272:0.127198)n3:0.0346502)n2:0.00163605)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000555_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000555_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e37c3d017e774d38bf7cec9a6f958346f782b0db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000555_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00561:0.004662,GCF_003691675_1_GCF_003691675.1_00283:0.004458)n1:0.0018235,((GCF_005280335_1_GCF_005280335.1_02385:0.159167,GCF_020097155_1_GCF_020097155.1_02269:0.215733)n3:0.107136,GCF_002008305_4_GCF_002008305.4_00558:0.0277455)n2:0.0018235)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000556_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000556_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55b58cae19749dcab04f038a6d61fd9652395c72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000556_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00562:0.0111969,(GCF_005280335_1_GCF_005280335.1_02384:0.10891,GCF_020097155_1_GCF_020097155.1_02268:0.132258)n2:0.0851656)n1:0.00143907,(GCF_003691675_1_GCF_003691675.1_00284:0.0201266,GCF_002008305_4_GCF_002008305.4_00559:0.00236237)n3:0.00143907)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000557_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000557_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0c1442b6a0458d3a9193659057b49ab7d44cd12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000557_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02383:0.0411742,GCF_020097155_1_GCF_020097155.1_02267:0.0799088)n2:0.0307029,GCF_023573625_1_GCF_023573625.1_00563:0.0251001)n1:0.0045177,(GCF_003691675_1_GCF_003691675.1_00285:0.00209634,GCF_002008305_4_GCF_002008305.4_00560:0.0142017)n3:0.0045177)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000558_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000558_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34c2f8beadd5afc381df767a5b0849aa7e77dece
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000558_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00286:0.00125963,GCF_002008305_4_GCF_002008305.4_00561:0.00381237)n1:0.00169956,(GCF_023573625_1_GCF_023573625.1_00564:0.00224688,(GCF_005280335_1_GCF_005280335.1_02382:0.135349,GCF_020097155_1_GCF_020097155.1_02266:0.163445)n3:0.0400021)n2:0.00169956)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000562_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000562_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d15b8136bd691da7b9195d01f199dfbdfd20cb2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000562_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00568:0,GCF_002008305_4_GCF_002008305.4_00565:0)n1:0.0266239,((GCF_005280335_1_GCF_005280335.1_02378:0.124591,GCF_020097155_1_GCF_020097155.1_02262:0.151455)n3:0.0360227,GCF_003691675_1_GCF_003691675.1_00290:0.00747612)n2:0.0266239)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000564_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000564_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..988492149dcf23e50d31bdd703141d70dcb9db22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000564_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00567:0.168457,GCF_020097155_1_GCF_020097155.1_02260:0.127043)n1:0.129509,((GCF_003691675_1_GCF_003691675.1_00292:0.0111956,GCF_023573625_1_GCF_023573625.1_00570:0.0145934)n3:0.0794074,GCF_005280335_1_GCF_005280335.1_02376:0.0531912)n2:0.129509)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000567_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000567_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07de777fadba02410ab9928842df0346d7435f1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000567_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00306:0.00716506,GCF_023573625_1_GCF_023573625.1_00575:0.00834594)n1:0.00105565,(GCF_002008305_4_GCF_002008305.4_00574:0.0147081,(GCF_005280335_1_GCF_005280335.1_02359:0.0684367,GCF_020097155_1_GCF_020097155.1_02250:0.0602833)n3:0.0295285)n2:0.00105565)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000571_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000571_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49dba79789d6a69c3a9f2f9049025161d5559394
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000571_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00316:0.00192181,GCF_023573625_1_GCF_023573625.1_00584:0.00726919)n1:0.00097195,((GCF_005280335_1_GCF_005280335.1_02351:0.0322092,GCF_020097155_1_GCF_020097155.1_02246:0.116711)n3:0.033705,GCF_002008305_4_GCF_002008305.4_00583:0.0033943)n2:0.00097195)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000575_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000575_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d53ce43f09d73ccd637f283f821eb046bdf1af31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000575_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_00634:0,((GCF_023573625_1_GCF_023573625.1_00597:0.093024,(GCF_005280335_1_GCF_005280335.1_00406:0,GCF_005280335_1_GCF_005280335.1_00753:1.62438)n3:0.180487)n2:0.011113,GCF_020097155_1_GCF_020097155.1_02195:0)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000578_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000578_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03c5e2c9c49da59cd2d7843ca61e68c5d1cb8435
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000578_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00378:0.0024245,GCF_023573625_1_GCF_023573625.1_00611:0.0073005)n1:0.00164625,(GCF_005280335_1_GCF_005280335.1_02321:0.0847823,(GCF_020097155_1_GCF_020097155.1_02184:0.0900827,GCF_002008305_4_GCF_002008305.4_00641:1.93337e-07)n3:0.00556641)n2:0.00164625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000579_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000579_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71faabafc02f24555706f7218e91db273fc85134
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000579_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00379:0.00213475,GCF_002008305_4_GCF_002008305.4_00642:0.00606825)n1:0.00185563,(GCF_005280335_1_GCF_005280335.1_02320:0.1387,(GCF_023573625_1_GCF_023573625.1_00612:0.00630525,GCF_020097155_1_GCF_020097155.1_02183:0.00601775)n3:0.00540625)n2:0.00185563)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000581_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000581_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cbb50fa89db46ca54bb9577d65a7fa1d2cc3890
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000581_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00615:0.013415,(GCF_005280335_1_GCF_005280335.1_02318:0.0521443,GCF_020097155_1_GCF_020097155.1_02177:0.251463)n2:0.006698)n1:0.0122265,(GCF_002008305_4_GCF_002008305.4_00645:3.50105e-07,GCF_003691675_1_GCF_003691675.1_00382:0.002734)n3:0.0122265)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000582_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000582_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e2b9d0735ab14b99ce5b18d67b83bc55df33782
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000582_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00647:0.0008285,GCF_003691675_1_GCF_003691675.1_00384:0.0016875)n1:0.00154237,((GCF_020097155_1_GCF_020097155.1_02175:0.217732,GCF_005280335_1_GCF_005280335.1_02316:0.0234133)n3:0.0425102,GCF_023573625_1_GCF_023573625.1_00617:0.00575925)n2:0.00154237)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000584_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000584_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ab3d21809253dd4da5fdf45106162bbf1508c1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000584_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00388:0.0204016,GCF_023573625_1_GCF_023573625.1_00621:0.00998937)n1:0.0213983,(GCF_002008305_4_GCF_002008305.4_00651:0.0465206,(GCF_020097155_1_GCF_020097155.1_02169:0.523564,GCF_005280335_1_GCF_005280335.1_02312:0.324887)n3:0.230785)n2:0.0213983)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000585_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000585_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9b7e3439333a30d31a27fb6d301dbefa0fcf4fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000585_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02311:0.0191222,GCF_020097155_1_GCF_020097155.1_02168:0.0647518)n2:0.0062191,GCF_003691675_1_GCF_003691675.1_00389:0.0100258)n1:0.0021221,(GCF_002008305_4_GCF_002008305.4_00652:0,GCF_023573625_1_GCF_023573625.1_00622:0)n3:0.0021221)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000587_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000587_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc2cfdbc0d97f3e9164ae2f374eb1eaf84f0e8b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000587_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02166:0.135398,GCF_005280335_1_GCF_005280335.1_02309:0.0204605)n2:0.0111925,GCF_003691675_1_GCF_003691675.1_00391:-0)n1:0,(GCF_002008305_4_GCF_002008305.4_00654:0,GCF_023573625_1_GCF_023573625.1_00624:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000588_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000588_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90e1fe769c5a6486b71b7745382537d5154092c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000588_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00392:0,GCF_023573625_1_GCF_023573625.1_00625:0)n1:0,(GCF_002008305_4_GCF_002008305.4_00655:0,(GCF_020097155_1_GCF_020097155.1_02165:0.076315,GCF_005280335_1_GCF_005280335.1_02308:0.010013)n3:0.021356)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000591_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000591_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75049275f34703bf5bd01cd2e01f8f07368da505
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000591_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00659:0.00346594,GCF_003691675_1_GCF_003691675.1_00396:0.00308706)n1:0.00011089,((GCF_005280335_1_GCF_005280335.1_02304:0.0133433,GCF_020097155_1_GCF_020097155.1_02160:0.141751)n3:0.0181613,GCF_023573625_1_GCF_023573625.1_00629:0.00014467)n2:0.00011089)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000592_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000592_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..261ef0810d9ac04fd6290956b83234b3a9afb20a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000592_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00397:0.00449426,GCF_002008305_4_GCF_002008305.4_00660:0.00188074)n1:0.0128638,((GCF_005280335_1_GCF_005280335.1_02303:0.088595,GCF_020097155_1_GCF_020097155.1_02159:0.399006)n3:0.0419303,GCF_023573625_1_GCF_023573625.1_00630:0.0230463)n2:0.0128638)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000594_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000594_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0ab31aa15488c67d37a5e48bab2e4ece83a25fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000594_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00662:0.00799913,GCF_003691675_1_GCF_003691675.1_00399:0.00275787)n1:0.00219259,(GCF_023573625_1_GCF_023573625.1_00632:0.00910144,(GCF_005280335_1_GCF_005280335.1_02301:0.118487,GCF_020097155_1_GCF_020097155.1_02157:0.441604)n3:0.099547)n2:0.00219259)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000595_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000595_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7b7635c5e40d1e6c1103dc4fc15810746a1448e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000595_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02299:0.0956002,GCF_005280335_1_GCF_005280335.1_01220:2.82543)n2:0.065718,GCF_002008305_4_GCF_002008305.4_00664:0.0324125)n1:0.0173853,(GCF_023573625_1_GCF_023573625.1_00634:0.00059625,GCF_003691675_1_GCF_003691675.1_00401:0.00211575)n3:0.0173853)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000596_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000596_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8396cb83d7f7df10caef865bf747069abd16ca3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000596_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00405:0.00296362,GCF_002008305_4_GCF_002008305.4_00668:0.00791838)n1:0.00651518,(GCF_023573625_1_GCF_023573625.1_00638:0.00343313,(GCF_005280335_1_GCF_005280335.1_02294:0.0321339,GCF_020097155_1_GCF_020097155.1_02156:0.202338)n3:0.0488994)n2:0.00651518)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000598_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000598_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a3c3492f71dc2eedb9f0354ec65a576d3394700
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000598_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02292:0.0702395,GCF_020097155_1_GCF_020097155.1_02154:0.140918)n2:0.0854532,GCF_003691675_1_GCF_003691675.1_00407:0.00945475)n1:0.00240938,(GCF_002008305_4_GCF_002008305.4_00670:0.00599275,GCF_023573625_1_GCF_023573625.1_00640:0.00094125)n3:0.00240938)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000603_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000603_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b0c7de9e03d6c8f8346ccdeb2d4c3e7064bf902
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000603_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00645:0,GCF_002008305_4_GCF_002008305.4_00675:0)n1:0.00171775,(GCF_003691675_1_GCF_003691675.1_00412:3.83476e-07,(GCF_020097155_1_GCF_020097155.1_02149:0.315493,GCF_005280335_1_GCF_005280335.1_02287:0.0210865)n3:0.0435183)n2:0.00171775)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000604_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000604_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59d6dbd8a9b2545ceac39a80991ea53495e99612
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000604_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00413:0,GCF_002008305_4_GCF_002008305.4_00676:0)n1:0.00325262,((GCF_005280335_1_GCF_005280335.1_02286:0.109873,GCF_020097155_1_GCF_020097155.1_02148:0.413846)n3:0.127323,GCF_023573625_1_GCF_023573625.1_00646:0.00038275)n2:0.00325262)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000608_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000608_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e345b4ab587b72b157188ff1c71ee26102c95c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000608_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00418:0.00389725,GCF_002008305_4_GCF_002008305.4_00681:2.93947e-07)n1:0.00038525,((GCF_005280335_1_GCF_005280335.1_02282:0.0444507,GCF_020097155_1_GCF_020097155.1_02143:0.22234)n3:0.02044,GCF_023573625_1_GCF_023573625.1_00651:0.002365)n2:0.00038525)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000609_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000609_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4fde880e9b390ae761fc350daabfce8f25e9090
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000609_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00682:0,GCF_003691675_1_GCF_003691675.1_00419:0)n1:0,(GCF_023573625_1_GCF_023573625.1_00652:0,(GCF_005280335_1_GCF_005280335.1_02281:0.034995,GCF_020097155_1_GCF_020097155.1_02142:0.106206)n3:0.060085)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000611_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000611_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d59d2c8273db14c0ed35a783ffa31401b8332681
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000611_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00421:0,GCF_002008305_4_GCF_002008305.4_00684:0)n1:0.00195713,(GCF_023573625_1_GCF_023573625.1_00654:0.00235275,(GCF_020097155_1_GCF_020097155.1_02140:0.182165,GCF_005280335_1_GCF_005280335.1_02279:0.0620412)n3:0.0881943)n2:0.00195713)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000612_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000612_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcc5cdb9900b56414b6def40e2e71744864133fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000612_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02278:0.159371,GCF_020097155_1_GCF_020097155.1_02139:0.23186)n2:0.135532,GCF_023573625_1_GCF_023573625.1_00655:0.0103229)n1:0.0032048,(GCF_003691675_1_GCF_003691675.1_00422:0.00152737,GCF_002008305_4_GCF_002008305.4_00685:0.0195166)n3:0.0032048)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000614_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000614_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc95c74491d57452a7a1d2c5d82050aaa956e73f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000614_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00687:0,(GCF_023573625_1_GCF_023573625.1_00657:0,GCF_005280335_1_GCF_005280335.1_02270:0)n2:0)n1:0,(GCF_020097155_1_GCF_020097155.1_02137:0,GCF_003691675_1_GCF_003691675.1_00424:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000619_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000619_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e24407ea3085f358a1584ca1cba956bc497f49c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000619_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00430:0.0032663,GCF_023573625_1_GCF_023573625.1_00663:0.0055447)n1:0.001222,(GCF_002008305_4_GCF_002008305.4_00693:0.0033592,(GCF_020097155_1_GCF_020097155.1_02131:0.169002,GCF_005280335_1_GCF_005280335.1_02261:0.035461)n3:0.0182221)n2:0.001222)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000621_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000621_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..452d5c4813950fcd1329713217d2ef48c8971bce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000621_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00665:0.0128395,GCF_002008305_4_GCF_002008305.4_00695:0.0199915)n1:0.0178195,(GCF_003691675_1_GCF_003691675.1_00432:0.0191118,(GCF_005280335_1_GCF_005280335.1_02259:0.186318,GCF_020097155_1_GCF_020097155.1_02130:0.211642)n3:0.0977)n2:0.0178195)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000623_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000623_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f117cecc1fbf07b6cd9fc91b789349fb8f4a466d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000623_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00697:0.0412383,(GCF_020097155_1_GCF_020097155.1_02128:0.513183,GCF_005280335_1_GCF_005280335.1_02257:0.128444)n2:0.165221)n1:0.00392886,(GCF_023573625_1_GCF_023573625.1_00667:0.0277173,GCF_003691675_1_GCF_003691675.1_00434:0.00792266)n3:0.00392886)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000626_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000626_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96b906d35eee222c685db09dc5856a00e2d6263a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000626_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00704:1.00671e-07,(GCF_020097155_1_GCF_020097155.1_02125:0.075227,GCF_005280335_1_GCF_005280335.1_02253:0.014369)n2:0.00885275)n1:9.875e-06,(GCF_023573625_1_GCF_023573625.1_00671:0.00224175,GCF_003691675_1_GCF_003691675.1_00438:1.00671e-07)n3:9.875e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000630_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000630_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c762fa8b8fd7c501e4eb1b2284c7041d88a7c2de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000630_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00442:0.00380038,(GCF_020097155_1_GCF_020097155.1_02121:0.0140979,GCF_005280335_1_GCF_005280335.1_02249:0.167687)n2:0.00136812)n1:0.00145306,(GCF_002008305_4_GCF_002008305.4_00708:0.00516987,GCF_023573625_1_GCF_023573625.1_00675:0.00509312)n3:0.00145306)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000632_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000632_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6d1be7ed97bfb91c34696b5034c0f474253a0b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000632_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00710:0.26989,(GCF_020097155_1_GCF_020097155.1_02118:0.014649,GCF_005280335_1_GCF_005280335.1_02245:0.055586)n2:0.246693)n1:0.0517829,(GCF_023573625_1_GCF_023573625.1_00677:0,GCF_003691675_1_GCF_003691675.1_00444:0)n3:0.0517829)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000634_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000634_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..add29ce5c86bbe0fe7f9a9f7af4a781aad22f70d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000634_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00679:0.00329744,GCF_003691675_1_GCF_003691675.1_00446:7.356e-05)n1:0.00220087,(GCF_002008305_4_GCF_002008305.4_00715:0.00565349,(GCF_005280335_1_GCF_005280335.1_02243:0.0331222,GCF_020097155_1_GCF_020097155.1_02115:0.0965708)n3:0.027334)n2:0.00220087)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000638_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000638_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f1e4380a7670573ab7360816cf805ddf1c93cbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000638_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00450:6.30931e-08,(GCF_020097155_1_GCF_020097155.1_02111:0.0458856,GCF_005280335_1_GCF_005280335.1_02239:0.0119164)n2:0.00162312)n1:1.9315e-05,(GCF_023573625_1_GCF_023573625.1_00683:0.00370663,GCF_002008305_4_GCF_002008305.4_00719:6.30931e-08)n3:1.9315e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000642_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000642_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d732f5a97ef36d932c1de6489a9fc7179507f27f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000642_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00723:0.00492125,GCF_023573625_1_GCF_023573625.1_00687:0.00426475)n1:0.0040765,(GCF_003691675_1_GCF_003691675.1_00454:0.0171335,(GCF_005280335_1_GCF_005280335.1_02235:0.050226,GCF_020097155_1_GCF_020097155.1_02107:0.187986)n3:0.053627)n2:0.0040765)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000643_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000643_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e079606fcf9b3480a1bed833fbae92cfcc30d9d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000643_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00455:0,GCF_002008305_4_GCF_002008305.4_00724:0)n1:0,((GCF_020097155_1_GCF_020097155.1_02106:0.579025,GCF_005280335_1_GCF_005280335.1_02234:0.103054)n3:0.124133,GCF_023573625_1_GCF_023573625.1_00688:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000646_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000646_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92c56e9cef6894404ee71ff67a0609812b20b17b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000646_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00691:0,GCF_002008305_4_GCF_002008305.4_00727:0)n1:0,(GCF_003691675_1_GCF_003691675.1_00458:0,(GCF_020097155_1_GCF_020097155.1_02103:0.0723905,GCF_005280335_1_GCF_005280335.1_02231:0.0416935)n3:0.0464835)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000647_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000647_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..feb8b475f6da13ba973fd2f9155d2802d69206c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000647_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02102:0.301533,GCF_005280335_1_GCF_005280335.1_02229:0.0650397)n2:0.0992681,GCF_003691675_1_GCF_003691675.1_00459:0.00584837)n1:0.00431681,(GCF_023573625_1_GCF_023573625.1_00692:0,GCF_002008305_4_GCF_002008305.4_00728:0)n3:0.00431681)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000648_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000648_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e5a8a41dd954c6c0a281755474cfc666a25a4ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000648_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00729:0,GCF_023573625_1_GCF_023573625.1_00693:0)n1:0.00364363,((GCF_005280335_1_GCF_005280335.1_02226:0.0995277,GCF_020097155_1_GCF_020097155.1_02100:0.224163)n3:0.0894738,GCF_003691675_1_GCF_003691675.1_00460:0.00521275)n2:0.00364363)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000649_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000649_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04c30975cf6407abaf221dcbf1df1c3bed1d36b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000649_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02223:0.212489,GCF_020097155_1_GCF_020097155.1_02099:0.241131)n2:0.121554,GCF_003691675_1_GCF_003691675.1_00461:0.00763025)n1:0.00173338,(GCF_023573625_1_GCF_023573625.1_00694:0.001963,GCF_002008305_4_GCF_002008305.4_00730:0.008427)n3:0.00173338)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000653_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000653_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fb09384555279593ddd2767d46712240f021207
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000653_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00466:0,GCF_002008305_4_GCF_002008305.4_00735:0)n1:0.0029768,(GCF_023573625_1_GCF_023573625.1_00699:0.00182839,(GCF_005280335_1_GCF_005280335.1_02195:0.106969,GCF_020097155_1_GCF_020097155.1_02094:0.322879)n3:0.0854001)n2:0.0029768)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000654_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000654_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..011505bb7ff4ba4bf98cc77129e083e976fe00f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000654_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02194:0.0822363,GCF_020097155_1_GCF_020097155.1_02093:0.355803)n2:0.0822143,GCF_003691675_1_GCF_003691675.1_00467:0.027699)n1:0.00765051,(GCF_002008305_4_GCF_002008305.4_00736:0.0118653,GCF_023573625_1_GCF_023573625.1_00700:0.0181857)n3:0.00765051)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000655_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000655_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..998b1b3256e1a87f77483e966aa0330fd4552f76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000655_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02092:0.625853,GCF_005280335_1_GCF_005280335.1_02193:0.182531)n2:0.147251,GCF_023573625_1_GCF_023573625.1_00701:0.00952475)n1:0.00195862,(GCF_002008305_4_GCF_002008305.4_00737:0,GCF_003691675_1_GCF_003691675.1_00468:0)n3:0.00195862)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000656_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000656_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..867ca6d9f4d18394d9578632e0a3ae7db9af326f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000656_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02091:0.636554,GCF_005280335_1_GCF_005280335.1_02192:0.136716)n2:0.147209,GCF_023573625_1_GCF_023573625.1_00702:0.008775)n1:0.0151155,(GCF_003691675_1_GCF_003691675.1_00469:0.00553025,GCF_002008305_4_GCF_002008305.4_00738:0.00174275)n3:0.0151155)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000664_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000664_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9ed0e2d631472f135fef745a8723f60d0f15e1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000664_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00715:0.00229275,(GCF_005280335_1_GCF_005280335.1_02179:0.0355035,GCF_020097155_1_GCF_020097155.1_02074:0.159394)n2:0.0140693)n1:0.000997375,(GCF_003691675_1_GCF_003691675.1_00481:0.00297175,GCF_002008305_4_GCF_002008305.4_00751:0.00559325)n3:0.000997375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000665_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000665_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc9dcc836697c7fd8a77292b0b74f1e9db82f60e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000665_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00752:0.00723938,GCF_003691675_1_GCF_003691675.1_00482:0.0164726)n1:0.000602815,((GCF_005280335_1_GCF_005280335.1_02178:0.150255,GCF_020097155_1_GCF_020097155.1_02073:0.385408)n3:0.134216,GCF_023573625_1_GCF_023573625.1_00716:0.0185139)n2:0.000602815)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000667_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000667_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a2dcb15de146b0c7d23cd881847d097bf3b08e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000667_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00718:0.00055213,GCF_003691675_1_GCF_003691675.1_00484:0.0102009)n1:0.0222689,((GCF_005280335_1_GCF_005280335.1_02176:0.127263,GCF_020097155_1_GCF_020097155.1_02071:0.293591)n3:0.0873744,GCF_002008305_4_GCF_002008305.4_00754:0.0198001)n2:0.0222689)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000669_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000669_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c8a3f78197a165fad9140ecf50cca04a80ba6dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000669_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00720:0.00836575,GCF_002008305_4_GCF_002008305.4_00756:0.00778825)n1:0.000811625,(GCF_003691675_1_GCF_003691675.1_00486:0.00440825,(GCF_020097155_1_GCF_020097155.1_02069:0.139023,GCF_005280335_1_GCF_005280335.1_02174:0.0396492)n3:0.0186942)n2:0.000811625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000670_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000670_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b130957284b03aea36124f7a3ce2924e69c76d67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000670_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00487:0.00240287,GCF_002008305_4_GCF_002008305.4_00757:0.00290813)n1:0.000838065,(GCF_023573625_1_GCF_023573625.1_00721:0.00739588,(GCF_005280335_1_GCF_005280335.1_02173:0.0485741,GCF_020097155_1_GCF_020097155.1_02068:0.216378)n3:0.0523776)n2:0.000838065)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000671_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000671_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a31a78d6563ba546562b72cfddabddb2007ce028
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000671_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02172:0.0646792,GCF_020097155_1_GCF_020097155.1_02067:0.125998)n2:0.0609502,GCF_023573625_1_GCF_023573625.1_00722:0.00352775)n1:0.00419912,(GCF_003691675_1_GCF_003691675.1_00488:0,GCF_002008305_4_GCF_002008305.4_00758:0)n3:0.00419912)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000676_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000676_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a15bf7e33e3cf85cdf2be4e9ab3d172d60d47858
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000676_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00764:0.00604348,(GCF_020097155_1_GCF_020097155.1_02061:0.277747,GCF_005280335_1_GCF_005280335.1_02165:0.181608)n2:0.171021)n1:0.00355851,(GCF_003691675_1_GCF_003691675.1_00494:6.52229e-07,GCF_023573625_1_GCF_023573625.1_00728:0.00903993)n3:0.00355851)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000681_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000681_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11f8a0689b90037bb5c1a02a31b49ee0857c9fe3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000681_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_02054:0.0371575,(GCF_023573625_1_GCF_023573625.1_00738:0.00769217,GCF_005280335_1_GCF_005280335.1_02159:0.00900983)n2:0.009275)n1:0.000832995,(GCF_003691675_1_GCF_003691675.1_00502:0.00620608,GCF_002008305_4_GCF_002008305.4_00771:0.00118592)n3:0.000832995)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000683_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000683_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6c6621efd686e3c523229a2d429e25b9329f79c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000683_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00740:3.73122e-07,GCF_002008305_4_GCF_002008305.4_00773:0.00236262)n1:0.00174394,(GCF_003691675_1_GCF_003691675.1_00504:0.00138912,(GCF_005280335_1_GCF_005280335.1_02157:0.0490044,GCF_020097155_1_GCF_020097155.1_02052:0.281487)n3:0.0358034)n2:0.00174394)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000684_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000684_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a3e3cb1c3b4e7ff1fc56753e9b31acec565af80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000684_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00775:0,GCF_003691675_1_GCF_003691675.1_00506:0)n1:0.0107157,(GCF_005280335_1_GCF_005280335.1_02155:0.0437955,(GCF_020097155_1_GCF_020097155.1_02050:0.0574675,GCF_023573625_1_GCF_023573625.1_00742:0.0198195)n3:0.002446)n2:0.0107157)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000690_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000690_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc84469bf2ecb74f8d145caf3b2d23b4bca3a3e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000690_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00781:0.00282575,GCF_003691675_1_GCF_003691675.1_00512:0.00255925)n1:0.00823113,(GCF_023573625_1_GCF_023573625.1_00748:0.00794875,(GCF_005280335_1_GCF_005280335.1_02149:0.0224145,GCF_020097155_1_GCF_020097155.1_02043:0.203247)n3:0.0103147)n2:0.00823113)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000691_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000691_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e721408343d9747e66880a69cbdcbc5a476b33f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000691_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00749:0.00017388,GCF_002008305_4_GCF_002008305.4_00782:2.36542e-07)n1:8.694e-05,(GCF_003691675_1_GCF_003691675.1_00513:2.36542e-07,(GCF_020097155_1_GCF_020097155.1_02042:0.180094,GCF_005280335_1_GCF_005280335.1_02148:0.0295279)n3:0.0269204)n2:8.694e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000692_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000692_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bbc087e72707fec56007524daed55e791fd1c5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000692_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02147:0.014508,GCF_020097155_1_GCF_020097155.1_02041:0.069583)n2:0.0238085,GCF_003691675_1_GCF_003691675.1_00514:5e-07)n1:0,(GCF_002008305_4_GCF_002008305.4_00783:5e-07,GCF_023573625_1_GCF_023573625.1_00750:5e-07)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000697_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000697_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..abcf46b36c72ef8b4e9f65625bd6600e54838079
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000697_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00756:0.00580827,(GCF_005280335_1_GCF_005280335.1_02142:0.0848205,GCF_020097155_1_GCF_020097155.1_02035:0.255331)n2:0.102704)n1:0.00445887,(GCF_003691675_1_GCF_003691675.1_00520:0,GCF_002008305_4_GCF_002008305.4_00789:0)n3:0.00445887)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000699_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000699_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fb3d89ca85a23ea5845bb136eea55682e9ca614
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000699_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00522:0,GCF_002008305_4_GCF_002008305.4_00791:0)n1:0.00020647,(GCF_023573625_1_GCF_023573625.1_00758:0.00251706,(GCF_020097155_1_GCF_020097155.1_02033:0.160578,GCF_005280335_1_GCF_005280335.1_02140:0.016194)n3:0.011102)n2:0.00020647)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000700_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000700_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f51eab3c49673812eee003977d5a11a94582a8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000700_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00523:0,(GCF_020097155_1_GCF_020097155.1_02032:0.049126,GCF_023573625_1_GCF_023573625.1_00759:0)n2:0)n1:0,(GCF_005280335_1_GCF_005280335.1_02139:0,GCF_002008305_4_GCF_002008305.4_00792:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000703_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000703_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82846c2391516edf00f5cfd0c73d79695df4ed45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000703_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00795:0.00263862,(GCF_020097155_1_GCF_020097155.1_02029:0.0623346,GCF_005280335_1_GCF_005280335.1_02136:0.0183864)n2:0.0125109)n1:0.00067244,(GCF_023573625_1_GCF_023573625.1_00762:9.86184e-08,GCF_003691675_1_GCF_003691675.1_00526:0.00159613)n3:0.00067244)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000704_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000704_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4833732e8e8c63b6be887fa5e7e146760784619b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000704_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00527:0,GCF_002008305_4_GCF_002008305.4_00796:0)n1:0.000153305,(GCF_023573625_1_GCF_023573625.1_00763:0.00329739,(GCF_020097155_1_GCF_020097155.1_02028:0.0608482,GCF_005280335_1_GCF_005280335.1_02135:0.0116748)n3:0.0282933)n2:0.000153305)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000705_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000705_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ff26e408e0072878c0c771ed343525f3a6c630e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000705_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00764:0.002373,GCF_003691675_1_GCF_003691675.1_00528:0.00292)n1:0.000286,((GCF_020097155_1_GCF_020097155.1_02027:0.0385178,GCF_005280335_1_GCF_005280335.1_02134:0.0170803)n3:0.004874,GCF_002008305_4_GCF_002008305.4_00797:0.001014)n2:0.000286)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000707_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000707_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8de334b957e95a232abc2afe17b27b8891dbe940
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000707_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00766:0.00906537,GCF_003691675_1_GCF_003691675.1_00530:0.0222936)n1:0.0107037,(GCF_002008305_4_GCF_002008305.4_00799:0.00817612,(GCF_020097155_1_GCF_020097155.1_02025:0.951274,GCF_005280335_1_GCF_005280335.1_02132:0.212982)n3:0.172867)n2:0.0107037)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000708_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000708_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b0e2f40c19cd41c63369257208810c56967a478
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000708_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00800:0,GCF_003691675_1_GCF_003691675.1_00531:0)n1:0.000207715,(GCF_023573625_1_GCF_023573625.1_00767:0.00507457,(GCF_005280335_1_GCF_005280335.1_02130:0.0476753,GCF_020097155_1_GCF_020097155.1_02023:0.0526947)n3:0.0269389)n2:0.000207715)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000709_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000709_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38e28f023ea95923f8c13ad705624aacb17f731f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000709_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02022:0.0750925,GCF_005280335_1_GCF_005280335.1_02129:0.131139)n2:0.060028,GCF_023573625_1_GCF_023573625.1_00768:0.0082865)n1:0.001383,(GCF_003691675_1_GCF_003691675.1_00532:0.0170462,GCF_002008305_4_GCF_002008305.4_00801:0.0175378)n3:0.001383)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000712_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000712_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09c2842aab37494a846677b2ad4f71540e5191b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000712_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_02019:0.0722472,GCF_005280335_1_GCF_005280335.1_02126:0.0750908)n2:0.0710772,GCF_002008305_4_GCF_002008305.4_00804:0.0148162)n1:0.00185216,(GCF_003691675_1_GCF_003691675.1_00535:0.00605745,GCF_023573625_1_GCF_023573625.1_00771:0.0118575)n3:0.00185216)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000714_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000714_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9f8aff721c135af2979df9041753b7dae88fbeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000714_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02124:0.0220345,GCF_020097155_1_GCF_020097155.1_02017:0.188802)n2:0.0904951,GCF_023573625_1_GCF_023573625.1_00773:0.0215127)n1:0.00323116,(GCF_002008305_4_GCF_002008305.4_00806:0,GCF_003691675_1_GCF_003691675.1_00537:0)n3:0.00323116)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000720_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000720_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..993e511e1ba870341d85edacbc0bfc636b454989
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000720_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02117:0.0516352,GCF_020097155_1_GCF_020097155.1_02008:0.117697)n2:0.122146,GCF_002008305_4_GCF_002008305.4_00813:0.00869991)n1:0.00714554,(GCF_003691675_1_GCF_003691675.1_00545:0,GCF_023573625_1_GCF_023573625.1_00782:0)n3:0.00714554)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000721_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000721_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..988c1e203fe3a33372e1b312d95a1a7e45546d10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000721_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00546:0.00272,GCF_023573625_1_GCF_023573625.1_00783:0.001749)n1:0.0033605,(GCF_002008305_4_GCF_002008305.4_00814:0.001803,(GCF_020097155_1_GCF_020097155.1_02007:0.162428,GCF_005280335_1_GCF_005280335.1_02116:0.0541012)n3:0.068636)n2:0.0033605)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000724_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000724_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c130de023a802dee324bda881452eda8f1aa48f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000724_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00786:0.00069175,GCF_002008305_4_GCF_002008305.4_00817:0.0435453)n1:0.00266237,((GCF_020097155_1_GCF_020097155.1_02004:0.347902,GCF_005280335_1_GCF_005280335.1_02113:0.12572)n3:0.0769448,GCF_003691675_1_GCF_003691675.1_00549:0.00332225)n2:0.00266237)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000726_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000726_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf0250885be044a9d2b0d8c5fd904aef42b06df7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000726_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00788:0.00064028,GCF_002008305_4_GCF_002008305.4_00819:0.00184572)n1:0.00135074,((GCF_020097155_1_GCF_020097155.1_02002:0.108255,GCF_005280335_1_GCF_005280335.1_02111:0.13377)n3:0.225865,GCF_003691675_1_GCF_003691675.1_00551:0.00433322)n2:0.00135074)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000727_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000727_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ec848ae5b568266b1bc050c52ea17eccd724a1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000727_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00820:0.00241088,GCF_023573625_1_GCF_023573625.1_00789:0.00345012)n1:0.0193669,(GCF_003691675_1_GCF_003691675.1_00552:0.0291131,(GCF_020097155_1_GCF_020097155.1_02001:0.348107,GCF_005280335_1_GCF_005280335.1_02110:0.278329)n3:0.344756)n2:0.0193669)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000728_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000728_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eda6a6b5a63d57859d690f5a4b711ef3996b1455
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000728_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00553:0.00015317,GCF_023573625_1_GCF_023573625.1_00790:0.00143683)n1:0.00338113,(GCF_002008305_4_GCF_002008305.4_00821:0.0125224,(GCF_020097155_1_GCF_020097155.1_02000:0.214778,GCF_005280335_1_GCF_005280335.1_02109:0.118645)n3:0.0902969)n2:0.00338113)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000732_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000732_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..991a89460220670f7c161a6fbd900247aff80509
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000732_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00559:6.02816e-07,GCF_023573625_1_GCF_023573625.1_00796:0.0068335)n1:0.000390125,((GCF_005280335_1_GCF_005280335.1_02095:0.103373,GCF_020097155_1_GCF_020097155.1_01994:0.345162)n3:0.115652,GCF_002008305_4_GCF_002008305.4_00827:0.0311088)n2:0.000390125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000733_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000733_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..853dcb0ddd1c960bb5d6bb77bedf77f0f3097ec2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000733_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00797:0.00382962,(GCF_020097155_1_GCF_020097155.1_01993:0.0340865,GCF_005280335_1_GCF_005280335.1_02094:0.0698695)n2:0.0273454)n1:0.00100469,(GCF_002008305_4_GCF_002008305.4_00828:0,GCF_003691675_1_GCF_003691675.1_00560:0)n3:0.00100469)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000737_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000737_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b44c05b681bc037cc9b998fcff18b4203605e24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000737_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_02091:0.002286,GCF_002008305_4_GCF_002008305.4_00833:0.003118)n1:0.00080975,(GCF_020097155_1_GCF_020097155.1_01990:0.057195,(GCF_023573625_1_GCF_023573625.1_00803:0.0032915,GCF_003691675_1_GCF_003691675.1_00565:6.8778e-08)n3:0.00147352)n2:0.00080975)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000738_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000738_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ecc59f74916b9c4c239ac1ef794e4d3d23b2e419
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000738_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00834:0.00446375,(GCF_005280335_1_GCF_005280335.1_02090:0.0264972,GCF_020097155_1_GCF_020097155.1_01989:0.174976)n2:0.0280218)n1:0.000364125,(GCF_023573625_1_GCF_023573625.1_00804:0,GCF_003691675_1_GCF_003691675.1_00566:0)n3:0.000364125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000739_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000739_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2703ebe7f7eb88c3049ac641fc6f136d20ba3348
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000739_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00569:0.00096652,(GCF_020097155_1_GCF_020097155.1_01988:0.154886,GCF_005280335_1_GCF_005280335.1_02088:0.0371925)n2:0.04165)n1:0.00020074,(GCF_023573625_1_GCF_023573625.1_00806:0,GCF_002008305_4_GCF_002008305.4_00847:0)n3:0.00020074)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000742_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000742_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a42562a4326eeaf696f265c94f5008e7d520e586
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000742_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00850:0.0164858,(GCF_005280335_1_GCF_005280335.1_02085:0.0384473,GCF_020097155_1_GCF_020097155.1_01985:0.113501)n2:0.0211987)n1:0.0157696,(GCF_003691675_1_GCF_003691675.1_00572:0,GCF_023573625_1_GCF_023573625.1_00809:0)n3:0.0157696)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000743_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000743_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e515bb12c8f0e1a6127328f9ac41871454946493
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000743_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00810:0,GCF_003691675_1_GCF_003691675.1_00573:0)n1:0.102326,((GCF_005280335_1_GCF_005280335.1_02084:0.284657,GCF_020097155_1_GCF_020097155.1_01984:0.0623187)n3:0.107181,GCF_002008305_4_GCF_002008305.4_00851:0.137534)n2:0.102326)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000746_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000746_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..729ee5ca02b72043374c26a8ac85c65b2b5db334
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000746_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01970:0.172668,GCF_005280335_1_GCF_005280335.1_02076:0.207454)n2:0.0736771,GCF_002008305_4_GCF_002008305.4_00859:0.00583683)n1:0.000923335,(GCF_003691675_1_GCF_003691675.1_00581:0.0076955,GCF_023573625_1_GCF_023573625.1_00818:0.0057895)n3:0.000923335)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000749_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000749_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b56cae12a01ab50aff469ac5b57fba97fb8e62a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000749_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00862:0,GCF_003691675_1_GCF_003691675.1_00584:0)n1:0.00241625,(GCF_023573625_1_GCF_023573625.1_00821:1.55851e-07,(GCF_020097155_1_GCF_020097155.1_01967:0.112661,GCF_005280335_1_GCF_005280335.1_02073:0.0232075)n3:0.015892)n2:0.00241625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000750_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000750_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..923326548c6384444f0bacc7a85dfac0285d6a6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000750_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00585:0.00435425,(GCF_020097155_1_GCF_020097155.1_01966:0.0582568,GCF_005280335_1_GCF_005280335.1_02072:0.0162512)n2:0.0164742)n1:0.00385187,(GCF_002008305_4_GCF_002008305.4_00863:0,GCF_023573625_1_GCF_023573625.1_00822:0)n3:0.00385187)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000752_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000752_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eede75bcbff0ce4e25c84d85da4a0f524327d8f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000752_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00824:0.00388244,GCF_002008305_4_GCF_002008305.4_00865:7.81363e-08)n1:0.00012799,((GCF_005280335_1_GCF_005280335.1_02070:0.0160413,GCF_020097155_1_GCF_020097155.1_01964:0.0407167)n3:0.0152439,GCF_003691675_1_GCF_003691675.1_00587:0.00250545)n2:0.00012799)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000753_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000753_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb1dd700eca7ba9259e32c5102507cccac67c855
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000753_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02069:0.072161,GCF_020097155_1_GCF_020097155.1_01963:0.227347)n2:0.132824,GCF_003691675_1_GCF_003691675.1_00588:0.00532572)n1:0.00036714,(GCF_023573625_1_GCF_023573625.1_00825:0.00715157,GCF_002008305_4_GCF_002008305.4_00866:0.0184424)n3:0.00036714)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000756_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000756_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ab22a7e4da9789fadb1c7312d021d096a8e9829
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000756_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00591:0.00156737,GCF_002008305_4_GCF_002008305.4_00869:0.00642663)n1:0.00375332,(GCF_023573625_1_GCF_023573625.1_00828:0.00138487,(GCF_005280335_1_GCF_005280335.1_02066:0.0810196,GCF_020097155_1_GCF_020097155.1_01960:0.307034)n3:0.0480256)n2:0.00375332)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000759_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000759_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..586fe650d6f433772eca6a7d034982306a219899
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000759_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01957:0.167615,GCF_005280335_1_GCF_005280335.1_02063:0.074134)n2:0.0219507,GCF_003691675_1_GCF_003691675.1_00594:0.00701419)n1:0.00160691,(GCF_002008305_4_GCF_002008305.4_00872:0.00544791,GCF_023573625_1_GCF_023573625.1_00831:0.00766109)n3:0.00160691)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000762_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000762_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0ca044476468fecc7792ead91e75dac9e27da2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000762_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00597:0.008373,GCF_002008305_4_GCF_002008305.4_00875:2.90199e-07)n1:0.0011815,(GCF_023573625_1_GCF_023573625.1_00834:0.000935,(GCF_005280335_1_GCF_005280335.1_02060:0.046933,GCF_020097155_1_GCF_020097155.1_01954:0.18226)n3:0.0494775)n2:0.0011815)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000765_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000765_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c157dc9cc9561008b54f9eb457c3ebd9d826805b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000765_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00878:0,GCF_003691675_1_GCF_003691675.1_00600:0)n1:0,(GCF_023573625_1_GCF_023573625.1_00837:0,(GCF_005280335_1_GCF_005280335.1_02057:0.0075155,GCF_020097155_1_GCF_020097155.1_01951:0.0386465)n3:0.0076945)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000766_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000766_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..042d1eeea8518997857af51b67237c140f7382ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000766_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00879:2.23094e-07,(GCF_005280335_1_GCF_005280335.1_02056:0.0396167,GCF_020097155_1_GCF_020097155.1_01950:0.173308)n2:0.00308425)n1:0.00358789,(GCF_003691675_1_GCF_003691675.1_00601:5e-07,GCF_023573625_1_GCF_023573625.1_00838:5e-07)n3:0.00358789)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000771_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000771_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b798dfc39b4cecfb97e874606993b3fc57f4640
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000771_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00895:0.0049595,GCF_003691675_1_GCF_003691675.1_00617:0.0051095)n1:0.0800756,((GCF_023573625_1_GCF_023573625.1_00846:0.796211,GCF_020097155_1_GCF_020097155.1_01940:0.509772)n3:0.252046,GCF_005280335_1_GCF_005280335.1_02042:0.193145)n2:0.0800756)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000773_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000773_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6817ec615c7305c957cd3cb777b49d59940134f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000773_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00848:0.00707738,GCF_002008305_4_GCF_002008305.4_00897:0.00881963)n1:0.000466815,((GCF_020097155_1_GCF_020097155.1_01942:0.300257,GCF_003691675_1_GCF_003691675.1_00619:0.0200641)n3:0.00547212,GCF_005280335_1_GCF_005280335.1_02044:0.00849688)n2:0.000466815)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000775_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000775_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..383ee68a2b8be198e4be1aa7d69183b1e8681a7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000775_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00621:0.00478483,GCF_023573625_1_GCF_023573625.1_00850:0.00504417)n1:0.0295857,(GCF_020097155_1_GCF_020097155.1_01938:0.182304,(GCF_002008305_4_GCF_002008305.4_00902:0.0198533,GCF_005280335_1_GCF_005280335.1_02040:0.0418337)n3:0.0421415)n2:0.0295857)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000777_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000777_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1852220357a70cc58a4c1884f61aa035a1882b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000777_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00623:0.00097325,GCF_023573625_1_GCF_023573625.1_00852:0.00107775)n1:0.00068425,(GCF_002008305_4_GCF_002008305.4_00904:0.009352,(GCF_020097155_1_GCF_020097155.1_01936:0.0946208,GCF_005280335_1_GCF_005280335.1_02038:0.0200033)n3:0.023689)n2:0.00068425)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000783_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000783_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c190e8bab81f793c573b32727a8dd4e1b8746bd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000783_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00858:0.00946688,GCF_003691675_1_GCF_003691675.1_00629:0.00816512)n1:0.00335294,((GCF_005280335_1_GCF_005280335.1_02032:0.167837,GCF_020097155_1_GCF_020097155.1_01930:0.313358)n3:0.0917619,GCF_002008305_4_GCF_002008305.4_00910:0.00737662)n2:0.00335294)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000784_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000784_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efe433ab4af0e6547be44d16ae881cca6155f479
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000784_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00859:0,GCF_003691675_1_GCF_003691675.1_00630:0)n1:0,(GCF_002008305_4_GCF_002008305.4_00911:0,(GCF_020097155_1_GCF_020097155.1_01929:0.635902,GCF_005280335_1_GCF_005280335.1_02031:0.215988)n3:0.100164)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000785_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000785_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3bdc07a1bc35acf25d7a90052eb5d6a015eee93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000785_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00912:0,GCF_003691675_1_GCF_003691675.1_00631:0)n1:0,((GCF_020097155_1_GCF_020097155.1_01928:0.3717,GCF_005280335_1_GCF_005280335.1_02030:0.105508)n3:0.0823165,GCF_023573625_1_GCF_023573625.1_00860:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000786_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000786_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e6ba2dfd95bc0c26626f7fd51baf22fb31313c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000786_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00632:0,GCF_023573625_1_GCF_023573625.1_00861:0)n1:0,(GCF_002008305_4_GCF_002008305.4_00913:0,(GCF_005280335_1_GCF_005280335.1_02029:0.005113,GCF_020097155_1_GCF_020097155.1_01927:0.150975)n3:0.052024)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000793_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000793_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0c3f840a6dfed2e19ac718ce527616fe4c7c8d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000793_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01920:0.0168426,GCF_005280335_1_GCF_005280335.1_02021:0.00643137)n2:0.0168436,GCF_023573625_1_GCF_023573625.1_00868:5.33626e-08)n1:4.8065e-05,(GCF_003691675_1_GCF_003691675.1_00639:0.0133411,GCF_002008305_4_GCF_002008305.4_00920:5.33626e-08)n3:4.8065e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000794_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000794_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..861a0580c687c73f9198f16258c3d8054ed98303
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000794_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02020:0.0835863,GCF_020097155_1_GCF_020097155.1_01919:0.112302)n2:0.0301696,GCF_003691675_1_GCF_003691675.1_00640:0.00046771)n1:0.000135645,(GCF_023573625_1_GCF_023573625.1_00869:0.00147995,GCF_002008305_4_GCF_002008305.4_00921:0.00073805)n3:0.000135645)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000799_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000799_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81e13897f61b21384b0d0718dea42199009b5838
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000799_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01914:0.517819,GCF_005280335_1_GCF_005280335.1_02015:0.101472)n2:0.159554,GCF_003691675_1_GCF_003691675.1_00645:0.0149808)n1:0.00213262,(GCF_023573625_1_GCF_023573625.1_00874:0,GCF_002008305_4_GCF_002008305.4_00926:0)n3:0.00213262)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000805_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000805_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a256720ed4fe09c16a207c6abae3dadc199d48f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000805_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00652:0.00438715,GCF_002008305_4_GCF_002008305.4_00933:0.00159785)n1:0.000609585,(GCF_023573625_1_GCF_023573625.1_00882:0.00535432,(GCF_020097155_1_GCF_020097155.1_01903:0.108911,GCF_005280335_1_GCF_005280335.1_02007:0.0186062)n3:0.0193353)n2:0.000609585)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000809_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000809_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bbca6c93eab46f82fbd0d599671e7e2122ee932d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000809_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_01899:0.578135,(GCF_023573625_1_GCF_023573625.1_00886:0.0106987,GCF_005280335_1_GCF_005280335.1_02002:0.0172083)n2:0.00208725)n1:0.00209713,(GCF_003691675_1_GCF_003691675.1_00656:0.0151287,GCF_002008305_4_GCF_002008305.4_00937:0.0242512)n3:0.00209713)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000811_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000811_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6f911d64d737cae71124fa6747cc0dc2cb28e54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000811_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00658:0.0153966,GCF_020097155_1_GCF_020097155.1_01897:0.324771)n1:0.00304781,((GCF_023573625_1_GCF_023573625.1_00888:0.0200589,GCF_005280335_1_GCF_005280335.1_02000:0.44078)n3:0.00897313,GCF_002008305_4_GCF_002008305.4_00939:0.00597288)n2:0.00304781)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000815_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000815_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d1e6245de97096178adf930123e57f8f720034b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000815_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00662:0.0029015,GCF_002008305_4_GCF_002008305.4_00943:0.0049925)n1:0.0153118,(GCF_023573625_1_GCF_023573625.1_00893:0.021022,(GCF_005280335_1_GCF_005280335.1_01995:0.107425,GCF_020097155_1_GCF_020097155.1_01892:0.177031)n3:0.0504055)n2:0.0153118)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000816_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000816_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..869aaf5174952cf32c1c4b7483bce7370e00da84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000816_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00895:0.00665333,GCF_003691675_1_GCF_003691675.1_00666:1.47561e-07)n1:0.000270585,(GCF_002008305_4_GCF_002008305.4_00947:0.00611216,(GCF_005280335_1_GCF_005280335.1_01990:0.098403,GCF_020097155_1_GCF_020097155.1_01891:0.031379)n3:0.00634061)n2:0.000270585)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000817_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000817_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81dd06532d5bbcd300d85a9ee884c9117981c5c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000817_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00902:0.00605012,(GCF_020097155_1_GCF_020097155.1_01883:0.0574811,GCF_005280335_1_GCF_005280335.1_01931:0.0891779)n2:0.0111884)n1:0.00127944,(GCF_002008305_4_GCF_002008305.4_00956:0.00215663,GCF_003691675_1_GCF_003691675.1_00669:0.00642838)n3:0.00127944)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000818_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000818_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9db948b382f195f3dddd46b15d8f7e9f686cde16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000818_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01930:0.0428219,GCF_020097155_1_GCF_020097155.1_01882:0.199828)n2:0.0421709,GCF_003691675_1_GCF_003691675.1_00670:0.00086162)n1:0.00153719,(GCF_023573625_1_GCF_023573625.1_00903:0.00801438,GCF_002008305_4_GCF_002008305.4_00957:0.00500863)n3:0.00153719)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000819_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000819_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b1fdca3ec6484bb7e4ccd92e79776649267801e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000819_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01880:0.202133,GCF_005280335_1_GCF_005280335.1_01929:0.369999)n2:0.0792476,GCF_003691675_1_GCF_003691675.1_00672:0.00558338)n1:0.00199981,(GCF_023573625_1_GCF_023573625.1_00905:0.0143151,GCF_002008305_4_GCF_002008305.4_00959:0.00430687)n3:0.00199981)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000823_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000823_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4be8fd646d2bff613aab03e3bd12b548eec4c953
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000823_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_01923:0.0896836,GCF_003691675_1_GCF_003691675.1_00677:0.0115385)n1:0.00606071,(GCF_020097155_1_GCF_020097155.1_01872:0.125922,(GCF_023573625_1_GCF_023573625.1_00910:0.0165565,GCF_002008305_4_GCF_002008305.4_00964:0.0046825)n3:0.0189308)n2:0.00606071)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000827_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000827_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42b1f85eaa0dbe7e72f1a6bcf96f998176894618
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000827_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00917:0.0050945,GCF_002008305_4_GCF_002008305.4_00974:5.66124e-07)n1:0.0074305,((GCF_005280335_1_GCF_005280335.1_01916:0.134046,GCF_020097155_1_GCF_020097155.1_01863:0.299825)n3:0.087649,GCF_003691675_1_GCF_003691675.1_00688:0.025162)n2:0.0074305)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000828_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000828_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6dff7ecb1464435cd1bf39537cc93e45cb37b3ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000828_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01861:0.141993,GCF_005280335_1_GCF_005280335.1_01914:0.0369873)n2:0.00884169,GCF_003691675_1_GCF_003691675.1_00690:0.00412507)n1:0.000921465,(GCF_023573625_1_GCF_023573625.1_00919:0.0054919,GCF_002008305_4_GCF_002008305.4_00976:0.0070621)n3:0.000921465)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000832_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000832_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a1144e05a14c935b02a54928623d8a63d76a379
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000832_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00980:0,GCF_003691675_1_GCF_003691675.1_00694:0)n1:0,(GCF_023573625_1_GCF_023573625.1_00923:0,(GCF_005280335_1_GCF_005280335.1_01910:0.0910805,GCF_020097155_1_GCF_020097155.1_01857:0.0722845)n3:0.334967)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000833_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000833_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae61f3252be9dbb789b021d5b345efad20048918
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000833_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00981:0,GCF_003691675_1_GCF_003691675.1_00695:0)n1:0,((GCF_005280335_1_GCF_005280335.1_01908:0.29369,GCF_020097155_1_GCF_020097155.1_01856:0.025752)n3:0.014603,GCF_023573625_1_GCF_023573625.1_00924:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000836_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000836_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdb50eaf7dfd1bd42a6553957b8610c659222183
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000836_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00984:0,GCF_023573625_1_GCF_023573625.1_00927:0)n1:0.008347,(GCF_003691675_1_GCF_003691675.1_00698:0.006346,(GCF_005280335_1_GCF_005280335.1_01905:0.01917,GCF_020097155_1_GCF_020097155.1_01852:0.007558)n3:0.026093)n2:0.008347)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000837_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000837_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2076c3b3ad2bb0e0dc1621aef1a28fdc57010ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000837_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00985:0,GCF_023573625_1_GCF_023573625.1_00928:0)n1:0.00185375,(GCF_003691675_1_GCF_003691675.1_00699:0.0010755,(GCF_005280335_1_GCF_005280335.1_01904:0.439624,GCF_020097155_1_GCF_020097155.1_01851:0.00120124)n3:0.0002285)n2:0.00185375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000838_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000838_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea2426481192ed13603e81d1eb1fad2d5d6d9688
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000838_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00986:0.00085275,GCF_023573625_1_GCF_023573625.1_00929:0.00417425)n1:0.00374288,(GCF_020097155_1_GCF_020097155.1_01850:2.66572e-08,(GCF_005280335_1_GCF_005280335.1_01903:0.0102562,GCF_003691675_1_GCF_003691675.1_00700:0.00391375)n3:0.00039275)n2:0.00374288)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000839_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000839_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32bac5a010e677e01b5d1c088a524fa178f959f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000839_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00701:0.0039935,GCF_023573625_1_GCF_023573625.1_00930:1.19745e-08)n1:2.75e-06,(GCF_002008305_4_GCF_002008305.4_00987:1.19745e-08,(GCF_020097155_1_GCF_020097155.1_01849:1.19745e-08,GCF_005280335_1_GCF_005280335.1_01902:0.0079865)n3:5.5e-06)n2:2.75e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000841_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000841_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..468dcc6945b22d9cc3d68200d351053ddde562d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000841_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00932:0,GCF_002008305_4_GCF_002008305.4_00989:0)n1:0.00069057,(GCF_003691675_1_GCF_003691675.1_00703:0.00184286,(GCF_005280335_1_GCF_005280335.1_01900:0.0165698,GCF_020097155_1_GCF_020097155.1_01847:0.0116572)n3:0.0227768)n2:0.00069057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000842_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000842_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d373ed2e8462084f4f0cd59d1c61c4b18fa5b06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000842_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00704:0.00390109,GCF_023573625_1_GCF_023573625.1_00933:0.00160891)n1:0.00556153,((GCF_005280335_1_GCF_005280335.1_01899:0.0308043,GCF_020097155_1_GCF_020097155.1_01846:0.00968067)n3:0.0161278,GCF_002008305_4_GCF_002008305.4_00990:0.00438916)n2:0.00556153)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000844_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000844_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0482539eeefcb9123d53672f8c02dbb3d4c4f4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000844_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00708:0.00253988,GCF_023573625_1_GCF_023573625.1_00937:0.00361712)n1:0.00037194,((GCF_020097155_1_GCF_020097155.1_01842:0.0973816,GCF_005280335_1_GCF_005280335.1_01895:0.0158574)n3:0.0106034,GCF_002008305_4_GCF_002008305.4_00994:0.00310912)n2:0.00037194)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000850_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000850_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bff1a39f9511dead99d2aed37157865aa8c22f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000850_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00944:0,GCF_002008305_4_GCF_002008305.4_01001:0)n1:0,(GCF_003691675_1_GCF_003691675.1_00715:0,(GCF_005280335_1_GCF_005280335.1_01889:0,GCF_020097155_1_GCF_020097155.1_01817:0.064144)n3:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000851_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000851_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4a621269fa153e0665276f344cb3c9d74405757
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000851_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00945:0,GCF_003691675_1_GCF_003691675.1_00716:0)n1:0,(GCF_002008305_4_GCF_002008305.4_01002:0,(GCF_005280335_1_GCF_005280335.1_01888:0.022658,GCF_020097155_1_GCF_020097155.1_01816:0.111838)n3:0.043309)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000853_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000853_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..515b9b318a6503115f902aac5f236a7ebf6af46a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000853_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00947:0.00204503,(GCF_020097155_1_GCF_020097155.1_01814:0.222906,GCF_005280335_1_GCF_005280335.1_01886:0.0561255)n2:0.0471718)n1:0.00406774,(GCF_002008305_4_GCF_002008305.4_01004:1.268e-05,GCF_003691675_1_GCF_003691675.1_00718:0.00058432)n3:0.00406774)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000855_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000855_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..599ec84e1c4a3c7aa327e76e41ec0793f858b4a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000855_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01006:0,GCF_003691675_1_GCF_003691675.1_00720:0)n1:0.00201033,((GCF_005280335_1_GCF_005280335.1_01884:0.0394398,GCF_020097155_1_GCF_020097155.1_01812:0.185975)n3:0.0174949,GCF_023573625_1_GCF_023573625.1_00949:0.0225833)n2:0.00201033)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000858_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000858_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cf7fd560bc8b5393936f567ee31c54696eea1ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000858_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01230:2.79151,GCF_005280335_1_GCF_005280335.1_01874:0.011889)n2:0.0061645,GCF_003691675_1_GCF_003691675.1_00728:0.002629)n1:0.00093375,(GCF_002008305_4_GCF_002008305.4_01014:5e-07,GCF_023573625_1_GCF_023573625.1_00957:5e-07)n3:0.00093375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000868_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000868_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b158a9846bcd4193f42ac56422f0a6bdff3f104
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000868_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01859:0.011463,GCF_020097155_1_GCF_020097155.1_01749:0.074488)n2:0.00619175,GCF_023573625_1_GCF_023573625.1_00970:0.00268626)n1:0.00075237,(GCF_002008305_4_GCF_002008305.4_01026:0,GCF_003691675_1_GCF_003691675.1_00741:0)n3:0.00075237)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000869_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000869_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e59a3cc3f96f7c704ddcfd67f4a8ae63f0295124
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000869_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01027:0.00365775,GCF_003691675_1_GCF_003691675.1_00742:0.00399925)n1:0.00113887,((GCF_020097155_1_GCF_020097155.1_01745:0.0636985,GCF_005280335_1_GCF_005280335.1_01858:0.0261625)n3:0.0287262,GCF_023573625_1_GCF_023573625.1_00971:0.00231625)n2:0.00113887)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000870_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000870_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14bb2ca1883519de92ee3c27556d8656a08a1533
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000870_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01741:0.00785662,GCF_023573625_1_GCF_023573625.1_00975:3.45111e-08)n2:0.00010312,GCF_005280335_1_GCF_005280335.1_01851:0.0128424)n1:6.131e-05,(GCF_002008305_4_GCF_002008305.4_01031:0.00329963,GCF_003691675_1_GCF_003691675.1_00746:0.0104344)n3:6.131e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000871_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000871_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f8da9de9800523b9d1901089039e45da8d92880
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000871_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00747:0.0292494,(GCF_020097155_1_GCF_020097155.1_01740:0.0191028,GCF_005280335_1_GCF_005280335.1_01850:0.0193392)n2:0.00612125)n1:0.0135877,(GCF_023573625_1_GCF_023573625.1_00976:1.03043e-07,GCF_002008305_4_GCF_002008305.4_01032:0.00264883)n3:0.0135877)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000872_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000872_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d35068a9f525a36efd559dd8566fa25d495c214
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000872_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00977:0.00235038,GCF_002008305_4_GCF_002008305.4_01035:0.0264156)n1:0.00055656,((GCF_003691675_1_GCF_003691675.1_00748:0.00702288,GCF_005280335_1_GCF_005280335.1_01849:0.00479312)n3:0.0256656,GCF_020097155_1_GCF_020097155.1_01739:0.00260388)n2:0.00055656)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000873_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000873_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27b4a874fff980f134dadcfd624d379feddb17bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000873_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00749:3.24459e-08,GCF_002008305_4_GCF_002008305.4_01036:0.00891963)n1:0.00210069,(GCF_023573625_1_GCF_023573625.1_00978:0.00580113,(GCF_005280335_1_GCF_005280335.1_01848:0.0127934,GCF_020097155_1_GCF_020097155.1_01738:0.00048162)n3:0.00030438)n2:0.00210069)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000874_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000874_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4a6729b48160ff3bda20c7270dd28a43a9ece3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000874_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00979:0.00120414,(GCF_020097155_1_GCF_020097155.1_01737:0.0247243,GCF_005280335_1_GCF_005280335.1_01847:0.0135437)n2:0.00328309)n1:0.00412404,(GCF_003691675_1_GCF_003691675.1_00750:0.00445767,GCF_002008305_4_GCF_002008305.4_01037:0.00043133)n3:0.00412404)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000879_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000879_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adee358766debd1d08acff7eb0e0a4fb74ddf4cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000879_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00987:0.00091363,GCF_002008305_4_GCF_002008305.4_01046:0.00093237)n1:0.00089144,(GCF_003691675_1_GCF_003691675.1_00759:1.39443e-07,(GCF_020097155_1_GCF_020097155.1_01730:0.0388079,GCF_005280335_1_GCF_005280335.1_01842:0.0469911)n3:0.0501354)n2:0.00089144)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000881_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000881_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b2e79fa0a8f22e74b4b5b2a59ebcb21331aae48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000881_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00989:0.00710866,GCF_003691675_1_GCF_003691675.1_00761:0.00502934)n1:0.00361123,(GCF_002008305_4_GCF_002008305.4_01048:0.0199721,(GCF_005280335_1_GCF_005280335.1_01840:0.0620358,GCF_020097155_1_GCF_020097155.1_01728:0.213885)n3:0.0740877)n2:0.00361123)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000885_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000885_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2629f2365b50362c23a848f916f725accff8b672
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000885_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00993:0.00144727,GCF_002008305_4_GCF_002008305.4_01052:0.00216373)n1:0.000237395,(GCF_003691675_1_GCF_003691675.1_00765:0.00169076,(GCF_005280335_1_GCF_005280335.1_01834:0.0685562,GCF_020097155_1_GCF_020097155.1_01724:0.0896158)n3:0.0519374)n2:0.000237395)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000889_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000889_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49a3297c1a558d25e2813251df05008e458ec65d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000889_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00779:0.00901813,(GCF_005280335_1_GCF_005280335.1_01826:0.0818516,GCF_020097155_1_GCF_020097155.1_01716:0.209638)n2:0.0691884)n1:0.00420568,(GCF_002008305_4_GCF_002008305.4_01060:0.00996387,GCF_023573625_1_GCF_023573625.1_01007:0.00617812)n3:0.00420568)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000890_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000890_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..269552e37cd592b66f79a1d9126bddd86fac9c0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000890_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01061:0.00024663,GCF_003691675_1_GCF_003691675.1_00780:0.00918737)n1:0.00440356,(GCF_023573625_1_GCF_023573625.1_01008:0.00790837,(GCF_005280335_1_GCF_005280335.1_01825:0.0651994,GCF_020097155_1_GCF_020097155.1_01715:0.16774)n3:0.0246146)n2:0.00440356)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000891_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000891_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85e449c14aba8f848ecea3c0685028d28a708620
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000891_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01824:0.0419588,GCF_020097155_1_GCF_020097155.1_01714:0.0864012)n2:0.0449665,GCF_023573625_1_GCF_023573625.1_01009:0.00105595)n1:0.00102002,(GCF_002008305_4_GCF_002008305.4_01062:0.00103185,GCF_003691675_1_GCF_003691675.1_00781:0.00309215)n3:0.00102002)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000892_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000892_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c38be1face5033b5cc410fa08858aafd210dc6ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000892_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01823:0.293622,GCF_020097155_1_GCF_020097155.1_01713:0.249053)n2:0.129764,GCF_003691675_1_GCF_003691675.1_00782:0.0122238)n1:0.00444812,(GCF_023573625_1_GCF_023573625.1_01010:0.0206237,GCF_002008305_4_GCF_002008305.4_01063:0.0118353)n3:0.00444812)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000893_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000893_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..503d7e0948b4754f2ade7395ac515eea147d564c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000893_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01013:0,GCF_003691675_1_GCF_003691675.1_00785:0)n1:0.0017885,(GCF_002008305_4_GCF_002008305.4_01066:3.13566e-07,(GCF_005280335_1_GCF_005280335.1_01821:0.0717158,GCF_020097155_1_GCF_020097155.1_01710:0.162074)n3:0.0764198)n2:0.0017885)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000897_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000897_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6bc59856075b6530de5e7ca576a819766afaf17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000897_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00800:0,GCF_023573625_1_GCF_023573625.1_01030:0)n1:0.00247212,((GCF_005280335_1_GCF_005280335.1_01816:0.106803,GCF_020097155_1_GCF_020097155.1_01704:0.271299)n3:0.106326,GCF_002008305_4_GCF_002008305.4_01081:0.00271875)n2:0.00247212)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000900_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000900_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4a35376851b9e9dad629840464d1046c66f0d02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000900_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00803:0,GCF_023573625_1_GCF_023573625.1_01033:0)n1:0.00333987,(GCF_002008305_4_GCF_002008305.4_01084:6.71402e-07,(GCF_005280335_1_GCF_005280335.1_01813:0.128987,GCF_020097155_1_GCF_020097155.1_01701:0.42343)n3:0.114142)n2:0.00333987)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000903_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000903_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e587488c5e37b29a1adbb2aca987f2885dab4be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000903_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01036:0,GCF_003691675_1_GCF_003691675.1_00806:0)n1:0.00813875,(GCF_002008305_4_GCF_002008305.4_01087:0.0110635,(GCF_005280335_1_GCF_005280335.1_01810:0.026908,GCF_020097155_1_GCF_020097155.1_01698:0.253706)n3:0.022982)n2:0.00813875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000905_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000905_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6d10fa39baebcf266b3c6482ecfe551671cef5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000905_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01807:0.231876,GCF_020097155_1_GCF_020097155.1_01696:0.040111)n2:0.051496,GCF_003691675_1_GCF_003691675.1_00808:0)n1:0,(GCF_023573625_1_GCF_023573625.1_01038:0,GCF_002008305_4_GCF_002008305.4_01089:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000913_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000913_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c581e000514e13f35358fad4fad407d65261d00b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000913_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01098:0,GCF_023573625_1_GCF_023573625.1_01047:0)n1:0,(GCF_003691675_1_GCF_003691675.1_00817:0,(GCF_020097155_1_GCF_020097155.1_01687:0.11339,GCF_005280335_1_GCF_005280335.1_01797:0.0632665)n3:0.0763365)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000915_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000915_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3479e962a764a2df294ce0143513c63d1159698b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000915_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01100:0.00935674,GCF_003691675_1_GCF_003691675.1_00819:0.0173073)n1:0.0034386,(GCF_023573625_1_GCF_023573625.1_01049:0.0219801,(GCF_020097155_1_GCF_020097155.1_01685:0.283803,GCF_005280335_1_GCF_005280335.1_01795:0.0889472)n3:0.109957)n2:0.0034386)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000916_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000916_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e8f63bdd7cfe62c54c2891b011f83b6ede49a57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000916_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01101:0.00579437,(GCF_005280335_1_GCF_005280335.1_01794:0.0402396,GCF_020097155_1_GCF_020097155.1_01684:0.167549)n2:0.0430501)n1:0.00103206,(GCF_003691675_1_GCF_003691675.1_00820:0.00288162,GCF_023573625_1_GCF_023573625.1_01050:0.00719137)n3:0.00103206)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000918_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000918_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8143ce1a882fa5ab15747b32572b7a468f29895d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000918_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01104:0.00761953,(GCF_020097155_1_GCF_020097155.1_01681:0.453571,GCF_005280335_1_GCF_005280335.1_01790:0.268574)n2:0.268933)n1:0.0108497,(GCF_003691675_1_GCF_003691675.1_00823:0.00191182,GCF_023573625_1_GCF_023573625.1_01053:1.02165e-06)n3:0.0108497)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000929_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000929_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c40bbb581bb7a838a7e3ab43bfe329faac039bcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000929_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01666:0.181826,GCF_005280335_1_GCF_005280335.1_01773:0.056425)n2:0.057879,GCF_003691675_1_GCF_003691675.1_00839:0)n1:0,(GCF_002008305_4_GCF_002008305.4_01120:0,GCF_023573625_1_GCF_023573625.1_01070:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000934_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000934_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d8d7afd000483f69113837f14a7b2c93de48a9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000934_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01661:0.139647,GCF_005280335_1_GCF_005280335.1_01767:0.0399704)n2:0.0317139,GCF_003691675_1_GCF_003691675.1_00844:0.00223513)n1:0.0107132,(GCF_023573625_1_GCF_023573625.1_01075:0.00060137,GCF_002008305_4_GCF_002008305.4_01125:0.00140763)n3:0.0107132)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000935_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000935_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5011c78e07a7400ab9383b6c6d14d605ed40a12c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000935_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01766:0.0467178,GCF_020097155_1_GCF_020097155.1_01660:0.165921)n2:0.0652679,GCF_023573625_1_GCF_023573625.1_01076:0.00062123)n1:0.00241214,(GCF_003691675_1_GCF_003691675.1_00845:0.00048549,GCF_002008305_4_GCF_002008305.4_01126:0.00247351)n3:0.00241214)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000940_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000940_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65f913eac5b2a6c7cbc0768630eb6f0a0c94ea26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000940_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01131:5e-07,GCF_003691675_1_GCF_003691675.1_00850:5e-07)n1:0.00126325,(GCF_023573625_1_GCF_023573625.1_01081:0.000372,(GCF_020097155_1_GCF_020097155.1_01655:0.196151,GCF_005280335_1_GCF_005280335.1_01761:0.0525805)n3:0.042721)n2:0.00126325)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000942_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000942_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c7cebbea8868bdd5b1b8920d2d032e9d7c5cd0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000942_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01759:0.0417566,GCF_020097155_1_GCF_020097155.1_01653:0.109005)n2:0.0320194,GCF_002008305_4_GCF_002008305.4_01133:1.8748e-07)n1:7.169e-05,(GCF_023573625_1_GCF_023573625.1_01083:0.00484237,GCF_003691675_1_GCF_003691675.1_00852:1.8748e-07)n3:7.169e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000943_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000943_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d1dfe36b00f89825c0552834be7c5582c9401b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000943_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01084:0.00652255,(GCF_005280335_1_GCF_005280335.1_01758:0.0877803,GCF_020097155_1_GCF_020097155.1_01652:0.547046)n2:0.101115)n1:0.00390422,(GCF_003691675_1_GCF_003691675.1_00853:0,GCF_002008305_4_GCF_002008305.4_01134:0)n3:0.00390422)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000945_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000945_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..960ff84f06efe73ec363fe44d765e9ce7619305a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000945_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00855:0,GCF_002008305_4_GCF_002008305.4_01136:0)n1:0.00152312,((GCF_005280335_1_GCF_005280335.1_01756:0.0771778,GCF_020097155_1_GCF_020097155.1_01650:0.304645)n3:0.0503333,GCF_023573625_1_GCF_023573625.1_01086:0.00773675)n2:0.00152312)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000947_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000947_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7e05827ba01607bc9e6cfee998b356479e61963
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000947_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01088:0.00043725,GCF_003691675_1_GCF_003691675.1_00857:0.00111275)n1:0.000297875,(GCF_002008305_4_GCF_002008305.4_01138:0.00095425,(GCF_005280335_1_GCF_005280335.1_01754:0.014045,GCF_020097155_1_GCF_020097155.1_01648:0.042257)n3:0.0110393)n2:0.000297875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000948_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000948_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a659f0d1f40c8358e32e5ecee036e0f9823cdeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000948_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00858:0.00222237,GCF_002008305_4_GCF_002008305.4_01139:0.00034663)n1:0.00114481,((GCF_005280335_1_GCF_005280335.1_01753:0.0311249,GCF_020097155_1_GCF_020097155.1_01647:0.19376)n3:0.0369711,GCF_023573625_1_GCF_023573625.1_01089:0.00510437)n2:0.00114481)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000951_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000951_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77596dbf9ed752e334a0eb050b5a288d6215d0e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000951_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00861:0,GCF_023573625_1_GCF_023573625.1_01092:0)n1:0.00289686,(GCF_002008305_4_GCF_002008305.4_01142:0.00672928,(GCF_005280335_1_GCF_005280335.1_01749:0.117275,GCF_020097155_1_GCF_020097155.1_01644:0.23764)n3:0.0921333)n2:0.00289686)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000956_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000956_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6508b0819b43e4d31713a52fc09d562802decaad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000956_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01149:0.00204429,(GCF_005280335_1_GCF_005280335.1_01743:0.0599527,GCF_020097155_1_GCF_020097155.1_01637:0.26919)n2:0.0350064)n1:0.000859355,(GCF_023573625_1_GCF_023573625.1_01099:0,GCF_003691675_1_GCF_003691675.1_00868:0)n3:0.000859355)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000958_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000958_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c1a3f69f7aaed7e7c2a15f196bd5de32e23a8c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000958_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00870:0,GCF_023573625_1_GCF_023573625.1_01101:0)n1:0.00183175,(GCF_002008305_4_GCF_002008305.4_01151:0.0021505,(GCF_005280335_1_GCF_005280335.1_01741:0.226101,GCF_020097155_1_GCF_020097155.1_01635:0.101414)n3:0.075814)n2:0.00183175)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000962_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000962_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0efcac4ab62530c7d4ac529abefd646ceb4deb37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000962_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01107:0,GCF_002008305_4_GCF_002008305.4_01157:0)n1:0,((GCF_005280335_1_GCF_005280335.1_01732:0.013534,GCF_020097155_1_GCF_020097155.1_01630:0.094825)n3:0.011777,GCF_003691675_1_GCF_003691675.1_00876:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000963_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000963_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..607a869fb4856db78b86c71083d836988235fabb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000963_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01158:0,GCF_023573625_1_GCF_023573625.1_01108:0)n1:0.000573015,(GCF_003691675_1_GCF_003691675.1_00877:0.00011797,(GCF_020097155_1_GCF_020097155.1_01629:0.132703,GCF_005280335_1_GCF_005280335.1_01731:0.0301507)n3:0.0406927)n2:0.000573015)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000965_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000965_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c727745c4ec6fde470bc633bd4bcbd481ff79210
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000965_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01161:0.00174177,GCF_023573625_1_GCF_023573625.1_01111:0.00292023)n1:0.00160936,(GCF_003691675_1_GCF_003691675.1_00880:0.00496332,(GCF_020097155_1_GCF_020097155.1_01626:0.102855,GCF_005280335_1_GCF_005280335.1_01729:0.0393852)n3:0.0505045)n2:0.00160936)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000967_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000967_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57f01f44ea71e776d2c68bcfc951619443202e07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000967_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00882:0.0150563,GCF_002008305_4_GCF_002008305.4_01163:0.00853366)n1:0.0044419,((GCF_005280335_1_GCF_005280335.1_01727:0.123701,GCF_020097155_1_GCF_020097155.1_01624:0.384144)n3:0.107503,GCF_023573625_1_GCF_023573625.1_01113:0.00634795)n2:0.0044419)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000968_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000968_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c951eca3898c2bf232f64db1c499dc7a7b76b4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000968_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01114:6.03814e-07,(GCF_020097155_1_GCF_020097155.1_01623:0.29282,GCF_005280335_1_GCF_005280335.1_01726:0.198064)n2:0.111572)n1:0.000792875,(GCF_003691675_1_GCF_003691675.1_00883:0,GCF_002008305_4_GCF_002008305.4_01164:0)n3:0.000792875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000971_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000971_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..217ea39caed2d3d342c7edfef221d6c9586ac2cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000971_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01721:0.0336045,GCF_020097155_1_GCF_020097155.1_01619:0.0945145)n2:0.0170745,GCF_003691675_1_GCF_003691675.1_00887:0)n1:0,(GCF_023573625_1_GCF_023573625.1_01118:0,GCF_002008305_4_GCF_002008305.4_01168:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000972_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000972_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1272f21f49bee44944a3c5cb9cd7f38c4cb77b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000972_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01720:0.0348035,GCF_020097155_1_GCF_020097155.1_01618:0.0692045)n2:0.0739665,GCF_023573625_1_GCF_023573625.1_01119:0)n1:0,(GCF_003691675_1_GCF_003691675.1_00888:0,GCF_002008305_4_GCF_002008305.4_01169:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000973_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000973_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34b19081e61d0bd3dfeafd97671502114b9552e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000973_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01120:0,GCF_002008305_4_GCF_002008305.4_01170:0)n1:0.000531375,(GCF_003691675_1_GCF_003691675.1_00889:0.00605025,(GCF_005280335_1_GCF_005280335.1_01719:0.0634217,GCF_020097155_1_GCF_020097155.1_01617:0.156198)n3:0.0586228)n2:0.000531375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000975_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000975_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8120bb8fe00c807865a3e17f1c07b2144b2ff17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000975_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00891:0.0137319,GCF_002008305_4_GCF_002008305.4_01172:0.0217351)n1:0.00209669,(GCF_023573625_1_GCF_023573625.1_01122:0.0261981,(GCF_005280335_1_GCF_005280335.1_01717:0.157383,GCF_020097155_1_GCF_020097155.1_01615:0.203246)n3:0.133686)n2:0.00209669)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000979_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000979_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30a51a3ab88ce8dcddae4919d28e0c23f006feaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000979_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00895:0.002076,GCF_002008305_4_GCF_002008305.4_01176:0.000986)n1:0.000851125,(GCF_023573625_1_GCF_023573625.1_01126:0.00887425,(GCF_005280335_1_GCF_005280335.1_01713:0.0102495,GCF_020097155_1_GCF_020097155.1_01611:0.268971)n3:0.00299025)n2:0.000851125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000982_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000982_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..200e21b2b63f912a96c8e989d12e3be943a0386c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000982_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01179:0,GCF_003691675_1_GCF_003691675.1_00898:0)n1:0.0106082,((GCF_020097155_1_GCF_020097155.1_01608:0.281766,GCF_005280335_1_GCF_005280335.1_01710:3.27985e-07)n3:0.00369375,GCF_023573625_1_GCF_023573625.1_01129:0.0252705)n2:0.0106082)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000989_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000989_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2498a5e5f4fb53aee44cc4b64eb5353cd942b275
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000989_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01187:0,GCF_023573625_1_GCF_023573625.1_01137:0)n1:0.00181066,(GCF_003691675_1_GCF_003691675.1_00906:0.00885567,(GCF_005280335_1_GCF_005280335.1_01701:0.211536,GCF_020097155_1_GCF_020097155.1_01600:0.352363)n3:0.142368)n2:0.00181066)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000991_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000991_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe3daa3e23832cc74aaaaa0c2ce335db7dafa3dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000991_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00908:0.00200125,GCF_005280335_1_GCF_005280335.1_01699:0.0257787)n1:0.00140913,(GCF_020097155_1_GCF_020097155.1_01598:0.188219,(GCF_002008305_4_GCF_002008305.4_01189:0,GCF_023573625_1_GCF_023573625.1_01139:0)n3:0.00235581)n2:0.00140913)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000993_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000993_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fc27c6c934a36d9c16bdc331a9baf20cd6905ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000993_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01191:0,GCF_023573625_1_GCF_023573625.1_01141:0)n1:0.00231774,(GCF_003691675_1_GCF_003691675.1_00910:0.00504153,(GCF_005280335_1_GCF_005280335.1_01697:0.0665802,GCF_020097155_1_GCF_020097155.1_01596:0.441349)n3:0.138442)n2:0.00231774)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000994_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000994_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e28ba6cd123c3942347d71864271f2deb2a76b45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000994_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00911:0.00885025,(GCF_020097155_1_GCF_020097155.1_01595:0.32406,GCF_005280335_1_GCF_005280335.1_01696:0.0864347)n2:0.0962724)n1:0.000778125,(GCF_023573625_1_GCF_023573625.1_01142:0.00407448,GCF_002008305_4_GCF_002008305.4_01192:0.00345552)n3:0.000778125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000996_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000996_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82af1dccb7bc25998e357c0b41ad696b966dbabf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000996_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01693:0.777813,GCF_020097155_1_GCF_020097155.1_01591:0.742784)n2:0.522677,GCF_002008305_4_GCF_002008305.4_01194:0.0897506)n1:0.0145949,(GCF_023573625_1_GCF_023573625.1_01148:0.119707,GCF_003691675_1_GCF_003691675.1_00914:0.0838496)n3:0.0145949)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000997_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000997_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b33019de76c40a77b3dcd987af93a9da7d7cbce3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000997_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01692:0.268741,GCF_020097155_1_GCF_020097155.1_01590:0.556902)n2:0.188156,GCF_023573625_1_GCF_023573625.1_01149:0.0217027)n1:0.00359791,(GCF_002008305_4_GCF_002008305.4_01195:0.0213929,GCF_003691675_1_GCF_003691675.1_00915:0.0189621)n3:0.00359791)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000999_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000999_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9195c4cd6d97ac97c4142adecbff4d8ffd15a529
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000999_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01151:0,GCF_003691675_1_GCF_003691675.1_00917:0)n1:5.5595e-05,((GCF_005280335_1_GCF_005280335.1_01690:0.0517957,GCF_020097155_1_GCF_020097155.1_01587:0.0993543)n3:0.0631383,GCF_002008305_4_GCF_002008305.4_01197:0.00439681)n2:5.5595e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001008_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001008_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1433373e310f9b35f526c92223abccda13cb341
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001008_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01207:0.0102884,GCF_023573625_1_GCF_023573625.1_01164:0.00990262)n1:0.00119743,((GCF_020097155_1_GCF_020097155.1_01578:0.196307,GCF_005280335_1_GCF_005280335.1_01680:0.0543596)n3:0.0488349,GCF_003691675_1_GCF_003691675.1_00926:0.0111146)n2:0.00119743)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001009_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001009_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4c1d398da48b4578e794af3dc79b9599612c7f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001009_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01679:0.205238,GCF_020097155_1_GCF_020097155.1_01577:0.270164)n2:0.0489001,GCF_003691675_1_GCF_003691675.1_00927:0.0243988)n1:0.00712258,(GCF_023573625_1_GCF_023573625.1_01165:0,GCF_002008305_4_GCF_002008305.4_01208:0)n3:0.00712258)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001010_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001010_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad47eb9132b1958ab61056e2cd2bfce10e46f887
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001010_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01166:0.0102026,GCF_002008305_4_GCF_002008305.4_01209:0.00561038)n1:0.00238244,(GCF_003691675_1_GCF_003691675.1_00928:0.00912662,(GCF_005280335_1_GCF_005280335.1_01678:0.0318366,GCF_020097155_1_GCF_020097155.1_01576:0.208351)n3:0.0343689)n2:0.00238244)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001015_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001015_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5dc16524f2c1f996c580b14fe72157b167dd441
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001015_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01172:0,GCF_002008305_4_GCF_002008305.4_01215:0)n1:0.000991875,((GCF_020097155_1_GCF_020097155.1_01570:0.2521,GCF_005280335_1_GCF_005280335.1_01673:0.0559673)n3:0.0699368,GCF_003691675_1_GCF_003691675.1_00934:0.00610225)n2:0.000991875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001017_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001017_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34e9c8ab8428dba7456faf43a9e6ce8663470c81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001017_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01568:0.169763,GCF_005280335_1_GCF_005280335.1_01671:0.0557555)n2:0.0805055,GCF_023573625_1_GCF_023573625.1_01174:0)n1:0,(GCF_003691675_1_GCF_003691675.1_00936:0,GCF_002008305_4_GCF_002008305.4_01217:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001019_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001019_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..596e1866be329f7dbe94106808a157be5836130f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001019_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01566:0.217178,GCF_005280335_1_GCF_005280335.1_01669:0.0496665)n2:0.0331405,GCF_023573625_1_GCF_023573625.1_01177:0.002738)n1:0.0004395,(GCF_002008305_4_GCF_002008305.4_01219:0,GCF_003691675_1_GCF_003691675.1_00938:0)n3:0.0004395)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001020_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001020_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13c05c05e5a78b0718861565c137d62f7fa51c21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001020_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01178:0.00142456,GCF_002008305_4_GCF_002008305.4_01220:0.00500644)n1:0.00300763,((GCF_005280335_1_GCF_005280335.1_01668:0.04644,GCF_020097155_1_GCF_020097155.1_01565:0.151858)n3:0.0478671,GCF_003691675_1_GCF_003691675.1_00939:0.00043161)n2:0.00300763)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001021_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001021_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b0c1f0cb36f5bb5e9b398c4355381030ccf43a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001021_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01564:0.111092,GCF_005280335_1_GCF_005280335.1_01667:0.0732408)n2:0.0287429,GCF_002008305_4_GCF_002008305.4_01221:0.00185807)n1:0.000814715,(GCF_003691675_1_GCF_003691675.1_00940:0.00702305,GCF_023573625_1_GCF_023573625.1_01179:0.00695995)n3:0.000814715)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001024_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001024_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e54c8b38afc8496113edeea4bfb8e745c0b1c136
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001024_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01225:0.0104369,GCF_023573625_1_GCF_023573625.1_01183:0.00689012)n1:0.00629982,((GCF_020097155_1_GCF_020097155.1_01560:0.388112,GCF_005280335_1_GCF_005280335.1_01663:0.209504)n3:0.219764,GCF_003691675_1_GCF_003691675.1_00944:0.0222399)n2:0.00629982)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001025_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001025_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afe8381b2c6ca6aef223afdd34f7d281a2e18024
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001025_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00945:0,GCF_005280335_1_GCF_005280335.1_01662:0)n1:0,((GCF_020097155_1_GCF_020097155.1_01559:0.124646,GCF_002008305_4_GCF_002008305.4_01226:0.0120275)n3:0.0166445,GCF_023573625_1_GCF_023573625.1_01184:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001027_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001027_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adc61db409b1281a743abb615e8fdec86e4cc804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001027_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01186:0.00045292,GCF_003691675_1_GCF_003691675.1_00947:0.00086308)n1:0.0131587,(GCF_002008305_4_GCF_002008305.4_01228:0.0309936,(GCF_005280335_1_GCF_005280335.1_01660:0.220827,GCF_020097155_1_GCF_020097155.1_01557:0.438344)n3:0.194261)n2:0.0131587)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001028_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001028_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b17989fd448ee7326de11f79d425acdd493e0e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001028_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01187:0.00232651,GCF_003691675_1_GCF_003691675.1_00948:0.0248925)n1:0.0406588,(GCF_002008305_4_GCF_002008305.4_01229:0.177444,(GCF_005280335_1_GCF_005280335.1_01659:0.380747,GCF_020097155_1_GCF_020097155.1_01556:0.562339)n3:0.222337)n2:0.0406588)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001035_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001035_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b03b08e498425c48d95e10da5d6b263ac3449ed6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001035_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01194:0.0013795,GCF_003691675_1_GCF_003691675.1_00955:4.16187e-07)n1:0.0076095,(GCF_002008305_4_GCF_002008305.4_01236:0.0160055,(GCF_020097155_1_GCF_020097155.1_01549:0.245639,GCF_005280335_1_GCF_005280335.1_01652:0.0934798)n3:0.0445915)n2:0.0076095)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001036_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001036_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87fd9b07e9e6e102851e86519230e4cd495eb6fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001036_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01195:0,GCF_003691675_1_GCF_003691675.1_00956:0)n1:0.00828062,(GCF_002008305_4_GCF_002008305.4_01237:0.0240348,(GCF_020097155_1_GCF_020097155.1_01548:0.482229,GCF_005280335_1_GCF_005280335.1_01651:0.0267572)n3:0.0250543)n2:0.00828062)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001039_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001039_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..505511b1a5c2008e1d24b02b0a5e868b311c62c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001039_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01240:0.00266937,GCF_023573625_1_GCF_023573625.1_01198:4.863e-05)n1:0.00142019,(GCF_003691675_1_GCF_003691675.1_00959:0.00125263,(GCF_005280335_1_GCF_005280335.1_01648:0.0840461,GCF_020097155_1_GCF_020097155.1_01545:0.25293)n3:0.116774)n2:0.00142019)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001040_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001040_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a76ea4714ab1b41c4f3e0390a5caebd92080c4c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001040_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01199:0,GCF_002008305_4_GCF_002008305.4_01241:0)n1:0.00011875,(GCF_003691675_1_GCF_003691675.1_00960:0.0007095,(GCF_020097155_1_GCF_020097155.1_01544:0.0604055,GCF_005280335_1_GCF_005280335.1_01647:0.0209355)n3:0.017533)n2:0.00011875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001043_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001043_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8cda98254bf9bfecfc26e88c879ab8e6dace450d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001043_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01203:0.006336,(GCF_020097155_1_GCF_020097155.1_01540:0.185406,GCF_005280335_1_GCF_005280335.1_01643:0.034329)n2:0.011915)n1:0.000834,(GCF_002008305_4_GCF_002008305.4_01245:0,GCF_003691675_1_GCF_003691675.1_00964:0)n3:0.000834)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001049_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001049_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46a50331f519613d5b4231f51183523cd514d179
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001049_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01534:0.05298,GCF_005280335_1_GCF_005280335.1_01637:0.022498)n2:0.0313208,GCF_002008305_4_GCF_002008305.4_01251:0.00318175)n1:0.00257163,(GCF_003691675_1_GCF_003691675.1_00970:0.00060725,GCF_023573625_1_GCF_023573625.1_01209:0.00130175)n3:0.00257163)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001051_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001051_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbf112826ce3432dc4a5c3aac704f79db6a34ad5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001051_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01254:0.0220883,GCF_005280335_1_GCF_005280335.1_01634:0.11078)n1:0.00962287,(GCF_020097155_1_GCF_020097155.1_01531:0.318082,(GCF_003691675_1_GCF_003691675.1_00973:0.0116193,GCF_023573625_1_GCF_023573625.1_01212:4.93971e-07)n3:0.0139063)n2:0.00962287)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001052_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001052_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c50d625a908b49e359964f5735a8878ecf61cf51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001052_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01633:0.0409356,GCF_020097155_1_GCF_020097155.1_01530:0.0536404)n2:0.0247176,GCF_002008305_4_GCF_002008305.4_01255:0.00929437)n1:0.00230657,(GCF_023573625_1_GCF_023573625.1_01213:0.00088188,GCF_003691675_1_GCF_003691675.1_00974:1.34074e-07)n3:0.00230657)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001053_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001053_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7059fef5012981ea5fbb6e1f3d8720541a9aee9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001053_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01529:0.953528,GCF_005280335_1_GCF_005280335.1_01632:0.191984)n2:0.33738,GCF_003691675_1_GCF_003691675.1_00975:0)n1:0,(GCF_023573625_1_GCF_023573625.1_01214:0,GCF_002008305_4_GCF_002008305.4_01256:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001055_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001055_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f01fa2a088b1a3cd9e71e53c22bfb8d419e6713
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001055_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01216:0,(GCF_020097155_1_GCF_020097155.1_01527:0.590433,GCF_005280335_1_GCF_005280335.1_01629:0.189386)n2:0.269757)n1:0,(GCF_002008305_4_GCF_002008305.4_01258:0,GCF_003691675_1_GCF_003691675.1_00977:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001056_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001056_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75c751f0dd00d47322d849b403f5f1261d89c63e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001056_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00978:0,GCF_023573625_1_GCF_023573625.1_01217:0)n1:0.0019905,(GCF_002008305_4_GCF_002008305.4_01259:0.00337,(GCF_005280335_1_GCF_005280335.1_01628:0.0674285,GCF_020097155_1_GCF_020097155.1_01526:0.126635)n3:0.055792)n2:0.0019905)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001058_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001058_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5b298b0ead723cd9cf01b8d4dc5d953879eebcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001058_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01524:0.0994617,GCF_005280335_1_GCF_005280335.1_01627:0.171319)n2:0.131099,GCF_002008305_4_GCF_002008305.4_01261:4.03676e-07)n1:0.00094779,(GCF_023573625_1_GCF_023573625.1_01219:0,GCF_003691675_1_GCF_003691675.1_00980:0)n3:0.00094779)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001064_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001064_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fa72f15b7f757cb04494d618006a033a93f5470
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001064_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01225:0,GCF_003691675_1_GCF_003691675.1_00986:0)n1:0.00709275,(GCF_002008305_4_GCF_002008305.4_01267:0.0121665,(GCF_005280335_1_GCF_005280335.1_01620:0.169405,GCF_020097155_1_GCF_020097155.1_01515:0.435966)n3:0.146307)n2:0.00709275)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001073_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001073_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c10439f63bdd5b69f3572f22c1b9c5a4d920f87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001073_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01277:0.0123392,(GCF_020097155_1_GCF_020097155.1_01505:0.233393,GCF_005280335_1_GCF_005280335.1_01610:0.0946967)n2:0.0923367)n1:0.00289887,(GCF_003691675_1_GCF_003691675.1_00996:0,GCF_023573625_1_GCF_023573625.1_01235:0)n3:0.00289887)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001074_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001074_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..176d3fa1e47c7a01b8b6cb6fd1e9aac484fa546b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001074_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01609:0.113441,GCF_020097155_1_GCF_020097155.1_01504:0.167809)n2:0.097141,GCF_002008305_4_GCF_002008305.4_01278:0)n1:0,(GCF_023573625_1_GCF_023573625.1_01236:0,GCF_003691675_1_GCF_003691675.1_00997:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001082_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001082_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f0b306d9aff9a03f5b53a1e47f65301087e1c1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001082_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01006:1.882e-07,GCF_002008305_4_GCF_002008305.4_01287:0.00196963)n1:0.00037119,(GCF_023573625_1_GCF_023573625.1_01245:0.00269962,(GCF_020097155_1_GCF_020097155.1_01494:0.125517,GCF_005280335_1_GCF_005280335.1_01598:0.0312284)n3:0.0261039)n2:0.00037119)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001086_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001086_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78a40dd21c79857ec38bec92ada6395c3852d08d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001086_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01594:0.0754718,GCF_020097155_1_GCF_020097155.1_01490:0.317421)n2:0.0586887,GCF_002008305_4_GCF_002008305.4_01298:0.00044875)n1:0.000883125,(GCF_003691675_1_GCF_003691675.1_01021:0,GCF_023573625_1_GCF_023573625.1_01256:0)n3:0.000883125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001087_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001087_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbf2884a6849ee20e1d405f2153de203dcd20c43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001087_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01022:0,GCF_002008305_4_GCF_002008305.4_01299:0)n1:0,(GCF_023573625_1_GCF_023573625.1_01257:0,(GCF_020097155_1_GCF_020097155.1_01489:0.162087,GCF_005280335_1_GCF_005280335.1_01593:0.11941)n3:0.0675125)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001091_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001091_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce8aa07b54995f7d1f0910b2f5ca6e5899568186
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001091_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01485:0.204226,GCF_005280335_1_GCF_005280335.1_01589:0.0554185)n2:0.0445385,GCF_003691675_1_GCF_003691675.1_01026:0)n1:0,(GCF_002008305_4_GCF_002008305.4_01303:0,GCF_023573625_1_GCF_023573625.1_01261:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001094_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001094_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c706f0693e2f28c0175bd3a511f123c6edcd1754
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001094_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01481:0.193487,GCF_005280335_1_GCF_005280335.1_01585:0.0388775)n2:0.0619304,GCF_002008305_4_GCF_002008305.4_01307:0.00775955)n1:0.00234723,(GCF_003691675_1_GCF_003691675.1_01030:0,GCF_023573625_1_GCF_023573625.1_01265:0)n3:0.00234723)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001105_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001105_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51a0814354081dd7564eed2a3bd6efa3a914b1ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001105_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01467:0.202194,GCF_005280335_1_GCF_005280335.1_01571:0.0218295)n2:0.0457403,GCF_003691675_1_GCF_003691675.1_01041:2.80667e-07)n1:0.000592125,(GCF_023573625_1_GCF_023573625.1_01276:0.0120873,GCF_002008305_4_GCF_002008305.4_01320:2.80667e-07)n3:0.000592125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001106_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001106_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..972e49bc465e0b56fb66701fcb06f6637181ce6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001106_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01570:0.0373928,GCF_020097155_1_GCF_020097155.1_01466:0.140868)n2:0.0547057,GCF_002008305_4_GCF_002008305.4_01321:0.0305876)n1:0.00605818,(GCF_023573625_1_GCF_023573625.1_01277:0.0322116,GCF_003691675_1_GCF_003691675.1_01042:0.0242464)n3:0.00605818)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001109_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001109_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d62f4e5713799dcbed9e38109c4ce65be0dcf8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001109_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01280:0.0072605,GCF_002008305_4_GCF_002008305.4_01324:0.0087235)n1:0.00268298,(GCF_003691675_1_GCF_003691675.1_01045:0.00354919,(GCF_005280335_1_GCF_005280335.1_01567:0.0922125,GCF_020097155_1_GCF_020097155.1_01463:0.198268)n3:0.0396397)n2:0.00268298)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001111_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001111_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1575a8d53d52f54c7594ccdddfb80b2a6f620090
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001111_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01047:0.00034137,GCF_002008305_4_GCF_002008305.4_01326:0.00229463)n1:0.0102608,(GCF_023573625_1_GCF_023573625.1_01282:0.0137214,(GCF_020097155_1_GCF_020097155.1_01461:0.152942,GCF_005280335_1_GCF_005280335.1_01565:0.136423)n3:0.0384991)n2:0.0102608)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001112_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001112_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..429bbbd34da457dbe836ed3fbbc1843c061ed87c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001112_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01327:0,GCF_005280335_1_GCF_005280335.1_01564:0)n1:0.000481375,(GCF_003691675_1_GCF_003691675.1_01048:0.00784825,(GCF_023573625_1_GCF_023573625.1_01283:0.00552175,GCF_020097155_1_GCF_020097155.1_01460:0.110061)n3:0.00110825)n2:0.000481375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001113_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001113_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc1159500ebacbc03ed68e3b0ffeec9c79630560
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001113_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01049:0.00254475,GCF_002008305_4_GCF_002008305.4_01328:0.0108492)n1:0.00927812,(GCF_023573625_1_GCF_023573625.1_01284:0.0307877,(GCF_005280335_1_GCF_005280335.1_01563:0.0579078,GCF_020097155_1_GCF_020097155.1_01459:0.945871)n3:0.0209247)n2:0.00927812)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001115_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001115_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5965b0acf9e299c83af06dea269541962341eea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001115_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01330:0,GCF_023573625_1_GCF_023573625.1_01286:0)n1:0.000554375,(GCF_003691675_1_GCF_003691675.1_01051:0.00260425,(GCF_005280335_1_GCF_005280335.1_01561:0.0142072,GCF_020097155_1_GCF_020097155.1_01457:0.0726648)n3:0.00150325)n2:0.000554375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001117_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001117_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a562a75432d63ec4bab87b01e9d131994ffc024
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001117_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_01559:0,GCF_002008305_4_GCF_002008305.4_01332:0)n1:0,(GCF_003691675_1_GCF_003691675.1_01053:0,(GCF_023573625_1_GCF_023573625.1_01288:0.111989,GCF_020097155_1_GCF_020097155.1_01455:0.24805)n3:0.1212)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001118_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001118_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1e8ca39c755335b3170634a4d63350e730c869f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001118_tree.txt
@@ -0,0 +1 @@
+(((GCF_023573625_1_GCF_023573625.1_01289:0.0130297,GCF_020097155_1_GCF_020097155.1_01454:0.0959292)n2:0.00144975,GCF_005280335_1_GCF_005280335.1_01558:0.00547975)n1:0.000667625,(GCF_002008305_4_GCF_002008305.4_01333:0,GCF_003691675_1_GCF_003691675.1_01054:0)n3:0.000667625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001119_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001119_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1515073b69e56c4f5945f04b89d2570817348a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001119_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01335:0.0141666,(GCF_020097155_1_GCF_020097155.1_01452:0.265922,GCF_005280335_1_GCF_005280335.1_01556:0.0535076)n2:0.0397439)n1:0.00205469,(GCF_003691675_1_GCF_003691675.1_01056:0.0124369,GCF_023573625_1_GCF_023573625.1_01291:0.00242613)n3:0.00205469)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001120_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001120_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..563869a50818b5d28691ace2c9ec730a2a659c50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001120_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01292:0.00332052,GCF_002008305_4_GCF_002008305.4_01336:0.00552748)n1:0.00519282,((GCF_020097155_1_GCF_020097155.1_01451:0.0903877,GCF_005280335_1_GCF_005280335.1_01555:0.0149733)n3:0.0140379,GCF_003691675_1_GCF_003691675.1_01057:0.00162819)n2:0.00519282)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001121_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001121_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e78b85d9f998f34f4dee4198f1b9bca461d31299
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001121_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01450:0.185497,GCF_005280335_1_GCF_005280335.1_01554:0.082895)n2:0.0521296,GCF_002008305_4_GCF_002008305.4_01338:0.00432871)n1:0.0015119,(GCF_003691675_1_GCF_003691675.1_01058:3.30622e-07,GCF_023573625_1_GCF_023573625.1_01293:0.00278035)n3:0.0015119)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001122_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001122_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82c4c7e9be2454389e352aad3c6e95809deb7f88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001122_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01294:0,GCF_003691675_1_GCF_003691675.1_01059:0)n1:0.00797126,(GCF_002008305_4_GCF_002008305.4_01339:0.0447575,(GCF_005280335_1_GCF_005280335.1_01553:0.126089,GCF_020097155_1_GCF_020097155.1_01449:0.358803)n3:0.123946)n2:0.00797126)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001124_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001124_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe20d65a366ee3e97d4487935838b9e0cde3847f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001124_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01297:0,GCF_002008305_4_GCF_002008305.4_01342:0)n1:0,((GCF_020097155_1_GCF_020097155.1_01446:0.07212,GCF_005280335_1_GCF_005280335.1_01550:0.033598)n3:0.024513,GCF_003691675_1_GCF_003691675.1_01062:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001125_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001125_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de0db3c7dc0f224f41c85444c5d299566d7686fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001125_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01445:0.0728413,GCF_005280335_1_GCF_005280335.1_01549:0.0155817)n2:0.0117795,GCF_003691675_1_GCF_003691675.1_01063:0.00233336)n1:0.00072707,(GCF_002008305_4_GCF_002008305.4_01343:0.00127348,GCF_023573625_1_GCF_023573625.1_01298:0.00103652)n3:0.00072707)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001127_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001127_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8c202da6af820d52de9a62dcfe6524f1dc5e360
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001127_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01300:0.00801216,(GCF_005280335_1_GCF_005280335.1_01547:0.0900038,GCF_020097155_1_GCF_020097155.1_01443:0.282465)n2:0.0721466)n1:0.00232892,(GCF_002008305_4_GCF_002008305.4_01345:0.002469,GCF_003691675_1_GCF_003691675.1_01065:0.000898)n3:0.00232892)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001130_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001130_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..198caff2e2e6f410e93b921bc1e990b827f62f28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001130_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01303:0.021373,(GCF_005280335_1_GCF_005280335.1_01544:0.149449,GCF_020097155_1_GCF_020097155.1_01440:0.30871)n2:0.0955185)n1:0.012922,(GCF_002008305_4_GCF_002008305.4_01348:0.0054418,GCF_003691675_1_GCF_003691675.1_01068:0.0274962)n3:0.012922)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001131_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001131_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f103525453d8e29a4291112ccda9906c7942409d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001131_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01349:0.0151054,GCF_023573625_1_GCF_023573625.1_01304:0.0129186)n1:0.00096741,((GCF_020097155_1_GCF_020097155.1_01439:0.260774,GCF_005280335_1_GCF_005280335.1_01543:0.104325)n3:0.128818,GCF_003691675_1_GCF_003691675.1_01069:0.0130393)n2:0.00096741)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001134_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001134_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5695c14e54179e8611f9407e6c595fa50d4a8ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001134_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01072:0.0198646,GCF_023573625_1_GCF_023573625.1_01307:0.0133615)n1:0.00345947,((GCF_005280335_1_GCF_005280335.1_01540:0.2599,GCF_020097155_1_GCF_020097155.1_01436:0.647207)n3:0.200426,GCF_002008305_4_GCF_002008305.4_01352:0.0162326)n2:0.00345947)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001135_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001135_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b96dce3ba3b6b68178e35908d1cd0b12fa3534c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001135_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01353:0.004012,GCF_003691675_1_GCF_003691675.1_01073:0.000888)n1:0.00192425,(GCF_023573625_1_GCF_023573625.1_01308:0.003521,(GCF_005280335_1_GCF_005280335.1_01539:0.0528173,GCF_020097155_1_GCF_020097155.1_01435:0.163949)n3:0.061275)n2:0.00192425)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001137_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001137_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c4329d4a6470ba1b79bd71189b66ea4ff67d272
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001137_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01433:0.432022,GCF_005280335_1_GCF_005280335.1_01537:0.086307)n2:0.0692845,GCF_003691675_1_GCF_003691675.1_01075:0.0044264)n1:0.0015383,(GCF_002008305_4_GCF_002008305.4_01355:0.00811698,GCF_023573625_1_GCF_023573625.1_01310:0.00506702)n3:0.0015383)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001139_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001139_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..050db1bb089527db987042101214a9b638344fb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001139_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01078:0.00371236,(GCF_005280335_1_GCF_005280335.1_01535:0.326034,GCF_020097155_1_GCF_020097155.1_01430:0.108079)n2:0.0599033)n1:0.00148057,(GCF_002008305_4_GCF_002008305.4_01358:0.00294122,GCF_023573625_1_GCF_023573625.1_01313:0.00024978)n3:0.00148057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001142_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001142_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc856ebca8d472c76fef49e42e4c4462e2940dd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001142_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01427:0.650887,GCF_005280335_1_GCF_005280335.1_01532:0.156895)n2:0.117113,GCF_003691675_1_GCF_003691675.1_01081:0.0423525)n1:0.008537,(GCF_002008305_4_GCF_002008305.4_01361:9.88613e-07,GCF_023573625_1_GCF_023573625.1_01316:0.00489875)n3:0.008537)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001144_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001144_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8838a599aacf62e88625abf79937507bf8c14531
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001144_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01425:0.0967507,GCF_005280335_1_GCF_005280335.1_01530:1.02948e-07)n2:0.00694575,GCF_003691675_1_GCF_003691675.1_01083:1.02948e-07)n1:0.000684875,(GCF_002008305_4_GCF_002008305.4_01363:0,GCF_023573625_1_GCF_023573625.1_01318:0)n3:0.000684875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001152_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001152_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f28b416ff013a6a8ab472c95ff0e602274170841
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001152_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01092:0.0027905,(GCF_005280335_1_GCF_005280335.1_01520:0.110385,GCF_020097155_1_GCF_020097155.1_01416:0.331147)n2:0.155274)n1:0.00195675,(GCF_002008305_4_GCF_002008305.4_01372:0,GCF_023573625_1_GCF_023573625.1_01327:0)n3:0.00195675)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001154_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001154_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..288bd26584df752aeb3459f211d7f11455b4d687
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001154_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01094:2.5e-05,GCF_023573625_1_GCF_023573625.1_01329:0.002042)n1:0.00440975,((GCF_005280335_1_GCF_005280335.1_01518:0.054526,GCF_020097155_1_GCF_020097155.1_01413:0.210631)n3:0.0739625,GCF_002008305_4_GCF_002008305.4_01374:0.0335125)n2:0.00440975)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001157_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001157_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c10a49b6bc20c41022f30f4fd02bb11fc213dcc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001157_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01515:0.0838669,GCF_020097155_1_GCF_020097155.1_01410:0.436151)n2:0.0697016,GCF_023573625_1_GCF_023573625.1_01332:0.0106484)n1:0.00218806,(GCF_003691675_1_GCF_003691675.1_01097:0.0162001,GCF_002008305_4_GCF_002008305.4_01377:6.20542e-07)n3:0.00218806)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001164_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001164_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98a1e7e2cc29515e4d1be000f826e4197194b489
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001164_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01490:0.086994,GCF_020097155_1_GCF_020097155.1_01401:0.251199)n2:0.062504,GCF_002008305_4_GCF_002008305.4_01406:4.05539e-07)n1:0.0001415,(GCF_023573625_1_GCF_023573625.1_01356:4.05539e-07,GCF_003691675_1_GCF_003691675.1_01136:0.005125)n3:0.0001415)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001167_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001167_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f30e910a232be22e4f7ed3609fc3257aa3ce900
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001167_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01393:0.335576,GCF_005280335_1_GCF_005280335.1_01486:0.0273035)n2:0.0409345,GCF_023573625_1_GCF_023573625.1_01363:0.001934)n1:0.0007955,(GCF_002008305_4_GCF_002008305.4_01413:0,GCF_003691675_1_GCF_003691675.1_01144:0)n3:0.0007955)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001168_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001168_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8d65f94088ec84886ace32227b478a29e07318c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001168_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01485:0.020302,GCF_020097155_1_GCF_020097155.1_01392:0.05587)n2:0.0343665,GCF_003691675_1_GCF_003691675.1_01145:0.0030035)n1:0.00100275,(GCF_023573625_1_GCF_023573625.1_01364:0.0036345,GCF_002008305_4_GCF_002008305.4_01414:0.0008665)n3:0.00100275)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001169_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001169_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c1524c16b77b490e5f01160b6c4ff6e83bc2aff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001169_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01484:0.0221166,GCF_020097155_1_GCF_020097155.1_01391:0.0138834)n2:0.0192096,GCF_023573625_1_GCF_023573625.1_01365:4.038e-05)n1:0.00577531,(GCF_003691675_1_GCF_003691675.1_01146:0.00340038,GCF_002008305_4_GCF_002008305.4_01415:0.00400363)n3:0.00577531)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001171_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001171_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31e9ab795ccde015913ee8dd7a58d0fc4d807047
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001171_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01389:0.280574,GCF_023573625_1_GCF_023573625.1_01368:0.037877)n2:0.0257927,GCF_002008305_4_GCF_002008305.4_01418:0.0272753)n1:0.00669813,(GCF_003691675_1_GCF_003691675.1_01149:0.00787925,GCF_005280335_1_GCF_005280335.1_01481:0.0139968)n3:0.00669813)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001178_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001178_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..181426122d616e8a650b06b251845eeb96b19c61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001178_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01428:2.31107e-07,GCF_023573625_1_GCF_023573625.1_01378:0.00193438)n1:0.00169531,(GCF_003691675_1_GCF_003691675.1_01159:0.00653587,(GCF_020097155_1_GCF_020097155.1_01378:0.13641,GCF_005280335_1_GCF_005280335.1_01471:0.0535699)n3:0.0295061)n2:0.00169531)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001181_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001181_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a802639322415d11ecc719733c1df1293511f08f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001181_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01381:4.9e-05,GCF_002008305_4_GCF_002008305.4_01431:0.003021)n1:0.00127575,((GCF_020097155_1_GCF_020097155.1_01375:0.0304148,GCF_005280335_1_GCF_005280335.1_01468:0.0161932)n3:0.0058995,GCF_003691675_1_GCF_003691675.1_01163:0.0026885)n2:0.00127575)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001182_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001182_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0563698dc2112229935cfc26b3d066ed1554f6ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001182_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01467:0.159597,GCF_020097155_1_GCF_020097155.1_01374:0.504456)n2:0.13454,GCF_002008305_4_GCF_002008305.4_01432:0.0709459)n1:0.0205578,(GCF_023573625_1_GCF_023573625.1_01382:0.0256626,GCF_003691675_1_GCF_003691675.1_01164:0.00413737)n3:0.0205578)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001184_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001184_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ed26b0e729c445fbb463533f85aa00f689cd38c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001184_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01464:0.041451,GCF_020097155_1_GCF_020097155.1_01372:0.12252)n2:0.037807,GCF_002008305_4_GCF_002008305.4_01434:0.000526)n1:0.0029785,(GCF_003691675_1_GCF_003691675.1_01166:0,GCF_023573625_1_GCF_023573625.1_01384:0)n3:0.0029785)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001186_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001186_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..051d5da398a5efe67b036b033ce78057248c1bc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001186_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01436:0.00225728,GCF_003691675_1_GCF_003691675.1_01168:0.00016872)n1:0.000890515,(GCF_023573625_1_GCF_023573625.1_01386:0.00299338,(GCF_020097155_1_GCF_020097155.1_01370:0.150904,GCF_005280335_1_GCF_005280335.1_01462:0.0628262)n3:0.0407118)n2:0.000890515)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001188_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001188_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58ae0ab17c0cf4667be7fdf79c3104cee0b57161
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001188_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01460:0.047114,GCF_020097155_1_GCF_020097155.1_01368:0.093914)n2:0.0341539,GCF_023573625_1_GCF_023573625.1_01388:0.00626676)n1:0.00046387,(GCF_003691675_1_GCF_003691675.1_01170:0.00643811,GCF_002008305_4_GCF_002008305.4_01438:0.00643389)n3:0.00046387)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001192_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001192_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a70b1267fb9226e8287ef8397de3bdd76a0a9b02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001192_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01175:0.0005039,GCF_002008305_4_GCF_002008305.4_01443:0.0013181)n1:0.00435908,(GCF_023573625_1_GCF_023573625.1_01393:0.00889477,(GCF_005280335_1_GCF_005280335.1_01455:0.0477692,GCF_020097155_1_GCF_020097155.1_01363:0.297061)n3:0.0512802)n2:0.00435908)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001197_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001197_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..25a0f1a7bfe416b2f49fa0f07ca60e5196a441ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001197_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01450:0.117939,GCF_020097155_1_GCF_020097155.1_01354:0.396737)n2:0.0966677,GCF_023573625_1_GCF_023573625.1_01399:0.0680977)n1:0.00944962,(GCF_002008305_4_GCF_002008305.4_01449:0,GCF_003691675_1_GCF_003691675.1_01181:0)n3:0.00944962)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001201_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001201_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40bd6a80de9db720df963e555ef5a27d10d85484
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001201_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01455:0.0121787,GCF_023573625_1_GCF_023573625.1_01405:0.0249453)n1:0.0477412,(GCF_003691675_1_GCF_003691675.1_01187:0.138185,(GCF_005280335_1_GCF_005280335.1_01445:0.050928,GCF_020097155_1_GCF_020097155.1_01348:0.320514)n3:0.0812676)n2:0.0477412)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001202_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001202_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b69db66e9293bb138f3869969bf73896f14b7fe1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001202_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01406:0,GCF_002008305_4_GCF_002008305.4_01456:0)n1:0.0256788,(GCF_005280335_1_GCF_005280335.1_01444:0.0300165,(GCF_003691675_1_GCF_003691675.1_01188:0.0222575,GCF_020097155_1_GCF_020097155.1_01347:0.0903555)n3:0.0130925)n2:0.0256788)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001204_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001204_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23b0a7ccda1e4570e81b6004c7ddb206925c0cd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001204_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01190:0,GCF_023573625_1_GCF_023573625.1_01408:0)n1:0,(GCF_020097155_1_GCF_020097155.1_01345:0.011976,(GCF_002008305_4_GCF_002008305.4_01458:0,GCF_005280335_1_GCF_005280335.1_01442:0)n3:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001207_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001207_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40827c659b62004802bbacb3f9fc624b41e0b01d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001207_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01461:0.00728263,GCF_023573625_1_GCF_023573625.1_01411:0.00014337)n1:0.00341437,(GCF_003691675_1_GCF_003691675.1_01193:0.00545285,(GCF_020097155_1_GCF_020097155.1_01342:0.429449,GCF_005280335_1_GCF_005280335.1_01439:0.148072)n3:0.063286)n2:0.00341437)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001211_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001211_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c95a647961366416b8b10e29161390d8b750f158
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001211_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01435:0.249465,GCF_020097155_1_GCF_020097155.1_01338:0.563968)n2:0.148911,GCF_003691675_1_GCF_003691675.1_01197:0.0091619)n1:0.00550705,(GCF_002008305_4_GCF_002008305.4_01465:0.0072609,GCF_023573625_1_GCF_023573625.1_01415:0.0006921)n3:0.00550705)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001215_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001215_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8052defba68ce3883be868ba41b7e20e56ff8540
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001215_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01333:0.513462,GCF_005280335_1_GCF_005280335.1_01431:0.0899266)n2:0.103718,GCF_023573625_1_GCF_023573625.1_01419:0.0199789)n1:0.00395856,(GCF_002008305_4_GCF_002008305.4_01469:0.0221456,GCF_003691675_1_GCF_003691675.1_01201:0.0160384)n3:0.00395856)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001216_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001216_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94616ec28cb6a2be52045c0e7546579d5eb05e04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001216_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01421:0,GCF_002008305_4_GCF_002008305.4_01471:0)n1:0.00668725,(GCF_003691675_1_GCF_003691675.1_01203:0.0068235,(GCF_020097155_1_GCF_020097155.1_01331:0.08761,GCF_005280335_1_GCF_005280335.1_01429:0.026791)n3:0.020505)n2:0.00668725)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001221_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001221_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51408bbc35e12c0c144d1bf7c7137ecfce08331a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001221_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01428:0,GCF_003691675_1_GCF_003691675.1_01210:0)n1:0,(GCF_002008305_4_GCF_002008305.4_01478:0,(GCF_020097155_1_GCF_020097155.1_01324:0.178444,GCF_005280335_1_GCF_005280335.1_01424:0.175867)n3:0.11632)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001222_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001222_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b9a8d33d5bc2e3d5208e614f5f5c6e96964f374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001222_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01479:0,GCF_003691675_1_GCF_003691675.1_01211:0)n1:0,((GCF_005280335_1_GCF_005280335.1_01423:0.244297,GCF_020097155_1_GCF_020097155.1_01323:0.199756)n3:0.374712,GCF_023573625_1_GCF_023573625.1_01429:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001224_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001224_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..959a7e303aff19c6f41ef580b6fddbaee15c4aa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001224_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01431:0,GCF_002008305_4_GCF_002008305.4_01481:0)n1:0.00399488,(GCF_003691675_1_GCF_003691675.1_01213:0.00711025,(GCF_020097155_1_GCF_020097155.1_01321:0.176967,GCF_005280335_1_GCF_005280335.1_01421:0.178176)n3:0.0695082)n2:0.00399488)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001225_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001225_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5dd9d377bfc377b5ce2e872e01ed8587e2b61d07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001225_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01482:0.012257,(GCF_020097155_1_GCF_020097155.1_01320:0.416971,GCF_005280335_1_GCF_005280335.1_01420:0.100321)n2:0.136088)n1:0.00298425,(GCF_003691675_1_GCF_003691675.1_01214:0.00535375,GCF_023573625_1_GCF_023573625.1_01432:0.00488625)n3:0.00298425)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001226_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001226_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be21d7f66b0cbfa59eddd7b13c4e249cd6c737a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001226_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01215:8.088e-05,GCF_023573625_1_GCF_023573625.1_01433:0.0118361)n1:0.00695956,((GCF_020097155_1_GCF_020097155.1_01319:0.204446,GCF_005280335_1_GCF_005280335.1_01419:0.0281474)n3:0.0495236,GCF_002008305_4_GCF_002008305.4_01483:0.0449194)n2:0.00695956)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001228_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001228_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87d01a51a7248b7d8342c165ba6a7d8d746976af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001228_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01435:0.00287663,GCF_003691675_1_GCF_003691675.1_01217:0.0158144)n1:0.0126714,(GCF_002008305_4_GCF_002008305.4_01485:0.0343046,(GCF_005280335_1_GCF_005280335.1_01417:0.0952066,GCF_020097155_1_GCF_020097155.1_01317:0.478205)n3:0.166547)n2:0.0126714)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001229_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001229_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6bdb30ad80a4bab604fd428e36016f30e12e480d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001229_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01486:0.00423563,GCF_023573625_1_GCF_023573625.1_01436:4.03087e-07)n1:0.00041831,(GCF_003691675_1_GCF_003691675.1_01218:4.03087e-07,(GCF_005280335_1_GCF_005280335.1_01416:0.0838459,GCF_020097155_1_GCF_020097155.1_01316:0.247267)n3:0.0685751)n2:0.00041831)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001233_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001233_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88b31ca5c48d11d3b5b638c33e363236227788f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001233_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01515:0,GCF_003691675_1_GCF_003691675.1_01224:0)n1:0.0302567,(GCF_023573625_1_GCF_023573625.1_01442:0.0521567,(GCF_020097155_1_GCF_020097155.1_01309:0.504686,GCF_005280335_1_GCF_005280335.1_01410:0.275023)n3:0.11116)n2:0.0302567)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001234_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001234_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4115571e729b497ba18ce2052b1b7be90bc4e9f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001234_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01516:0.0082855,GCF_003691675_1_GCF_003691675.1_01225:1.43455e-06)n1:0.008665,((GCF_005280335_1_GCF_005280335.1_01409:0.243316,GCF_020097155_1_GCF_020097155.1_01308:1.03731)n3:0.128922,GCF_023573625_1_GCF_023573625.1_01443:0.000276)n2:0.008665)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001235_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001235_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..873a051fa3d544e83e77bae21b795a741d97ec01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001235_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01307:0.139183,GCF_005280335_1_GCF_005280335.1_01408:0.039433)n2:0.0191646,GCF_023573625_1_GCF_023573625.1_01444:0.00179071)n1:0.000557145,(GCF_003691675_1_GCF_003691675.1_01226:0,GCF_002008305_4_GCF_002008305.4_01517:0)n3:0.000557145)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001239_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001239_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb0a1eff2bdcc8471218368c47f932d484fa36a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001239_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01448:0.00486188,GCF_002008305_4_GCF_002008305.4_01521:0.00454112)n1:0.000563435,((GCF_020097155_1_GCF_020097155.1_01303:0.31047,GCF_005280335_1_GCF_005280335.1_01404:0.0859131)n3:0.0640364,GCF_003691675_1_GCF_003691675.1_01230:0.00747913)n2:0.000563435)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001240_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001240_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f1d0a606d037b4f03265f864d1e2c59770af160
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001240_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01231:0.00930838,GCF_002008305_4_GCF_002008305.4_01522:0.00916263)n1:0.0102261,(GCF_023573625_1_GCF_023573625.1_01449:0.00960337,(GCF_005280335_1_GCF_005280335.1_01403:0.0960334,GCF_020097155_1_GCF_020097155.1_01302:0.484046)n3:0.206332)n2:0.0102261)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001241_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001241_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..172d53839559d148fa24682b0a841292103d1c0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001241_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01450:0.00681162,(GCF_020097155_1_GCF_020097155.1_01301:0.196154,GCF_005280335_1_GCF_005280335.1_01402:0.0402656)n2:0.0427104)n1:0.00059369,(GCF_003691675_1_GCF_003691675.1_01232:0.00879588,GCF_002008305_4_GCF_002008305.4_01523:0.00841513)n3:0.00059369)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001242_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001242_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c25e152e8330a7c154d9f9d458b974e9744a3d18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001242_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01524:0.003227,(GCF_005280335_1_GCF_005280335.1_01401:0.0382325,GCF_020097155_1_GCF_020097155.1_01300:0.0318135)n2:0.0216925)n1:0.000172,(GCF_003691675_1_GCF_003691675.1_01233:0,GCF_023573625_1_GCF_023573625.1_01451:0)n3:0.000172)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001249_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001249_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a1651d1c27c63235009dc15eef567f72debbd79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001249_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01458:0,GCF_002008305_4_GCF_002008305.4_01531:0)n1:0.000360815,(GCF_003691675_1_GCF_003691675.1_01241:0.00038037,(GCF_020097155_1_GCF_020097155.1_01285:0.180721,GCF_005280335_1_GCF_005280335.1_01394:0.0653512)n3:0.0431866)n2:0.000360815)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001252_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001252_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a13f3c59bc51e5f2dc245e67421a13266902ffa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001252_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01244:0.0013775,(GCF_005280335_1_GCF_005280335.1_01391:0.052432,GCF_020097155_1_GCF_020097155.1_01282:0.155873)n2:0.068487)n1:0.00026575,(GCF_002008305_4_GCF_002008305.4_01534:0,GCF_023573625_1_GCF_023573625.1_01461:0)n3:0.00026575)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001253_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001253_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15d0f4cdbb75e20bc10a7547bab05dc9925bf5a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001253_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01245:0.00139293,GCF_002008305_4_GCF_002008305.4_01535:0.00481007)n1:0.00087688,(GCF_023573625_1_GCF_023573625.1_01462:0.00430555,(GCF_005280335_1_GCF_005280335.1_01390:0.0939705,GCF_020097155_1_GCF_020097155.1_01281:0.238074)n3:0.0823453)n2:0.00087688)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001254_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001254_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac543f80d5b1973d4715984778f82c2bc6eccd2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001254_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01463:0.0295117,GCF_003691675_1_GCF_003691675.1_01246:0.00218425)n1:0.0026225,(GCF_002008305_4_GCF_002008305.4_01536:0.008256,(GCF_005280335_1_GCF_005280335.1_01389:0.226117,GCF_020097155_1_GCF_020097155.1_01280:0.986904)n3:0.0438625)n2:0.0026225)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001257_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001257_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17f5f8990272ca36cc8d8734b1c198e6bbdd5813
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001257_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01385:0.120719,GCF_020097155_1_GCF_020097155.1_01276:0.10775)n2:0.101498,GCF_002008305_4_GCF_002008305.4_01540:0.007674)n1:0.0042175,(GCF_023573625_1_GCF_023573625.1_01467:0,GCF_003691675_1_GCF_003691675.1_01250:0)n3:0.0042175)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001267_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001267_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..092e420bc99f57c5060b243332b4cfa8d40d6085
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001267_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01551:0.0235107,GCF_003691675_1_GCF_003691675.1_01261:0.0155323)n1:0.0107201,((GCF_005280335_1_GCF_005280335.1_01374:0.202714,GCF_020097155_1_GCF_020097155.1_01265:0.407247)n3:0.249168,GCF_023573625_1_GCF_023573625.1_01478:0.0687933)n2:0.0107201)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001270_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001270_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24ec6e759f7977242da204fd43435be8931403db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001270_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01481:0.00228775,GCF_002008305_4_GCF_002008305.4_01554:0.00052025)n1:0.009643,(GCF_003691675_1_GCF_003691675.1_01264:0.007392,(GCF_005280335_1_GCF_005280335.1_01371:0.0638173,GCF_020097155_1_GCF_020097155.1_01262:0.112238)n3:0.0652575)n2:0.009643)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001271_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001271_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ba1bf2a9d4f02208395d64383bd277412d0378a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001271_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01482:0,GCF_003691675_1_GCF_003691675.1_01265:0)n1:0.00279462,(GCF_002008305_4_GCF_002008305.4_01555:0.00400275,(GCF_020097155_1_GCF_020097155.1_01261:0.125137,GCF_005280335_1_GCF_005280335.1_01370:0.0135458)n3:0.00771575)n2:0.00279462)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001275_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001275_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3337f6870a94ad583cec9e3c11d7e2186cdf0f8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001275_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01270:0.00106092,GCF_002008305_4_GCF_002008305.4_01560:0.00535108)n1:0.00079102,((GCF_005280335_1_GCF_005280335.1_01366:0.0182755,GCF_020097155_1_GCF_020097155.1_01257:0.0550635)n3:0.0126455,GCF_023573625_1_GCF_023573625.1_01487:0.00071496)n2:0.00079102)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001276_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001276_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edc45fa49d2264953fd24af2d6c26bb6c66b658f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001276_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01365:0.0414763,GCF_020097155_1_GCF_020097155.1_01256:0.150349)n2:0.0479004,GCF_002008305_4_GCF_002008305.4_01561:0.00371029)n1:0.00371061,(GCF_003691675_1_GCF_003691675.1_01271:0.00365154,GCF_023573625_1_GCF_023573625.1_01488:0.00918646)n3:0.00371061)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001277_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001277_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1f8aad22057ea00ab4b4157f412aeed787695cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001277_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01364:0.00543533,GCF_020097155_1_GCF_020097155.1_01255:0.0512247)n2:0.0292339,GCF_023573625_1_GCF_023573625.1_01489:0.00657863)n1:0.000966185,(GCF_002008305_4_GCF_002008305.4_01562:0,GCF_003691675_1_GCF_003691675.1_01272:0)n3:0.000966185)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001278_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001278_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f1f9aab2ecb61f33f3dbb3e201b37752862bf56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001278_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01274:0.00277179,GCF_002008305_4_GCF_002008305.4_01564:0.00048921)n1:0.000378255,((GCF_005280335_1_GCF_005280335.1_01362:0.0594098,GCF_020097155_1_GCF_020097155.1_01253:0.0321632)n3:0.0140913,GCF_023573625_1_GCF_023573625.1_01491:0.00069354)n2:0.000378255)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001283_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001283_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..011c5f5123c0ec28002129c5d0fcc16f5c0e76fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001283_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01280:0.0292282,(GCF_005280335_1_GCF_005280335.1_01354:0.126238,GCF_020097155_1_GCF_020097155.1_01247:0.764072)n2:0.0854522)n1:0.00939714,(GCF_002008305_4_GCF_002008305.4_01570:0.00292941,GCF_023573625_1_GCF_023573625.1_01497:0.00571659)n3:0.00939714)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001285_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001285_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddf01fd87179abee235a1fb9de3fbc207a67895f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001285_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01282:0.00669632,(GCF_020097155_1_GCF_020097155.1_01245:0.239557,GCF_005280335_1_GCF_005280335.1_01352:0.0412672)n2:0.0516109)n1:0.00540009,(GCF_002008305_4_GCF_002008305.4_01572:0.0160936,GCF_023573625_1_GCF_023573625.1_01499:0.00926541)n3:0.00540009)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001286_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001286_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c579da3b2c3ae98f170edd0fb9aaa2fcc8fe0989
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001286_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01573:0.00077194,GCF_023573625_1_GCF_023573625.1_01500:0.00681306)n1:0.00178047,(GCF_003691675_1_GCF_003691675.1_01283:0.00416975,(GCF_020097155_1_GCF_020097155.1_01244:0.116036,GCF_005280335_1_GCF_005280335.1_01351:0.0368487)n3:0.0510753)n2:0.00178047)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001287_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001287_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aabc18fe49e17842a55b583e04a3b8903b3241f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001287_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01350:0.157761,GCF_020097155_1_GCF_020097155.1_01243:0.222303)n2:0.131152,GCF_023573625_1_GCF_023573625.1_01501:0.00677225)n1:0.000755625,(GCF_002008305_4_GCF_002008305.4_01574:0.00127,GCF_003691675_1_GCF_003691675.1_01284:0.001733)n3:0.000755625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001288_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001288_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd36caa09db0d130a5379552deae335fd34d3fa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001288_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01285:8.96086e-07,GCF_023573625_1_GCF_023573625.1_01502:0.0043325)n1:0.00066225,(GCF_002008305_4_GCF_002008305.4_01575:8.96086e-07,(GCF_005280335_1_GCF_005280335.1_01349:0.65569,GCF_020097155_1_GCF_020097155.1_01242:0.116437)n3:0.120951)n2:0.00066225)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001289_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001289_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e196947270bede427e8aabc8e17789035a5a606a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001289_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01286:0.00297238,GCF_023573625_1_GCF_023573625.1_01503:4.02264e-07)n1:0.00164694,((GCF_020097155_1_GCF_020097155.1_01241:0.174935,GCF_005280335_1_GCF_005280335.1_01348:0.0852294)n3:0.13382,GCF_002008305_4_GCF_002008305.4_01576:0.00237462)n2:0.00164694)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001290_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001290_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94418ea06c6f0e1a894c99871e9a8e599dabb9dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001290_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01504:0.00619025,(GCF_005280335_1_GCF_005280335.1_01346:0.109865,GCF_020097155_1_GCF_020097155.1_01239:0.119765)n2:0.0428878)n1:0.00591562,(GCF_003691675_1_GCF_003691675.1_01287:0.00533375,GCF_002008305_4_GCF_002008305.4_01577:0.00535225)n3:0.00591562)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001294_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001294_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc7cd948546f7b8101368ebabc2d4e5ee4d9213c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001294_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01233:0.407375,GCF_005280335_1_GCF_005280335.1_01335:0.300913)n2:0.00273552,GCF_002008305_4_GCF_002008305.4_01587:0.00199806)n1:0.00060897,(GCF_003691675_1_GCF_003691675.1_01298:0.00257841,GCF_023573625_1_GCF_023573625.1_01514:7.16811e-07)n3:0.00060897)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001296_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001296_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..136c09fb31d3bc3f7c09cbf639b6042a66f2e1fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001296_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01591:0,GCF_003691675_1_GCF_003691675.1_01303:0)n1:0.00309519,(GCF_023573625_1_GCF_023573625.1_01518:0.0297646,(GCF_005280335_1_GCF_005280335.1_01300:0.101504,GCF_020097155_1_GCF_020097155.1_01219:0.138075)n3:0.10692)n2:0.00309519)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001300_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001300_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6d9c659951cbcda5dd2ca97ca7ae62aaa4c6bf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001300_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01598:0,GCF_003691675_1_GCF_003691675.1_01310:0)n1:0.014465,(GCF_023573625_1_GCF_023573625.1_01525:0.003955,(GCF_005280335_1_GCF_005280335.1_01295:0.969055,GCF_020097155_1_GCF_020097155.1_01204:1.02118e-06)n3:0.033708)n2:0.014465)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001302_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001302_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33b3289395a7518b2c29d1944c5d69812b632388
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001302_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01527:0.00341104,GCF_003691675_1_GCF_003691675.1_01312:0.00312496)n1:0.0144453,(GCF_002008305_4_GCF_002008305.4_01600:0.00152683,(GCF_005280335_1_GCF_005280335.1_01293:0.0159385,GCF_020097155_1_GCF_020097155.1_01202:0.0149305)n3:0.0485751)n2:0.0144453)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001312_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001312_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbd0b452444f91d1c6dde1f115b1a5525222d860
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001312_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01335:0.00705658,(GCF_020097155_1_GCF_020097155.1_01174:0.288554,GCF_005280335_1_GCF_005280335.1_01266:0.0665898)n2:0.054886)n1:0.00231321,(GCF_002008305_4_GCF_002008305.4_01630:0.01713,GCF_023573625_1_GCF_023573625.1_01559:0.00618305)n3:0.00231321)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001318_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001318_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5eeb695b0c01fdc9e66766cba08cbd94c3b16333
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001318_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01637:0.00010963,GCF_003691675_1_GCF_003691675.1_01342:0.00820837)n1:0.0140114,(GCF_023573625_1_GCF_023573625.1_01566:0.0237851,(GCF_005280335_1_GCF_005280335.1_01258:0.0861196,GCF_020097155_1_GCF_020097155.1_01167:0.353179)n3:0.0638124)n2:0.0140114)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001320_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001320_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49922b3e918cb557f76e446721058d57f6612328
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001320_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01639:0.0218819,GCF_023573625_1_GCF_023573625.1_01568:0.13392)n1:0.0319645,((GCF_020097155_1_GCF_020097155.1_01165:0.572587,GCF_005280335_1_GCF_005280335.1_01256:0.415469)n3:0.279419,GCF_003691675_1_GCF_003691675.1_01344:0.032975)n2:0.0319645)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001322_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001322_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3794357319813a0dba8d97a7528b4968694c1ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001322_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01163:0.557169,GCF_005280335_1_GCF_005280335.1_01254:0.0979493)n2:0.103247,GCF_003691675_1_GCF_003691675.1_01346:0.0156897)n1:0.00206038,(GCF_023573625_1_GCF_023573625.1_01571:0.00650984,GCF_002008305_4_GCF_002008305.4_01641:0.00275116)n3:0.00206038)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001323_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001323_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f620a34b17d3202cd9c16d090fb45188ef1eeda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001323_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01347:0.0589966,GCF_002008305_4_GCF_002008305.4_01642:0.0142604)n1:0.0104302,(GCF_023573625_1_GCF_023573625.1_01572:0.0255346,(GCF_020097155_1_GCF_020097155.1_01162:0.991978,GCF_005280335_1_GCF_005280335.1_01251:0.24093)n3:0.200414)n2:0.0104302)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001324_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001324_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29775af31eacc12331077392dd507ac077261303
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001324_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01161:1.53434,GCF_005280335_1_GCF_005280335.1_01250:0.472919)n2:0.0968049,GCF_003691675_1_GCF_003691675.1_01348:0.0146596)n1:0.0269159,(GCF_002008305_4_GCF_002008305.4_01643:0.0245764,GCF_023573625_1_GCF_023573625.1_01573:0.00492963)n3:0.0269159)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001325_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001325_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8970422a7d8e479e18bd8a442ea06bd69386700c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001325_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01644:0.00841522,GCF_023573625_1_GCF_023573625.1_01574:0.00550578)n1:0.00247562,((GCF_020097155_1_GCF_020097155.1_01160:0.245307,GCF_005280335_1_GCF_005280335.1_01249:0.0489565)n3:0.0213626,GCF_003691675_1_GCF_003691675.1_01349:0.0156286)n2:0.00247562)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001326_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001326_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..496fb71fc4d17b361b8a6a20c8b38fbff2cb38da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001326_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01248:0.0897353,GCF_020097155_1_GCF_020097155.1_01159:0.493854)n2:0.0731135,GCF_002008305_4_GCF_002008305.4_01645:0.002694)n1:0.00536525,(GCF_003691675_1_GCF_003691675.1_01350:0.007384,GCF_023573625_1_GCF_023573625.1_01575:0.00353)n3:0.00536525)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001328_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001328_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..101bc113546996da5ad5fef548a294e5aede3d05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001328_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01647:0.0169769,GCF_003691675_1_GCF_003691675.1_01352:0.0418051)n1:0.0112873,(GCF_023573625_1_GCF_023573625.1_01577:0.0551126,(GCF_005280335_1_GCF_005280335.1_01246:0.305066,GCF_020097155_1_GCF_020097155.1_01157:0.687812)n3:0.336012)n2:0.0112873)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001329_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001329_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e8659c419508cb0df86e6d360bee055a32e1bbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001329_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01578:0.00900126,GCF_002008305_4_GCF_002008305.4_01648:0.00278274)n1:0.00109169,(GCF_003691675_1_GCF_003691675.1_01353:0.00513886,(GCF_020097155_1_GCF_020097155.1_01156:0.259897,GCF_005280335_1_GCF_005280335.1_01245:0.0621282)n3:0.0566525)n2:0.00109169)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001332_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001332_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02ca2b1b30a67f44d18900707348f250072f4f48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001332_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01581:0.00186375,GCF_002008305_4_GCF_002008305.4_01651:0.0111022)n1:0.00279575,(GCF_003691675_1_GCF_003691675.1_01356:0.007417,(GCF_005280335_1_GCF_005280335.1_01242:0.107367,GCF_020097155_1_GCF_020097155.1_01153:0.262142)n3:0.12305)n2:0.00279575)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001333_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001333_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6df33c4de09906c88d22c0b4e4290b42794f3dbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001333_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01152:0.0880983,GCF_005280335_1_GCF_005280335.1_01241:0.0134907)n2:0.023671,GCF_003691675_1_GCF_003691675.1_01357:0.00472996)n1:0.00036502,(GCF_002008305_4_GCF_002008305.4_01652:0.00685558,GCF_023573625_1_GCF_023573625.1_01582:0.00270642)n3:0.00036502)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001337_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001337_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff12a24169b7f79982eea285af09791db2a24720
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001337_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_01235:0.045883,GCF_002008305_4_GCF_002008305.4_01659:6.75495e-08)n1:0.0015185,(GCF_023573625_1_GCF_023573625.1_01589:0.006556,(GCF_003691675_1_GCF_003691675.1_01364:0.00704978,GCF_020097155_1_GCF_020097155.1_01146:0.00503522)n3:0.0005065)n2:0.0015185)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001339_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001339_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd5978dbec7f5413e7aa4382b909bbdec5367cf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001339_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_01233:0.0821657,GCF_003691675_1_GCF_003691675.1_01366:0.00221233)n1:0.0024527,(GCF_023573625_1_GCF_023573625.1_01591:0.00830024,(GCF_002008305_4_GCF_002008305.4_01661:0.0047061,GCF_020097155_1_GCF_020097155.1_01144:0.0076229)n3:0.00173676)n2:0.0024527)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001343_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001343_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b458e01e6a6666ddd59f6aeddd7b07339ed3e430
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001343_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01140:0.125053,GCF_005280335_1_GCF_005280335.1_01229:0.0375918)n2:0.0371348,GCF_002008305_4_GCF_002008305.4_01665:0.0116299)n1:0.00022405,(GCF_023573625_1_GCF_023573625.1_01595:0.00373761,GCF_003691675_1_GCF_003691675.1_01370:0.00322239)n3:0.00022405)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001349_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001349_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a5efdb55751ad83a42fa196abc9d70eebbb10f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001349_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01672:0.00309847,GCF_003691675_1_GCF_003691675.1_01377:0.00980453)n1:0.0019437,(GCF_023573625_1_GCF_023573625.1_01602:0.0060139,(GCF_020097155_1_GCF_020097155.1_01134:0.221804,GCF_005280335_1_GCF_005280335.1_01206:0.0278053)n3:0.0366309)n2:0.0019437)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001350_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001350_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e744b3002a455ff9699b501ea1d086dbd7814608
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001350_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01673:0.00078601,GCF_003691675_1_GCF_003691675.1_01378:0.00920799)n1:0.0101747,((GCF_005280335_1_GCF_005280335.1_01205:0.0567192,GCF_020097155_1_GCF_020097155.1_01133:0.325978)n3:0.046982,GCF_023573625_1_GCF_023573625.1_01603:0.0171336)n2:0.0101747)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001352_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001352_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34dedf5a17e0a1b75c67cc1761626c44f787d6d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001352_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01380:0.0150198,GCF_023573625_1_GCF_023573625.1_01605:0.00867224)n1:0.00214855,(GCF_002008305_4_GCF_002008305.4_01675:0.0142693,(GCF_020097155_1_GCF_020097155.1_01131:0.438375,GCF_005280335_1_GCF_005280335.1_01203:0.104136)n3:0.0909312)n2:0.00214855)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001354_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001354_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..634615e9a7707b68578b25c29f3e9797a43d06fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001354_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01677:0.00422587,GCF_003691675_1_GCF_003691675.1_01382:0.00193413)n1:0.0125378,(GCF_023573625_1_GCF_023573625.1_01607:0.0131784,(GCF_020097155_1_GCF_020097155.1_01129:0.55185,GCF_005280335_1_GCF_005280335.1_01201:0.156573)n3:0.116991)n2:0.0125378)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001357_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001357_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f1fd2ff6b2c0a9204cf01d1576a65bd35c80b09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001357_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01386:0.00343575,GCF_002008305_4_GCF_002008305.4_01682:3.28283e-07)n1:0.000215375,(GCF_023573625_1_GCF_023573625.1_01611:3.28283e-07,(GCF_005280335_1_GCF_005280335.1_01196:0.046702,GCF_020097155_1_GCF_020097155.1_01125:0.203239)n3:0.0753372)n2:0.000215375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001361_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001361_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9618779889471cbba719d80f50dc54cd1418239f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001361_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01392:0.0506683,GCF_005280335_1_GCF_005280335.1_01190:0.682369)n1:0.0144215,(GCF_023573625_1_GCF_023573625.1_01617:0.0848741,(GCF_020097155_1_GCF_020097155.1_01120:0.226766,GCF_002008305_4_GCF_002008305.4_01688:0.047134)n3:0.110229)n2:0.0144215)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001366_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001366_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bac5d2a4f4d0069a16f1bc5b5a2de6a115fa3bb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001366_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01693:0.00214887,(GCF_020097155_1_GCF_020097155.1_01115:0.0470998,GCF_005280335_1_GCF_005280335.1_01185:0.00258617)n2:0.0117928)n1:0.000490565,(GCF_023573625_1_GCF_023573625.1_01622:0.00161355,GCF_003691675_1_GCF_003691675.1_01400:0.00308145)n3:0.000490565)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001369_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001369_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3270d469a5b6a8c3f6c8136cad2231f87b535559
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001369_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_01182:0,(GCF_023573625_1_GCF_023573625.1_01625:0,GCF_020097155_1_GCF_020097155.1_01112:0.022633)n2:0)n1:0,(GCF_003691675_1_GCF_003691675.1_01403:0,GCF_002008305_4_GCF_002008305.4_01696:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001375_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001375_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..434f204605dce82a7880d811d2173e28a99efdab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001375_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01409:0,GCF_002008305_4_GCF_002008305.4_01702:0)n1:0,((GCF_005280335_1_GCF_005280335.1_01176:0.0105235,GCF_020097155_1_GCF_020097155.1_01106:0.0806025)n3:0.0174515,GCF_023573625_1_GCF_023573625.1_01631:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001376_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001376_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1be9ae2d5fe16b1e3f8dd43b71361f448f92c83a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001376_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01175:0.0134805,GCF_020097155_1_GCF_020097155.1_01105:0.0773595)n2:0.0555785,GCF_002008305_4_GCF_002008305.4_01703:0)n1:0,(GCF_023573625_1_GCF_023573625.1_01632:0,GCF_003691675_1_GCF_003691675.1_01410:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001384_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001384_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c838cb21e5ea482482cd98c67a5fc6e80c1888bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001384_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01418:0,(GCF_020097155_1_GCF_020097155.1_01097:0.101671,GCF_005280335_1_GCF_005280335.1_01167:0.022228)n2:0.005749)n1:0,(GCF_002008305_4_GCF_002008305.4_01711:0,GCF_023573625_1_GCF_023573625.1_01640:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001385_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001385_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5e109f88e61a63028a3e6d3232780c8a7784bb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001385_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01419:-0,(GCF_020097155_1_GCF_020097155.1_01096:0.0107725,GCF_005280335_1_GCF_005280335.1_01166:0.0017615)n2:0.0107215)n1:0,(GCF_023573625_1_GCF_023573625.1_01641:0,GCF_002008305_4_GCF_002008305.4_01712:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001391_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001391_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c847e4e54e5251e60ee5690a9bb1ccc76647b2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001391_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01718:0,GCF_003691675_1_GCF_003691675.1_01425:0)n1:0,((GCF_005280335_1_GCF_005280335.1_01160:3.70405e-08,GCF_020097155_1_GCF_020097155.1_01090:0.0307325)n3:0.0076845,GCF_023573625_1_GCF_023573625.1_01647:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001395_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001395_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffa8cefde41a119a50326e61fe13d2bb9b0f28c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001395_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01651:0,GCF_002008305_4_GCF_002008305.4_01722:0)n1:0.0252773,((GCF_005280335_1_GCF_005280335.1_01156:0.106222,GCF_020097155_1_GCF_020097155.1_01086:0.467616)n3:0.182533,GCF_003691675_1_GCF_003691675.1_01429:8.05161e-07)n2:0.0252773)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001396_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001396_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b742fc1be601e902ff7077cf3b5735b09348b66e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001396_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01430:0.0033065,GCF_002008305_4_GCF_002008305.4_01723:3.3437e-08)n1:4.75e-05,((GCF_005280335_1_GCF_005280335.1_01155:0.0053855,GCF_020097155_1_GCF_020097155.1_01085:0.0159945)n3:0.0088445,GCF_023573625_1_GCF_023573625.1_01652:3.3437e-08)n2:4.75e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001397_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001397_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3874622f011b03277fa0a32a28eeef8dfbe9b34d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001397_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01724:0,GCF_023573625_1_GCF_023573625.1_01653:0)n1:8.057e-05,(GCF_003691675_1_GCF_003691675.1_01431:0.00131386,(GCF_005280335_1_GCF_005280335.1_01154:0.0184975,GCF_020097155_1_GCF_020097155.1_01084:0.0284875)n3:0.0252208)n2:8.057e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001398_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001398_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86d464e89f6d1d6e2c254713ef5b63159d999b81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001398_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01725:0,GCF_023573625_1_GCF_023573625.1_01654:0)n1:0,(GCF_003691675_1_GCF_003691675.1_01432:0,(GCF_020097155_1_GCF_020097155.1_01083:0.0049075,GCF_005280335_1_GCF_005280335.1_01153:4.9075e-09)n3:0.0016395)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001399_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001399_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3505b6685db5d968d5995dfe9100dc601e299aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001399_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01082:0.0041665,GCF_005280335_1_GCF_005280335.1_01152:0.0041665)n2:0.0062615,GCF_002008305_4_GCF_002008305.4_01726:0.0020705)n1:0.00103525,(GCF_003691675_1_GCF_003691675.1_01433:0,GCF_023573625_1_GCF_023573625.1_01655:0)n3:0.00103525)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001400_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001400_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77cb015c9f7389b5bffab72cd279957ec1a1a111
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001400_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01727:5e-07,GCF_023573625_1_GCF_023573625.1_01656:5e-07)n1:0.000419625,((GCF_005280335_1_GCF_005280335.1_01151:0.0138858,GCF_020097155_1_GCF_020097155.1_01080:0.0402252)n3:0.00964375,GCF_003691675_1_GCF_003691675.1_01434:0.00114825)n2:0.000419625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001401_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001401_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7c17008cbb7a38dba16f3d486cc1b531c08a50e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001401_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01150:0.0135525,GCF_020097155_1_GCF_020097155.1_01079:0.0274155)n2:0.0085085,GCF_002008305_4_GCF_002008305.4_01728:0)n1:0,(GCF_023573625_1_GCF_023573625.1_01657:0,GCF_003691675_1_GCF_003691675.1_01435:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001402_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001402_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efb223e6200232d511b41fdc200fbd26a1d9f16f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001402_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01729:0.00130463,GCF_023573625_1_GCF_023573625.1_01658:1.16501e-07)n1:0.00065231,((GCF_005280335_1_GCF_005280335.1_01149:0.00507462,GCF_020097155_1_GCF_020097155.1_01078:0.0822034)n3:0.0292226,GCF_003691675_1_GCF_003691675.1_01436:1.16501e-07)n2:0.00065231)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001403_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001403_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4247a5730cddbcd4376c3e7d7ad27fc5a4e9817b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001403_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01437:0,GCF_023573625_1_GCF_023573625.1_01659:0)n1:0.000549125,(GCF_002008305_4_GCF_002008305.4_01730:0.00525075,(GCF_020097155_1_GCF_020097155.1_01077:0.0626547,GCF_005280335_1_GCF_005280335.1_01148:0.00634125)n3:0.0152772)n2:0.000549125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001406_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001406_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e8b61c185118cec385fddd9bdca1759277b8c10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001406_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01662:0.0181802,GCF_003691675_1_GCF_003691675.1_01440:0.0103118)n1:0.0110165,(GCF_002008305_4_GCF_002008305.4_01733:0.0185744,(GCF_020097155_1_GCF_020097155.1_01074:0.198483,GCF_005280335_1_GCF_005280335.1_01145:0.101769)n3:0.05614)n2:0.0110165)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001410_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001410_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0f5eb3e75e8a576adbc8df8eb9daa074cbdfc9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001410_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01738:0.01023,GCF_023573625_1_GCF_023573625.1_01667:0.014234)n1:0.00695677,(GCF_003691675_1_GCF_003691675.1_01445:0.0153712,(GCF_020097155_1_GCF_020097155.1_01069:0.213873,GCF_005280335_1_GCF_005280335.1_01140:0.138775)n3:0.103174)n2:0.00695677)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001414_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001414_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed7c3de15289b60892790080ee9d5796fa3966d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001414_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01742:0,GCF_003691675_1_GCF_003691675.1_01449:0)n1:0.00267478,(GCF_023573625_1_GCF_023573625.1_01671:0.00099144,(GCF_005280335_1_GCF_005280335.1_01135:0.0856343,GCF_020097155_1_GCF_020097155.1_01064:0.269486)n3:0.0504495)n2:0.00267478)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001422_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001422_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77096ca6a24e73e072d50a52367b9762c17cdf2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001422_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01457:5e-07,GCF_002008305_4_GCF_002008305.4_01750:5e-07)n1:0.00615135,((GCF_005280335_1_GCF_005280335.1_01127:0.0128995,GCF_020097155_1_GCF_020097155.1_01052:0.284685)n3:0.0020925,GCF_023573625_1_GCF_023573625.1_01679:0.0058558)n2:0.00615135)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001425_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001425_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3bdd44042e5b8394354457cf7f2d2480bdbb061d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001425_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01124:0.0795002,GCF_020097155_1_GCF_020097155.1_01049:0.196584)n2:0.0672167,GCF_023573625_1_GCF_023573625.1_01682:0.00832946)n1:0.00336877,(GCF_003691675_1_GCF_003691675.1_01460:0,GCF_002008305_4_GCF_002008305.4_01753:0)n3:0.00336877)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001427_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001427_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f76d9d635e0321412287a5b83ca384e240addfe6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001427_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01755:0,GCF_003691675_1_GCF_003691675.1_01462:0)n1:0.00490038,(GCF_023573625_1_GCF_023573625.1_01684:2.65682e-07,(GCF_005280335_1_GCF_005280335.1_01122:0.0510162,GCF_020097155_1_GCF_020097155.1_01047:0.182485)n3:0.0232317)n2:0.00490038)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001429_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001429_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da00ff6060aaf2f792a3ce570c1809c7a16c4e70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001429_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01688:0.016029,(GCF_005280335_1_GCF_005280335.1_01118:0.0741615,GCF_020097155_1_GCF_020097155.1_01043:0.216097)n2:0.0543482)n1:0.00999901,(GCF_002008305_4_GCF_002008305.4_01759:0,GCF_003691675_1_GCF_003691675.1_01466:0)n3:0.00999901)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001431_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001431_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e44e21e9ddd5aeefcd27f32ca9d93b5d0cf1558c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001431_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01761:0,GCF_003691675_1_GCF_003691675.1_01468:0)n1:0.00266838,(GCF_023573625_1_GCF_023573625.1_01690:0.00151425,(GCF_005280335_1_GCF_005280335.1_01116:0.0403698,GCF_020097155_1_GCF_020097155.1_01041:0.0645753)n3:0.0364322)n2:0.00266838)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001434_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001434_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ecd423e136c7a03e803604daed455eb3e732cd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001434_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01038:0.30426,GCF_005280335_1_GCF_005280335.1_01113:0.0621217)n2:0.0590418,GCF_002008305_4_GCF_002008305.4_01764:0.0271515)n1:0.00159874,(GCF_023573625_1_GCF_023573625.1_01693:0.00997448,GCF_003691675_1_GCF_003691675.1_01471:0.0197355)n3:0.00159874)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001435_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001435_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80af681055fe94030a689f5d1796294060397d8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001435_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01037:0.854795,GCF_005280335_1_GCF_005280335.1_01112:0.105874)n2:0.12733,GCF_002008305_4_GCF_002008305.4_01765:0.00054063)n1:0.00285318,(GCF_003691675_1_GCF_003691675.1_01472:0.0234746,GCF_023573625_1_GCF_023573625.1_01694:0.00856038)n3:0.00285318)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001437_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001437_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f954b6136ed94cd40756f7daaae696137242607b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001437_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01698:0,GCF_003691675_1_GCF_003691675.1_01476:0)n1:0.00359393,(GCF_002008305_4_GCF_002008305.4_01769:0.0178921,(GCF_020097155_1_GCF_020097155.1_01034:0.41382,GCF_005280335_1_GCF_005280335.1_01108:0.0965015)n3:0.0643035)n2:0.00359393)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001438_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001438_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1439ad19f0b78640db297a76d8a468b05ccc8ca8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001438_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01033:0.209459,GCF_005280335_1_GCF_005280335.1_01107:0.0432399)n2:0.0690059,GCF_002008305_4_GCF_002008305.4_01770:0.00963613)n1:0.00082294,(GCF_003691675_1_GCF_003691675.1_01477:0.0103611,GCF_023573625_1_GCF_023573625.1_01699:0.00334288)n3:0.00082294)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001448_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001448_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fd1a81bb597f9d8ee5541596cb4fc8d54f06096
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001448_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01713:0.00400537,GCF_003691675_1_GCF_003691675.1_01491:0.00568863)n1:0.000736935,(GCF_002008305_4_GCF_002008305.4_01784:0.00045663,(GCF_005280335_1_GCF_005280335.1_01094:0.0328689,GCF_020097155_1_GCF_020097155.1_01017:0.108069)n3:0.0180979)n2:0.000736935)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001451_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001451_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15472edacfbefea2d39e9a3444c292a5419124e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001451_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01798:0.0036549,GCF_023573625_1_GCF_023573625.1_01717:0.0079711)n1:0.000540685,(GCF_003691675_1_GCF_003691675.1_01495:0.00385276,(GCF_020097155_1_GCF_020097155.1_01013:0.208697,GCF_005280335_1_GCF_005280335.1_01078:0.0523395)n3:0.0342649)n2:0.000540685)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001455_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001455_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b5da76247fa63aca33e3690d779e77f726259eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001455_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_01007:0.223181,GCF_003691675_1_GCF_003691675.1_01499:0.0168022)n1:0.0138913,(GCF_005280335_1_GCF_005280335.1_01071:0.00859455,(GCF_002008305_4_GCF_002008305.4_01802:0.00639331,GCF_023573625_1_GCF_023573625.1_01723:0.00376869)n3:0.00724045)n2:0.0138913)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001456_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001456_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f894d2bf078848e8ee38dc8c7a530558216d4390
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001456_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_01070:6.48958e-07,GCF_003691675_1_GCF_003691675.1_01500:0.00693275)n1:0.111587,(GCF_020097155_1_GCF_020097155.1_01006:0.230647,(GCF_023573625_1_GCF_023573625.1_01724:0.0324168,GCF_002008305_4_GCF_002008305.4_01803:0.0616963)n3:0.094946)n2:0.111587)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001460_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001460_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7e864ebd24330f14e4cc6715fbf96fe6880a822
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001460_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01508:0.0006557,GCF_023573625_1_GCF_023573625.1_01732:0.0162463)n1:0.0103244,(GCF_002008305_4_GCF_002008305.4_01811:0.00970098,(GCF_020097155_1_GCF_020097155.1_00998:0.196296,GCF_005280335_1_GCF_005280335.1_01063:0.0876908)n3:0.0322274)n2:0.0103244)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001461_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001461_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c86e6cba6d93f9a967632425a69d7bea093c26c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001461_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01733:0,GCF_002008305_4_GCF_002008305.4_01812:0)n1:0,(GCF_020097155_1_GCF_020097155.1_00997:0.046606,(GCF_003691675_1_GCF_003691675.1_01509:0,GCF_005280335_1_GCF_005280335.1_01062:0)n3:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001462_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001462_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffc0cbaf0e1915f0959b5485aec8e1bdf5abd019
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001462_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01734:0.0082275,GCF_002008305_4_GCF_002008305.4_01813:0.0072585)n1:0.0008635,(GCF_003691675_1_GCF_003691675.1_01510:0.001212,(GCF_020097155_1_GCF_020097155.1_00996:0.172684,GCF_005280335_1_GCF_005280335.1_01061:0.064426)n3:0.0468415)n2:0.0008635)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001467_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001467_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5661391543a086aa9ece2b7c6848650cab1a3c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001467_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01515:2.38365e-07,GCF_023573625_1_GCF_023573625.1_01739:0.00304236)n1:0.00615993,(GCF_002008305_4_GCF_002008305.4_01818:0.00365352,(GCF_005280335_1_GCF_005280335.1_01052:0.0346273,GCF_020097155_1_GCF_020097155.1_00990:0.140051)n3:0.044695)n2:0.00615993)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001469_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001469_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71e4f387cc9544d4088368d1995e9e2834cdab15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001469_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01820:0.00835912,GCF_023573625_1_GCF_023573625.1_01741:0.00528488)n1:0.00144068,(GCF_003691675_1_GCF_003691675.1_01517:0.0184806,(GCF_020097155_1_GCF_020097155.1_00988:0.130412,GCF_005280335_1_GCF_005280335.1_01049:0.140884)n3:0.0992789)n2:0.00144068)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001471_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001471_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8bd6a523fe898aa2a44fa214de0de007b2973cb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001471_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01743:0,GCF_002008305_4_GCF_002008305.4_01822:0)n1:0.0227642,(GCF_003691675_1_GCF_003691675.1_01519:0.0139275,(GCF_005280335_1_GCF_005280335.1_01047:0.0773269,GCF_020097155_1_GCF_020097155.1_00986:0.441899)n3:0.0393245)n2:0.0227642)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001474_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001474_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8622e9c668aedf70797909c428d8d02897a5d06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001474_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01825:0.0145773,GCF_023573625_1_GCF_023573625.1_01746:0.0151997)n1:0.0511509,((GCF_005280335_1_GCF_005280335.1_01044:0.189105,GCF_020097155_1_GCF_020097155.1_00983:0.641369)n3:0.081126,GCF_003691675_1_GCF_003691675.1_01522:0.0287075)n2:0.0511509)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001477_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001477_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..770ce9a5e6efaeb00f73d5d91f1ee8673c99ecc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001477_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01828:0.0184836,GCF_003691675_1_GCF_003691675.1_01525:0.0108034)n1:0.00356188,((GCF_005280335_1_GCF_005280335.1_01041:0.0947215,GCF_020097155_1_GCF_020097155.1_00980:0.445935)n3:0.140566,GCF_023573625_1_GCF_023573625.1_01749:0.0219393)n2:0.00356188)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001479_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001479_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b369e3cfd024804b8625bb6d7919ae83b90a845c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001479_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01528:0.00288163,GCF_002008305_4_GCF_002008305.4_01831:0.00565237)n1:0.00206094,((GCF_020097155_1_GCF_020097155.1_00977:0.123754,GCF_005280335_1_GCF_005280335.1_01037:0.0578031)n3:0.0531819,GCF_023573625_1_GCF_023573625.1_01752:0.0203891)n2:0.00206094)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001480_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001480_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c4491a095f02db6f78f6d1fb128906d9fb33a05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001480_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01753:0.00273963,GCF_003691675_1_GCF_003691675.1_01529:1.42459e-07)n1:0.00138693,(GCF_002008305_4_GCF_002008305.4_01832:1.42459e-07,(GCF_020097155_1_GCF_020097155.1_00976:0.0841228,GCF_005280335_1_GCF_005280335.1_01036:0.0215762)n3:0.0313519)n2:0.00138693)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001481_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001481_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a900494c2849e7629b19c72858ca05d79ab636ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001481_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01754:0.0689742,GCF_002008305_4_GCF_002008305.4_01833:0.0557278)n1:0.00165869,((GCF_020097155_1_GCF_020097155.1_01055:1.16896,GCF_005280335_1_GCF_005280335.1_01035:0.119902)n3:0.0486031,GCF_003691675_1_GCF_003691675.1_01530:0.0431064)n2:0.00165869)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001484_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001484_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f85c205c60e8d09a89c93eea772fe916bcc780d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001484_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_01031:0.0041365,GCF_020097155_1_GCF_020097155.1_00972:0.0648745)n2:0.0029975,GCF_002008305_4_GCF_002008305.4_01837:-0)n1:0,(GCF_023573625_1_GCF_023573625.1_01758:0,GCF_003691675_1_GCF_003691675.1_01534:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001486_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001486_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29865b61b72adedd3382a5d7b47843d89a393dc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001486_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01536:0,GCF_023573625_1_GCF_023573625.1_01760:0)n1:0.0103958,(GCF_002008305_4_GCF_002008305.4_01839:0.00756737,(GCF_005280335_1_GCF_005280335.1_01029:0.0410058,GCF_020097155_1_GCF_020097155.1_00970:0.156317)n3:0.0320463)n2:0.0103958)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001487_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001487_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71b9e95a057f20c0dbb954416d7821417f569e77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001487_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01840:0,GCF_023573625_1_GCF_023573625.1_01761:0)n1:0,(GCF_003691675_1_GCF_003691675.1_01537:0,(GCF_020097155_1_GCF_020097155.1_00969:0.0649585,GCF_005280335_1_GCF_005280335.1_01028:0.0691335)n3:0.0136845)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001488_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001488_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41d5289182d3756780156386bc86691d39708b87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001488_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01841:0.0014934,GCF_003691675_1_GCF_003691675.1_01538:0.0059226)n1:0.00255658,(GCF_023573625_1_GCF_023573625.1_01762:0.00712455,(GCF_005280335_1_GCF_005280335.1_01027:0.0419435,GCF_020097155_1_GCF_020097155.1_00968:0.309544)n3:0.0388687)n2:0.00255658)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001497_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001497_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9053f79fa2cc9c7fad3b6db8544495df91ad222a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001497_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01550:0.0121055,GCF_023573625_1_GCF_023573625.1_01774:0.00338346)n1:0.00317336,(GCF_002008305_4_GCF_002008305.4_01854:0.00100879,(GCF_020097155_1_GCF_020097155.1_00956:0.058318,GCF_005280335_1_GCF_005280335.1_01014:0.089398)n3:0.0547909)n2:0.00317336)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001501_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001501_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4fba8217cea79255b66ead82528f89ae49e1200
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001501_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01554:0.00497138,(GCF_020097155_1_GCF_020097155.1_00950:0.16577,GCF_005280335_1_GCF_005280335.1_01006:0.224311)n2:0.143702)n1:0.00273406,(GCF_023573625_1_GCF_023573625.1_01778:0.00620713,GCF_002008305_4_GCF_002008305.4_01858:0.00300687)n3:0.00273406)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001504_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001504_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..930fb4f170af3295ff1136ecae8449b7045f7591
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001504_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01861:0.02002,GCF_023573625_1_GCF_023573625.1_01781:0.015937)n1:0.00498737,((GCF_005280335_1_GCF_005280335.1_00999:0.173538,GCF_005280335_1_GCF_005280335.1_01510:2.07843)n3:0.239128,GCF_003691675_1_GCF_003691675.1_01557:0.0340027)n2:0.00498737)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001508_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001508_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fd5758d985f2512141bc0302f5e4d911a6cfd43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001508_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01561:0.00321613,(GCF_005280335_1_GCF_005280335.1_00995:0.0710494,GCF_020097155_1_GCF_020097155.1_00933:0.212829)n2:0.0649584)n1:0.000575935,(GCF_023573625_1_GCF_023573625.1_01785:0.00807637,GCF_002008305_4_GCF_002008305.4_01865:0.00063963)n3:0.000575935)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001511_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001511_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..36a7169ac1ee424b568f95b178b23a097e7918c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001511_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00992:0.0692332,GCF_020097155_1_GCF_020097155.1_00930:0.137748)n2:0.0768338,GCF_003691675_1_GCF_003691675.1_01564:0.00421676)n1:0.00325762,(GCF_002008305_4_GCF_002008305.4_01868:3.06083e-07,GCF_023573625_1_GCF_023573625.1_01788:0.0123557)n3:0.00325762)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001514_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001514_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b514a64b82f754fe6d73d577917b8e7be606789c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001514_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00926:0.17888,GCF_005280335_1_GCF_005280335.1_00989:0.0653544)n2:0.0725761,GCF_023573625_1_GCF_023573625.1_01791:0.0222539)n1:0.0189596,(GCF_002008305_4_GCF_002008305.4_01871:0.00164238,GCF_003691675_1_GCF_003691675.1_01567:0.00520362)n3:0.0189596)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001515_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001515_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8f7ec7ae2d79c402ab1d4557e8d54151a9ec526
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001515_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01872:0.0146361,GCF_003691675_1_GCF_003691675.1_01568:0.0256169)n1:0.00776418,((GCF_020097155_1_GCF_020097155.1_00925:0.731189,GCF_005280335_1_GCF_005280335.1_00988:0.161375)n3:0.0908789,GCF_023573625_1_GCF_023573625.1_01792:0.0259176)n2:0.00776418)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001517_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001517_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78eca772b605a66a7f02ada7898d7bd1172b94ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001517_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01570:0.0195795,GCF_002008305_4_GCF_002008305.4_01874:0.0131455)n1:0.0226772,(GCF_023573625_1_GCF_023573625.1_01794:0.029707,(GCF_005280335_1_GCF_005280335.1_00986:0.266956,GCF_020097155_1_GCF_020097155.1_00923:0.288905)n3:0.0168285)n2:0.0226772)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001518_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001518_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8fee77ddf57bb088eb4c8b937cc890e861e25c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001518_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01795:0.0147445,GCF_002008305_4_GCF_002008305.4_01875:0.0011965)n1:0.00395325,((GCF_020097155_1_GCF_020097155.1_00922:0.375611,GCF_005280335_1_GCF_005280335.1_00984:0.0188955)n3:0.0066095,GCF_003691675_1_GCF_003691675.1_01571:0.0193765)n2:0.00395325)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001524_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001524_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c8cd7be3a6acf3948a9426e9fd6543c05cf262e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001524_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01804:0,GCF_002008305_4_GCF_002008305.4_01884:0)n1:0.00826459,(GCF_003691675_1_GCF_003691675.1_01580:0.0192598,(GCF_005280335_1_GCF_005280335.1_00974:0.11263,GCF_020097155_1_GCF_020097155.1_00912:0.247221)n3:0.119517)n2:0.00826459)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001525_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001525_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37e7f764599e420b93711da5822e887343b94ef2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001525_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00973:0.0551975,GCF_020097155_1_GCF_020097155.1_00911:0.300841)n2:0.0514175,GCF_003691675_1_GCF_003691675.1_01581:0.0107654)n1:0.0442038,(GCF_023573625_1_GCF_023573625.1_01805:0,GCF_002008305_4_GCF_002008305.4_01885:0)n3:0.0442038)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001526_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001526_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a54c1bb3b0ab0599413f743cfb11896442f5ad17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001526_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01886:0,GCF_023573625_1_GCF_023573625.1_01806:0)n1:0.0498642,((GCF_020097155_1_GCF_020097155.1_00910:0.438238,GCF_005280335_1_GCF_005280335.1_00972:0.141741)n3:0.088281,GCF_003691675_1_GCF_003691675.1_01582:0.0409745)n2:0.0498642)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001527_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001527_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8005baea780e39cd0800127391156b26f405c49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001527_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01807:0,GCF_002008305_4_GCF_002008305.4_01887:0)n1:0.00143633,(GCF_003691675_1_GCF_003691675.1_01583:0.00324334,(GCF_005280335_1_GCF_005280335.1_00971:0.0377557,GCF_020097155_1_GCF_020097155.1_00909:0.145874)n3:0.0466058)n2:0.00143633)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001529_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001529_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..450d2fd908fd6937120cf98be12cec54e4dfd3ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001529_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01889:0.0108451,GCF_003691675_1_GCF_003691675.1_01585:0.0180739)n1:0.00437236,(GCF_023573625_1_GCF_023573625.1_01809:0.00348706,(GCF_005280335_1_GCF_005280335.1_00969:0.0275183,GCF_020097155_1_GCF_020097155.1_00907:0.243776)n3:0.0212726)n2:0.00437236)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001531_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001531_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d45c4b22d12c75b1b9e6f6373dfe6b6b42afa916
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001531_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01811:0.00082875,GCF_002008305_4_GCF_002008305.4_01891:0.00306125)n1:0.000574135,((GCF_005280335_1_GCF_005280335.1_00967:0.0209495,GCF_020097155_1_GCF_020097155.1_00905:0.0939055)n3:0.0221889,GCF_003691675_1_GCF_003691675.1_01587:0.00330327)n2:0.000574135)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001532_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001532_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f8fb0c7072fd97ac55b891bf570fb54c4f31229
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001532_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01592:0.0018125,(GCF_005280335_1_GCF_005280335.1_00962:0.10244,GCF_020097155_1_GCF_020097155.1_00901:0.193896)n2:0.0931665)n1:0.00211725,(GCF_023573625_1_GCF_023573625.1_01816:0,GCF_002008305_4_GCF_002008305.4_01896:0)n3:0.00211725)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001534_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001534_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3bd4f135255836ceb6a3e2874642f3edf7c2debd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001534_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01596:0.00105099,GCF_023573625_1_GCF_023573625.1_01820:0.00253101)n1:0.00450568,((GCF_005280335_1_GCF_005280335.1_00958:0.0378777,GCF_020097155_1_GCF_020097155.1_00898:0.180691)n3:0.0792111,GCF_002008305_4_GCF_002008305.4_01900:0.00393572)n2:0.00450568)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001535_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001535_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf0c719d5a8eafbe78f25e156f854ba69f9086fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001535_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01901:0,GCF_023573625_1_GCF_023573625.1_01821:0)n1:0.0270241,(GCF_003691675_1_GCF_003691675.1_01597:0.0294727,(GCF_020097155_1_GCF_020097155.1_00897:0.520811,GCF_005280335_1_GCF_005280335.1_00957:0.147347)n3:0.0952018)n2:0.0270241)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001536_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001536_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79aad0f1f299949e999409a4d690cc24a675ba7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001536_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00896:0.168951,GCF_005280335_1_GCF_005280335.1_00956:0.0981291)n2:0.0781351,GCF_003691675_1_GCF_003691675.1_01598:0.00744637)n1:0.00071931,(GCF_023573625_1_GCF_023573625.1_01822:0.00068763,GCF_002008305_4_GCF_002008305.4_01902:0.00101637)n3:0.00071931)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001538_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001538_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3002ab4c7e520feb9f31ff56c38c7a87b479d167
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001538_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00894:0.471149,GCF_005280335_1_GCF_005280335.1_00954:0.180192)n2:0.122573,GCF_002008305_4_GCF_002008305.4_01904:0.0335659)n1:0.0242343,(GCF_023573625_1_GCF_023573625.1_01824:0.0196392,GCF_003691675_1_GCF_003691675.1_01600:8.74457e-07)n3:0.0242343)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001541_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001541_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6dedd2328f7c5ceb9c5b8bcaa84aec6653798272
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001541_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01907:3.52776e-08,(GCF_020097155_1_GCF_020097155.1_00891:0.008218,GCF_005280335_1_GCF_005280335.1_00951:0.006254)n2:0.0120976)n1:0.000242615,(GCF_023573625_1_GCF_023573625.1_01827:0.008708,GCF_003691675_1_GCF_003691675.1_01603:0)n3:0.000242615)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001547_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001547_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5ff44e82a3e183ba731da22b8b13aef5ff512c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001547_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01919:0.00822213,GCF_003691675_1_GCF_003691675.1_01615:0.00503588)n1:0.00290881,(GCF_023573625_1_GCF_023573625.1_01839:0.00035138,(GCF_005280335_1_GCF_005280335.1_00941:0.0268134,GCF_020097155_1_GCF_020097155.1_00876:0.248811)n3:0.0198911)n2:0.00290881)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001549_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001549_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c1d2f452b713a0ed65fbb8d69cef8f09d7bf2ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001549_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01842:0,GCF_002008305_4_GCF_002008305.4_01922:0)n1:0.00099364,((GCF_005280335_1_GCF_005280335.1_00938:0.0740405,GCF_020097155_1_GCF_020097155.1_00873:0.116568)n3:0.0591587,GCF_003691675_1_GCF_003691675.1_01618:0.00462172)n2:0.00099364)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001551_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001551_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..017324489e55831e39167c6fe76044e8af6bba2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001551_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00936:1.52308,GCF_020097155_1_GCF_020097155.1_00868:0.0811545)n2:0.0904773,GCF_003691675_1_GCF_003691675.1_01620:0.00637345)n1:0.00716977,(GCF_002008305_4_GCF_002008305.4_01924:1.75412e-06,GCF_023573625_1_GCF_023573625.1_01844:0.0400688)n3:0.00716977)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001554_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001554_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5042325ba03c97cdbda2b8f355a9bb3286a28156
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001554_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01624:0.00457287,GCF_002008305_4_GCF_002008305.4_01928:0.0125411)n1:0.00115594,(GCF_023573625_1_GCF_023573625.1_01847:0.00897662,(GCF_005280335_1_GCF_005280335.1_00931:0.125805,GCF_020097155_1_GCF_020097155.1_00863:0.266244)n3:0.112359)n2:0.00115594)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001556_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001556_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65e34e6b2d1bc69a4eaf396dc6fa92db6d6ab6fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001556_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00862:0.12305,GCF_005280335_1_GCF_005280335.1_00928:0.130447)n2:0.14693,GCF_003691675_1_GCF_003691675.1_01626:4.07955e-07)n1:0.00031225,(GCF_002008305_4_GCF_002008305.4_01930:4.07955e-07,GCF_023573625_1_GCF_023573625.1_01849:0.0081525)n3:0.00031225)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001558_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001558_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccddd4d8b2547d6e3b0f256b4c51f5b6d4e87d1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001558_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01629:0.00710987,GCF_002008305_4_GCF_002008305.4_01933:0.0183251)n1:0.00240522,(GCF_023573625_1_GCF_023573625.1_01852:0.00606091,(GCF_020097155_1_GCF_020097155.1_00860:0.199512,GCF_005280335_1_GCF_005280335.1_00926:0.127617)n3:0.0899093)n2:0.00240522)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001561_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001561_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..408219217d7ed16538dd58446c0c26b3393c5cf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001561_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01855:0,GCF_002008305_4_GCF_002008305.4_01936:0)n1:0.00309912,(GCF_003691675_1_GCF_003691675.1_01632:0.00662875,(GCF_005280335_1_GCF_005280335.1_00923:0.20156,GCF_020097155_1_GCF_020097155.1_00857:0.193657)n3:0.123977)n2:0.00309912)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001564_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001564_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e56f35da9c5ac44ba21de0db9610f4680642ae6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001564_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01637:0.0339269,(GCF_020097155_1_GCF_020097155.1_00853:0.33512,GCF_005280335_1_GCF_005280335.1_00918:0.428337)n2:0.155379)n1:0.00091056,(GCF_023573625_1_GCF_023573625.1_01860:0,GCF_002008305_4_GCF_002008305.4_01941:0)n3:0.00091056)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001566_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001566_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37f7aae69a69662043eddaf8ffd204334dae84f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001566_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01639:0.00086287,GCF_023573625_1_GCF_023573625.1_01862:0.00205012)n1:0.00419119,((GCF_005280335_1_GCF_005280335.1_00913:0.0795884,GCF_020097155_1_GCF_020097155.1_00851:0.0102046)n3:0.00107487,GCF_002008305_4_GCF_002008305.4_01943:0.00902362)n2:0.00419119)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001569_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001569_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1248f8c2118b27fef5c5dd12d5a1a37fd5b28d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001569_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01642:0,GCF_020097155_1_GCF_020097155.1_00846:0)n1:0,(GCF_002008305_4_GCF_002008305.4_01948:0,(GCF_005280335_1_GCF_005280335.1_00907:0.0017525,GCF_023573625_1_GCF_023573625.1_01871:0.0554055)n3:0.0056825)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001575_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001575_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df711df687b1250f6431cec42741ad126bfe078d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001575_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00830:0.341361,GCF_005280335_1_GCF_005280335.1_00889:0.014514)n2:0.0113603,GCF_003691675_1_GCF_003691675.1_01664:0.011094)n1:0.00108552,(GCF_023573625_1_GCF_023573625.1_01896:0.00525768,GCF_002008305_4_GCF_002008305.4_01970:0.00736232)n3:0.00108552)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001581_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001581_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19b4ee554d53a88ddc33d252ad5e869660b7ddfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001581_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01906:0,GCF_002008305_4_GCF_002008305.4_01980:0)n1:0.00197313,(GCF_003691675_1_GCF_003691675.1_01674:0.00579373,(GCF_020097155_1_GCF_020097155.1_00813:0.0106162,GCF_005280335_1_GCF_005280335.1_00878:0.233419)n3:0.0157727)n2:0.00197313)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001582_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001582_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..077620d41877d89bc278a6960597c866d2597627
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001582_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01675:0.00098176,GCF_023573625_1_GCF_023573625.1_01907:3.29924e-07)n1:0.00121834,(GCF_002008305_4_GCF_002008305.4_01981:0.00098409,(GCF_020097155_1_GCF_020097155.1_00812:0.0046275,GCF_005280335_1_GCF_005280335.1_00877:0.318682)n3:0.00221785)n2:0.00121834)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001584_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001584_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d6b5a0907a6f07c0c746959c53696bfc403fbef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001584_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00809:0.007545,GCF_005280335_1_GCF_005280335.1_00873:0.084894)n2:0.0009275,GCF_003691675_1_GCF_003691675.1_01678:0.00210805)n1:0.00246197,(GCF_002008305_4_GCF_002008305.4_01984:0,GCF_023573625_1_GCF_023573625.1_01910:0)n3:0.00246197)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001587_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001587_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c980d68ac651e007304c0224f730ceca8682902
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001587_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01683:0.0538496,GCF_023573625_1_GCF_023573625.1_01915:0.0542854)n1:0.00829866,(GCF_002008305_4_GCF_002008305.4_01989:0.0531575,(GCF_005280335_1_GCF_005280335.1_00868:0.387309,GCF_020097155_1_GCF_020097155.1_00805:0.731475)n3:0.232517)n2:0.00829866)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001588_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001588_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0af7876ec9d7239f9cccdd527a3f5fc5c9eecbb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001588_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01684:0.0133062,GCF_023573625_1_GCF_023573625.1_01916:0.00048283)n1:0.00101622,(GCF_002008305_4_GCF_002008305.4_01990:0.00687877,(GCF_020097155_1_GCF_020097155.1_01757:0.213322,GCF_005280335_1_GCF_005280335.1_00867:0.0380662)n3:0.0336061)n2:0.00101622)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001595_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001595_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98e40fb9ce32398ed4f66e0c276e94a43324a0c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001595_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01925:0,GCF_003691675_1_GCF_003691675.1_01693:0)n1:0.00386545,(GCF_002008305_4_GCF_002008305.4_01999:0.0191331,(GCF_005280335_1_GCF_005280335.1_00858:0.138332,GCF_020097155_1_GCF_020097155.1_00794:0.425901)n3:0.10517)n2:0.00386545)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001601_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001601_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fa6b53d5fad1e8abb2374af1abd47221e95bed8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001601_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02008:0.004093,GCF_003691675_1_GCF_003691675.1_01718:7.11238e-08)n1:0.000703375,(GCF_023573625_1_GCF_023573625.1_01946:0.00635025,(GCF_005280335_1_GCF_005280335.1_00834:0.0259648,GCF_020097155_1_GCF_020097155.1_00771:0.0198212)n3:0.0139087)n2:0.000703375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001602_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001602_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..872da03757fa07acc4eee2f8fc61be8268649030
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001602_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01947:0,GCF_003691675_1_GCF_003691675.1_01719:0)n1:0,(GCF_002008305_4_GCF_002008305.4_02009:0,(GCF_020097155_1_GCF_020097155.1_00770:0.0492855,GCF_005280335_1_GCF_005280335.1_00833:0.0139735)n3:0.0374305)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001604_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001604_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f128961e5cae72bd83dd38c8a6048fa3f98897e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001604_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01721:0.00673456,GCF_005280335_1_GCF_005280335.1_00831:0.0390844)n1:0.00472194,((GCF_002008305_4_GCF_002008305.4_02011:0.010488,GCF_020097155_1_GCF_020097155.1_00768:0.115256)n3:0.0115301,GCF_023573625_1_GCF_023573625.1_01949:0.00623039)n2:0.00472194)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001605_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001605_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0c6848430dc467aac5d0509a4e4e8fa8311e242
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001605_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00767:0.102175,GCF_005280335_1_GCF_005280335.1_00830:0.031163)n2:0.0253876,GCF_023573625_1_GCF_023573625.1_01950:0.00402369)n1:0.00195916,(GCF_002008305_4_GCF_002008305.4_02012:0.00788526,GCF_003691675_1_GCF_003691675.1_01722:0.00265474)n3:0.00195916)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001606_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001606_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..407c8f78c39341337ee73256cfa899f8936480ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001606_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01951:0,GCF_003691675_1_GCF_003691675.1_01723:0)n1:0.00159512,(GCF_002008305_4_GCF_002008305.4_02013:0.00389775,(GCF_020097155_1_GCF_020097155.1_00766:0.104175,GCF_005280335_1_GCF_005280335.1_00829:0.0723328)n3:0.0529888)n2:0.00159512)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001612_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001612_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2afbc836ff527164277fcf1a0a7a49b6502e39c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001612_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00797:0.369239,(GCF_020097155_1_GCF_020097155.1_00758:0.0315035,GCF_023573625_1_GCF_023573625.1_01959:0.0061425)n2:0.00120675)n1:0.00111912,(GCF_003691675_1_GCF_003691675.1_01731:0.0137035,GCF_002008305_4_GCF_002008305.4_02022:0.0069485)n3:0.00111912)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001618_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001618_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bced151e23490d576f7369f05e230e374f23292
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001618_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01965:0,GCF_003691675_1_GCF_003691675.1_01737:0)n1:0,((GCF_020097155_1_GCF_020097155.1_00752:0.123655,GCF_005280335_1_GCF_005280335.1_00791:0.163077)n3:0.0308025,GCF_002008305_4_GCF_002008305.4_02028:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001619_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001619_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cab9a92685e35bd8a8020d26dbd611b4e72892d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001619_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02033:0,GCF_023573625_1_GCF_023573625.1_01968:0)n1:0,(GCF_003691675_1_GCF_003691675.1_01740:0,(GCF_005280335_1_GCF_005280335.1_00787:0.0180615,GCF_020097155_1_GCF_020097155.1_01226:0.812149)n3:0.0375705)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001625_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001625_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09926a759e431ac6da833cb5303c1f066fa534df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001625_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02052:0.00075462,GCF_003691675_1_GCF_003691675.1_01758:0.00822437)n1:0.00331206,((GCF_005280335_1_GCF_005280335.1_00770:0.106996,GCF_020097155_1_GCF_020097155.1_00740:0.185007)n3:0.169457,GCF_023573625_1_GCF_023573625.1_01986:4.75602e-07)n2:0.00331206)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001626_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001626_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0215bd8c728378c87b1da96eeadeb0646ae2f62d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001626_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01987:0.0127823,GCF_003691675_1_GCF_003691675.1_01759:0.0125127)n1:0.00152208,(GCF_002008305_4_GCF_002008305.4_02053:0.0125189,(GCF_020097155_1_GCF_020097155.1_00126:0.319521,GCF_005280335_1_GCF_005280335.1_00769:0.095852)n3:0.0966926)n2:0.00152208)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001627_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001627_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d3038a31f436e2d75549e04afdef7f7758176e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001627_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00711:0.0976693,GCF_020097155_1_GCF_020097155.1_00726:0.0961227)n2:0.161518,GCF_023573625_1_GCF_023573625.1_01989:0.164964)n1:0.000467815,(GCF_003691675_1_GCF_003691675.1_01761:5.27865e-07,GCF_002008305_4_GCF_002008305.4_02055:0.00698655)n3:0.000467815)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001628_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001628_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffa13dcf305219eb073998bf0a5a1acda4a7fdc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001628_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00764:0.115221,GCF_020097155_1_GCF_020097155.1_00728:0.133919)n2:0.147236,GCF_002008305_4_GCF_002008305.4_02056:0.013587)n1:0.003265,(GCF_003691675_1_GCF_003691675.1_01762:0,GCF_023573625_1_GCF_023573625.1_01990:0)n3:0.003265)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001630_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001630_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b153942717471dcee311ad2a4a7a6ca94809068
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001630_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01994:0.049236,(GCF_020097155_1_GCF_020097155.1_00723:0.522283,GCF_005280335_1_GCF_005280335.1_00760:0.259758)n2:0.146461)n1:0.029104,(GCF_002008305_4_GCF_002008305.4_02058:0.00416675,GCF_003691675_1_GCF_003691675.1_01764:0.00584625)n3:0.029104)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001632_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001632_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee21bee9c6b042dd66cc05412d90013dd165e806
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001632_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_00614:0.0182976,GCF_002008305_4_GCF_002008305.4_02080:0.0189964)n1:0.0024099,(GCF_005280335_1_GCF_005280335.1_00704:0.313757,(GCF_023573625_1_GCF_023573625.1_02018:0.00590517,GCF_003691675_1_GCF_003691675.1_01784:0.00637583)n3:0.00738002)n2:0.0024099)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001634_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001634_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de76973190f85729f7f4886a5058cc7f5c228f00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001634_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01787:0,GCF_002008305_4_GCF_002008305.4_02082:0)n1:0.000321625,(GCF_020097155_1_GCF_020097155.1_00611:0.0180497,(GCF_023573625_1_GCF_023573625.1_02021:0.00143225,GCF_005280335_1_GCF_005280335.1_00701:0.0172017)n3:0.00246275)n2:0.000321625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001636_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001636_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3742f8a6a2a71af38b1703120dc44f2eef85e901
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001636_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00609:0.002928,GCF_023573625_1_GCF_023573625.1_02023:0.005883)n2:0.00221875,GCF_003691675_1_GCF_003691675.1_01789:2.28197e-08)n1:9.125e-06,(GCF_002008305_4_GCF_002008305.4_02084:2.28197e-08,GCF_005280335_1_GCF_005280335.1_00699:0.0118082)n3:9.125e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001637_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001637_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a88b00137a9f86947cfa2078faccef270caba7ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001637_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_00608:0.00535725,(GCF_023573625_1_GCF_023573625.1_02024:2.61782e-08,GCF_005280335_1_GCF_005280335.1_00698:0.0100787)n2:0.00326225)n1:0.00376838,(GCF_003691675_1_GCF_003691675.1_01790:0,GCF_002008305_4_GCF_002008305.4_02085:0)n3:0.00376838)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001640_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001640_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b028505300e84f16315d29bbe772a1de63bbb53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001640_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02088:0,GCF_003691675_1_GCF_003691675.1_01793:0)n1:0.00598788,((GCF_005280335_1_GCF_005280335.1_00586:0.189345,GCF_005280335_1_GCF_005280335.1_00695:0.0102557)n3:0.0350772,GCF_023573625_1_GCF_023573625.1_02027:0.0157592)n2:0.00598788)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001641_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001641_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ee8206bee43646ffe2af366d1bd8f9442b39f94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001641_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_02092:0.00603031,(GCF_005280335_1_GCF_005280335.1_00686:0.00552938,((GCF_020097155_1_GCF_020097155.1_00937:2.17161,GCF_020097155_1_GCF_020097155.1_00413:0.169521)n3:0.19721,GCF_020097155_1_GCF_020097155.1_00602:0.0359394)n2:0.00399326)n1:0.0143609)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001643_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001643_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9957e17516de91b183a980ba01c97b9cedc10a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001643_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02039:0.00244929,GCF_002008305_4_GCF_002008305.4_02099:3.04501e-07)n1:9.1645e-05,(GCF_003691675_1_GCF_003691675.1_01806:0,(GCF_020097155_1_GCF_020097155.1_00594:0.175989,GCF_005280335_1_GCF_005280335.1_00680:0.0688557)n3:0.0572066)n2:9.1645e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001652_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001652_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe630f4ca2e16871124538c2078c5772b1a4e88c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001652_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01820:0.00909462,GCF_002008305_4_GCF_002008305.4_02113:0.00808838)n1:0.0048462,((GCF_020097155_1_GCF_020097155.1_00583:0.227996,GCF_005280335_1_GCF_005280335.1_00667:0.165378)n3:0.0425768,GCF_023573625_1_GCF_023573625.1_02051:0.0225881)n2:0.0048462)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001653_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001653_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35dd11535207dbcab15b6fa6f854fbabe325912a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001653_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02052:0.0117197,GCF_002008305_4_GCF_002008305.4_02114:0.0177582)n1:0.004187,(GCF_003691675_1_GCF_003691675.1_01822:0.0359605,(GCF_020097155_1_GCF_020097155.1_00582:0.296427,GCF_005280335_1_GCF_005280335.1_00666:0.0807372)n3:0.0733435)n2:0.004187)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001654_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001654_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97fa56ed42330ef2426730184ee8633ccda6e4ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001654_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00581:0.0683322,GCF_005280335_1_GCF_005280335.1_00665:0.0180848)n2:0.0194672,GCF_002008305_4_GCF_002008305.4_02115:1.14029e-07)n1:5.8875e-05,(GCF_023573625_1_GCF_023573625.1_02053:0.0054675,GCF_003691675_1_GCF_003691675.1_01823:0.0026865)n3:5.8875e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001657_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001657_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbe7bc0e66a02bb2b6b1d8f9979200018ed5eaed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001657_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00661:0.147724,GCF_020097155_1_GCF_020097155.1_00578:0.350967)n2:0.13588,GCF_023573625_1_GCF_023573625.1_02057:0.0211038)n1:0.0264914,(GCF_003691675_1_GCF_003691675.1_01827:0.00343961,GCF_002008305_4_GCF_002008305.4_02119:0.0110474)n3:0.0264914)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001659_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001659_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3b70945ba7d7e36da38c7d1dc28a1f399491f65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001659_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01829:0,GCF_023573625_1_GCF_023573625.1_02059:0)n1:0.00750775,(GCF_020097155_1_GCF_020097155.1_00576:0.0264085,(GCF_002008305_4_GCF_002008305.4_02121:0.018846,GCF_005280335_1_GCF_005280335.1_00659:0.054391)n3:0.01578)n2:0.00750775)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001660_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001660_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e1301a40e8157a2f4ca8b22897ea0828cb505f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001660_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01831:0,GCF_023573625_1_GCF_023573625.1_02061:0)n1:0.0075495,(GCF_020097155_1_GCF_020097155.1_00574:0.005363,(GCF_005280335_1_GCF_005280335.1_00656:0.0764091,GCF_002008305_4_GCF_002008305.4_02123:0.0146599)n3:0.0017835)n2:0.0075495)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001662_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001662_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98cdea485e80dfa41c29583382495700f0b44b29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001662_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02126:0.00438617,(GCF_005280335_1_GCF_005280335.1_00654:0.00877454,GCF_023573625_1_GCF_023573625.1_02064:0.0140905)n2:0.00082954)n1:0.000198885,(GCF_003691675_1_GCF_003691675.1_01834:0.000455,GCF_020097155_1_GCF_020097155.1_00570:0.027666)n3:0.000198885)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001664_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001664_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00885fefce1fe5bfe62b62c6cd3b89c3300f52d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001664_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02128:0.00231775,(GCF_005280335_1_GCF_005280335.1_00652:0.00263175,GCF_020097155_1_GCF_020097155.1_00568:0.0116443)n2:0.00770475)n1:0.000259625,(GCF_003691675_1_GCF_003691675.1_01836:0,GCF_023573625_1_GCF_023573625.1_02066:0)n3:0.000259625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001666_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001666_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3da4a0f000472aa2f117e6fc1322cad3332668a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001666_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01838:0.00421883,GCF_023573625_1_GCF_023573625.1_02068:0.00320117)n1:0.0175679,((GCF_002008305_4_GCF_002008305.4_02130:0.0190155,GCF_005280335_1_GCF_005280335.1_00650:0.0175794)n3:0.0038165,GCF_020097155_1_GCF_020097155.1_00566:0.0240147)n2:0.0175679)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001667_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001667_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..350d06b24044f16d574e18d852e6d9e285661687
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001667_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02131:0.00041763,GCF_003691675_1_GCF_003691675.1_01839:0.0132524)n1:0.00179219,((GCF_020097155_1_GCF_020097155.1_00565:0.0338949,GCF_005280335_1_GCF_005280335.1_00649:0.00762213)n3:0.00039787,GCF_023573625_1_GCF_023573625.1_02069:0.0269811)n2:0.00179219)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001669_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001669_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4ec88b369446230720a7f55e7f48bca2fba10b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001669_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01841:0.00521025,(GCF_005280335_1_GCF_005280335.1_00647:0.0349327,GCF_020097155_1_GCF_020097155.1_00563:0.0548172)n2:0.0172677)n1:0.00377288,(GCF_002008305_4_GCF_002008305.4_02133:0.00457175,GCF_023573625_1_GCF_023573625.1_02071:0.00176025)n3:0.00377288)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001671_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001671_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b174a563bc4e6bbe88f7dd71052943b0d0336344
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001671_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02074:0,GCF_003691675_1_GCF_003691675.1_01844:0)n1:0.00529573,((GCF_005280335_1_GCF_005280335.1_00636:0.0344062,GCF_020097155_1_GCF_020097155.1_00560:0.220673)n3:0.027155,GCF_002008305_4_GCF_002008305.4_02136:0.00190855)n2:0.00529573)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001672_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001672_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e54eb7c7ff217a8bbbb0ff9200f66a4274888bfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001672_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01845:0,GCF_002008305_4_GCF_002008305.4_02137:0)n1:0,((GCF_005280335_1_GCF_005280335.1_00635:0.0612255,GCF_020097155_1_GCF_020097155.1_00559:0.139294)n3:0.0349035,GCF_023573625_1_GCF_023573625.1_02075:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001673_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001673_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cf0aaf91a3026b435c4b78bf452da61a54ab708
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001673_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02076:0,GCF_003691675_1_GCF_003691675.1_01846:0)n1:0.00208793,(GCF_002008305_4_GCF_002008305.4_02138:0.00361415,(GCF_020097155_1_GCF_020097155.1_00558:0.200396,GCF_005280335_1_GCF_005280335.1_00634:0.058274)n3:0.0945087)n2:0.00208793)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001676_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001676_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..729c586cd043e0cb48a18dce75fd1bfb49e5ea59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001676_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00716:0.272102,GCF_020097155_1_GCF_020097155.1_00554:0.0668437)n2:0.0516655,GCF_003691675_1_GCF_003691675.1_01849:0.0103934)n1:0.00342978,(GCF_023573625_1_GCF_023573625.1_02079:0.0188281,GCF_002008305_4_GCF_002008305.4_02141:0.0164669)n3:0.00342978)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001677_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001677_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d62dfb228c1ed38a04e1c47248ce870b922c37b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001677_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00629:0.0538145,GCF_002008305_4_GCF_002008305.4_02143:0.0305055)n1:0.077162,(GCF_020097155_1_GCF_020097155.1_00553:0.00451247,(GCF_003691675_1_GCF_003691675.1_01850:0.00509121,GCF_023573625_1_GCF_023573625.1_02080:2.54665e-07)n3:0.00644953)n2:0.077162)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001678_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001678_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb742771eae3a84d87d7faf534a88f4e38f0a450
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001678_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02144:0.0225797,GCF_005280335_1_GCF_005280335.1_00628:0.0109813)n1:0.054672,(GCF_020097155_1_GCF_020097155.1_00552:0.00676787,(GCF_003691675_1_GCF_003691675.1_01851:1.59462e-07,GCF_023573625_1_GCF_023573625.1_02081:0.00354784)n3:0.00627013)n2:0.054672)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001683_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001683_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8e897afd25ed047f7a84c19d42d6c2eb0b5bb04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001683_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02092:0.006834,GCF_002008305_4_GCF_002008305.4_02149:0.006175)n1:0.00421375,(GCF_003691675_1_GCF_003691675.1_01862:0.0138045,(GCF_020097155_1_GCF_020097155.1_00537:0.331009,GCF_005280335_1_GCF_005280335.1_00613:0.081979)n3:0.0656465)n2:0.00421375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001685_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001685_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4ce146cdcb49ad1b692a51428cc89e1b2707687
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001685_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02151:0.00630825,GCF_003691675_1_GCF_003691675.1_01864:7.70958e-07)n1:0.003111,(GCF_023573625_1_GCF_023573625.1_02094:0.0048605,(GCF_020097155_1_GCF_020097155.1_00535:0.474348,GCF_005280335_1_GCF_005280335.1_00611:0.098459)n3:0.181582)n2:0.003111)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001686_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001686_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa0b1d1c8ab511b5fe503ac03a80d8ad92237dfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001686_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01865:0.00350728,GCF_023573625_1_GCF_023573625.1_02095:0.0115287)n1:0.00886964,(GCF_002008305_4_GCF_002008305.4_02152:0.013516,(GCF_020097155_1_GCF_020097155.1_00534:0.0984072,GCF_005280335_1_GCF_005280335.1_00610:0.186086)n3:0.204687)n2:0.00886964)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001687_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001687_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33964bc96c0ff260ae3356b8891eb7702a24eae6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001687_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01867:0.00394712,GCF_023573625_1_GCF_023573625.1_02097:0.00251088)n1:0.000829935,(GCF_002008305_4_GCF_002008305.4_02154:0.00718563,(GCF_005280335_1_GCF_005280335.1_00609:0.0514656,GCF_020097155_1_GCF_020097155.1_00533:0.125643)n3:0.0325739)n2:0.000829935)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001688_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001688_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..280d93b3b6fe996aca9f8d368ef649d5337074ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001688_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02100:0.00047,GCF_002008305_4_GCF_002008305.4_02157:0.002325)n1:0.00116138,(GCF_003691675_1_GCF_003691675.1_01870:3.29248e-07,(GCF_020097155_1_GCF_020097155.1_00523:0.0997605,GCF_005280335_1_GCF_005280335.1_00601:0.118887)n3:0.105565)n2:0.00116138)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001692_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001692_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bff88ec5281e9dfec3f3ea836fadc76e43f86f41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001692_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02163:0.0121127,GCF_003691675_1_GCF_003691675.1_01877:4.63644e-07)n1:0.00022633,(GCF_023573625_1_GCF_023573625.1_02108:0,(GCF_005280335_1_GCF_005280335.1_00594:0.117894,GCF_020097155_1_GCF_020097155.1_00517:0.235188)n3:0.0984491)n2:0.00022633)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001695_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001695_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2223db1d4d6af392d443305d918c637f6b7f649e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001695_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02169:0.0202708,(GCF_005280335_1_GCF_005280335.1_00583:0.249946,GCF_020097155_1_GCF_020097155.1_00509:0.414204)n2:0.18214)n1:0.00511813,(GCF_003691675_1_GCF_003691675.1_01883:0.015055,GCF_023573625_1_GCF_023573625.1_02114:0.013876)n3:0.00511813)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001696_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001696_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0f4cbc497c607ce1418f7c41c8dc6523f096e50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001696_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01884:0.00422746,GCF_002008305_4_GCF_002008305.4_02170:0.00574654)n1:0.00128958,(GCF_023573625_1_GCF_023573625.1_02115:0.004693,(GCF_005280335_1_GCF_005280335.1_00582:0.0717363,GCF_020097155_1_GCF_020097155.1_00508:0.268358)n3:0.0797568)n2:0.00128958)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001697_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001697_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90fee61c29262f0ac76c9a58618f75b108006c85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001697_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02118:0.00066293,(GCF_005280335_1_GCF_005280335.1_00579:0.0389445,GCF_020097155_1_GCF_020097155.1_00506:0.285326)n2:0.0410471)n1:0.00330803,(GCF_002008305_4_GCF_002008305.4_02173:0,GCF_003691675_1_GCF_003691675.1_01887:0)n3:0.00330803)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001698_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001698_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00648436df11a364cf58b1a1e61dcfb87e7b49ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001698_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01889:0.00159887,GCF_023573625_1_GCF_023573625.1_02120:0.00073413)n1:0.00136006,(GCF_002008305_4_GCF_002008305.4_02175:0.00704688,(GCF_005280335_1_GCF_005280335.1_00577:0.216617,GCF_020097155_1_GCF_020097155.1_00504:0.122737)n3:0.101347)n2:0.00136006)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001701_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001701_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45f6faabdb653cd52ba5d5f1bea425689ea3fe0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001701_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02123:0.00666978,(GCF_020097155_1_GCF_020097155.1_00501:0.165279,GCF_005280335_1_GCF_005280335.1_00574:0.278716)n2:0.122809)n1:0.00151186,(GCF_002008305_4_GCF_002008305.4_02178:0.00314416,GCF_003691675_1_GCF_003691675.1_01892:0.00052884)n3:0.00151186)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001702_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001702_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24918f5103d302bfe892bb14a772968a05b289ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001702_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02179:0.00088087,GCF_003691675_1_GCF_003691675.1_01893:0.00336213)n1:0.00361281,(GCF_023573625_1_GCF_023573625.1_02124:0.00237187,(GCF_005280335_1_GCF_005280335.1_00573:0.0489676,GCF_020097155_1_GCF_020097155.1_00500:0.258931)n3:0.0248476)n2:0.00361281)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001707_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001707_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7cf2b48b14002b3a44b4ed790f4812020a24e605
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001707_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00565:0.186199,GCF_020097155_1_GCF_020097155.1_00490:0.358883)n2:0.208821,GCF_023573625_1_GCF_023573625.1_02130:7.60526e-07)n1:0.00433987,(GCF_002008305_4_GCF_002008305.4_02185:0,GCF_003691675_1_GCF_003691675.1_01899:0)n3:0.00433987)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001709_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001709_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51d95a36c6c12e412c46405f1048fc4b8c41a69c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001709_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02134:4.13626e-07,(GCF_020097155_1_GCF_020097155.1_00484:0.3032,GCF_005280335_1_GCF_005280335.1_00557:0.0300423)n2:0.0790533)n1:0.00100503,(GCF_003691675_1_GCF_003691675.1_01903:0,GCF_002008305_4_GCF_002008305.4_02189:0)n3:0.00100503)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001710_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001710_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41a4e93c4e4f7ae65d0edd9ec220b12f2f159c57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001710_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01904:0.00266508,GCF_023573625_1_GCF_023573625.1_02135:0.0105419)n1:0.00111865,(GCF_002008305_4_GCF_002008305.4_02190:0.00620608,(GCF_020097155_1_GCF_020097155.1_00483:0.392479,GCF_005280335_1_GCF_005280335.1_00554:0.120196)n3:0.138732)n2:0.00111865)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001711_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001711_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2a67b0b1e926af7f4054f7f9c5a7bcaefae9ab5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001711_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02138:0.0014115,GCF_003691675_1_GCF_003691675.1_01907:0.0043355)n1:0.00381112,(GCF_002008305_4_GCF_002008305.4_02194:0.0126313,(GCF_020097155_1_GCF_020097155.1_00482:0.810851,GCF_005280335_1_GCF_005280335.1_00546:0.246676)n3:0.126122)n2:0.00381112)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001717_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001717_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ca6535757702f2794d1b2fd5654ad7bc81171ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001717_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01914:0,GCF_023573625_1_GCF_023573625.1_02145:0)n1:0,(GCF_002008305_4_GCF_002008305.4_02201:0,(GCF_005280335_1_GCF_005280335.1_00496:0.23072,GCF_020097155_1_GCF_020097155.1_01297:0.322682)n3:0.294693)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001722_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001722_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62f3a7f1227550de5610b2aad5022a627f42dbe0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001722_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02158:0.00651737,GCF_002008305_4_GCF_002008305.4_02219:0.00080062)n1:0.00807744,(GCF_003691675_1_GCF_003691675.1_01932:0.0141006,(GCF_005280335_1_GCF_005280335.1_00527:0.374859,GCF_020097155_1_GCF_020097155.1_00465:0.432504)n3:0.425343)n2:0.00807744)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001723_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001723_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2c13e79c6ba798f35aacb3d9815a04b32712aa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001723_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02159:0.00843275,GCF_003691675_1_GCF_003691675.1_01933:0.0104362)n1:0.00557013,(GCF_002008305_4_GCF_002008305.4_02220:0.0111892,(GCF_005280335_1_GCF_005280335.1_00515:0.126861,GCF_020097155_1_GCF_020097155.1_00462:0.146884)n3:0.244167)n2:0.00557013)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001725_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001725_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8335fac6f0f4aab3b3ea620eabc22f488803d53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001725_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02172:0,GCF_002008305_4_GCF_002008305.4_02240:0)n1:0.00160363,(GCF_003691675_1_GCF_003691675.1_01942:8.375e-05,(GCF_005280335_1_GCF_005280335.1_00505:0.102565,GCF_020097155_1_GCF_020097155.1_00441:0.0582638)n3:0.0854977)n2:0.00160363)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001727_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001727_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f96dfde9b00f0f1ea24265f1c530c0810c2bea1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001727_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02176:0.00092585,GCF_002008305_4_GCF_002008305.4_02244:0.00363315)n1:0.00141479,(GCF_003691675_1_GCF_003691675.1_01946:0.00210949,(GCF_020097155_1_GCF_020097155.1_02088:0.522839,GCF_005280335_1_GCF_005280335.1_00502:1.12563)n3:0.0998507)n2:0.00141479)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001728_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001728_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9734582c170f712a5b99cd2396a4d5645f7e0f00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001728_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00511:0.656168,GCF_005280335_1_GCF_005280335.1_00500:0.0766255)n2:0.0687975,GCF_002008305_4_GCF_002008305.4_02245:-0)n1:0,(GCF_003691675_1_GCF_003691675.1_01947:0,GCF_023573625_1_GCF_023573625.1_02177:0)n3:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001731_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001731_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4f799b289fd91c409c56c8df3c7dbe2f5bc9d20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001731_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02186:3.3945e-08,GCF_002008305_4_GCF_002008305.4_02255:0.008158)n1:9e-06,((GCF_020097155_1_GCF_020097155.1_00431:0.004685,GCF_005280335_1_GCF_005280335.1_00476:0.016435)n3:0.004685,GCF_003691675_1_GCF_003691675.1_01955:3.3945e-08)n2:9e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001734_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001734_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fa73a7cc02a1ab852a5a173cd51678e153cc190
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001734_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02268:0.00738317,GCF_020097155_1_GCF_020097155.1_00493:0.324254)n1:0.000357735,(GCF_005280335_1_GCF_005280335.1_00462:0.0401999,(GCF_023573625_1_GCF_023573625.1_02200:0.00557818,GCF_003691675_1_GCF_003691675.1_01961:0.0166698)n3:0.0015941)n2:0.000357735)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001736_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001736_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e29d343ea298b64091febd65b66551a64b4e91ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001736_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00406:0.0164617,GCF_005280335_1_GCF_005280335.1_00454:0.0116443)n2:0.00190462,GCF_023573625_1_GCF_023573625.1_02221:0.00346986)n1:0.00083057,(GCF_002008305_4_GCF_002008305.4_02282:0.00127625,GCF_003691675_1_GCF_003691675.1_01973:0.00099775)n3:0.00083057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001737_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001737_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d96a5cc2840ec357ca0a992be854c0c768e50f2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001737_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01976:1.37513e-07,(GCF_005280335_1_GCF_005280335.1_00452:0.00013067,GCF_020097155_1_GCF_020097155.1_00405:0.129012)n2:0.0032406)n1:8.16e-05,(GCF_002008305_4_GCF_002008305.4_02285:0.005129,GCF_023573625_1_GCF_023573625.1_02224:0)n3:8.16e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001738_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001738_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4aaf21c264b78430faf88170c4d921395d533469
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001738_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02286:0.00147262,(GCF_020097155_1_GCF_020097155.1_00404:0.377407,GCF_005280335_1_GCF_005280335.1_00451:0.0274256)n2:0.0104254)n1:0.000320185,(GCF_003691675_1_GCF_003691675.1_01977:0.00040387,GCF_023573625_1_GCF_023573625.1_02225:0.00523812)n3:0.000320185)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001742_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001742_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c32580ae6e191ac85023d5567f349a57f731ce0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001742_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02291:0.0029125,GCF_003691675_1_GCF_003691675.1_01983:0.0051845)n1:0.00276413,(GCF_023573625_1_GCF_023573625.1_02231:0.00761975,(GCF_020097155_1_GCF_020097155.1_00399:0.151531,GCF_005280335_1_GCF_005280335.1_00447:0.0820078)n3:0.0235027)n2:0.00276413)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001743_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001743_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a6943f8824ea1d8193823ea9e3be94a26ecab55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001743_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01984:5e-07,GCF_002008305_4_GCF_002008305.4_02292:5e-07)n1:0,((GCF_005280335_1_GCF_005280335.1_00446:0.00091,GCF_020097155_1_GCF_020097155.1_00398:0.038202)n3:0.0222505,GCF_023573625_1_GCF_023573625.1_02232:5e-07)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001746_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001746_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa503700051e564524e7d7fdd623616385637fb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001746_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01988:0.00195025,GCF_023573625_1_GCF_023573625.1_02236:0.00534975)n1:0.0018125,(GCF_002008305_4_GCF_002008305.4_02295:0.0087365,(GCF_020097155_1_GCF_020097155.1_00394:0.264463,GCF_005280335_1_GCF_005280335.1_00441:0.091292)n3:0.107642)n2:0.0018125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001747_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001747_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80538b620477559a64376eded7949fd2ad30f363
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001747_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00440:0.0207658,GCF_020097155_1_GCF_020097155.1_00393:0.0716692)n2:0.0117995,GCF_002008305_4_GCF_002008305.4_02296:0.00469395)n1:0.000476775,(GCF_003691675_1_GCF_003691675.1_01989:0.00631282,GCF_023573625_1_GCF_023573625.1_02237:3.118e-05)n3:0.000476775)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001749_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001749_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdc983cc7c5e2f05f88248c03060d4e32c7aed5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001749_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00388:0.308232,GCF_005280335_1_GCF_005280335.1_00436:0.200246)n2:0.0429521,GCF_023573625_1_GCF_023573625.1_02242:0.00470788)n1:0.00123856,(GCF_002008305_4_GCF_002008305.4_02301:5.59539e-07,GCF_003691675_1_GCF_003691675.1_01994:0.00122838)n3:0.00123856)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001750_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001750_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1683c2869c82c5cfcf4bc4fa002b91d1eebf4fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001750_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01995:0.0327827,GCF_023573625_1_GCF_023573625.1_02243:0.0432932)n1:0.017589,((GCF_005280335_1_GCF_005280335.1_00435:0.684919,GCF_020097155_1_GCF_020097155.1_00387:0.665091)n3:0.044299,GCF_002008305_4_GCF_002008305.4_02302:0.078317)n2:0.017589)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001751_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001751_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f26a74878383daff2ea9d49a2dd72035a0c7816
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001751_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01997:0,GCF_023573625_1_GCF_023573625.1_02245:0)n1:0,((GCF_020097155_1_GCF_020097155.1_00385:0.087898,GCF_005280335_1_GCF_005280335.1_00433:0.016439)n3:0.04794,GCF_002008305_4_GCF_002008305.4_02304:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001758_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001758_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75fd1f771593f8670b41654330f1f6e8923479b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001758_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02253:5e-07,GCF_003691675_1_GCF_003691675.1_02005:5e-07)n1:0,(GCF_002008305_4_GCF_002008305.4_02312:5e-07,(GCF_020097155_1_GCF_020097155.1_00377:0.0223085,GCF_005280335_1_GCF_005280335.1_00424:0.0144475)n3:0.029689)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001759_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001759_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c56844dcfde842cf28fba9be741107deb86de702
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001759_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_02432:0.508635,(GCF_003691675_1_GCF_003691675.1_00206:1.02833,GCF_003691675_1_GCF_003691675.1_00237:0.452652)n2:0.0502946)n1:0.23034,(GCF_020097155_1_GCF_020097155.1_02316:0.308798,GCF_023573625_1_GCF_023573625.1_00516:0.152319)n3:0.692559)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001760_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001760_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d8c0479bb784e76e77db810b88f4a92e62c779b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001760_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00303:0.0218486,GCF_005280335_1_GCF_005280335.1_02372:0.0479534)n1:0.491682,(GCF_003691675_1_GCF_003691675.1_02232:0.673447,(GCF_005280335_1_GCF_005280335.1_02198:1.5088,GCF_005280335_1_GCF_005280335.1_02196:0.929004)n3:0.0275186)n2:0.491682)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001761_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001761_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14d166173f7b500c8570a8d7a582691f10ecb80b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001761_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_00329:0,((GCF_003691675_1_GCF_003691675.1_00368:0,GCF_003691675_1_GCF_003691675.1_01110:0.27663)n2:0,(GCF_003691675_1_GCF_003691675.1_01967:0,GCF_003691675_1_GCF_003691675.1_02017:0)n3:0)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001762_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001762_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7856dcf93defa1fbd88a13cde1556a880f3d421e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001762_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01858:0.0019765,(GCF_023573625_1_GCF_023573625.1_02088:0.003488,(GCF_020097155_1_GCF_020097155.1_00540:0.398996,(GCF_005280335_1_GCF_005280335.1_00616:0.118973,GCF_005280335_1_GCF_005280335.1_02658:0.369289)n3:0.0410321)n2:0.08975)n1:0.0019765)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001764_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001764_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8c3d1078d7932d798357537e53071eb3bdb5c88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001764_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_02133:0,(GCF_023573625_1_GCF_023573625.1_00125:0,(GCF_020097155_1_GCF_020097155.1_00135:0.538285,(GCF_005280335_1_GCF_005280335.1_00267:0.0154805,GCF_005280335_1_GCF_005280335.1_00090:0.536878)n3:0.0596531)n2:0.891348)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001769_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001769_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4962e891cb63efeaa88b85303ec30abc1971846
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001769_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_1_GCF_020097155.1_00886:0.0659238,(((GCF_005280335_1_GCF_005280335.1_00811:0.669371,GCF_005280335_1_GCF_005280335.1_02387:1.10963)n3:0.266512,GCF_005280335_1_GCF_005280335.1_00518:1.17097)n2:0.657395,GCF_005280335_1_GCF_005280335.1_00946:0.0437365)n1:0.0659238)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001771_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001771_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..591abd11924d2a8b6010511dd1723b2b9e6443d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001771_tree.txt
@@ -0,0 +1 @@
+(GCF_023573625_1_GCF_023573625.1_00036:2.26548e-06,(GCF_002008305_4_GCF_002008305.4_00041:0.0274863,(GCF_003691675_1_GCF_003691675.1_02171:2.23308,GCF_003691675_1_GCF_003691675.1_02054:2.26548e-06)n2:2.26548e-06)n1:0.0163802)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001779_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001779_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dadb6fcb85dd3e76f97d460a11ad6e30e7310cdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001779_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_00200:0.291944,GCF_002008305_4_GCF_002008305.4_00118:0.0166565)n1:0.00531175,(GCF_003691675_1_GCF_003691675.1_02131:0,GCF_023573625_1_GCF_023573625.1_00123:0)n2:0.00531175)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001782_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001782_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cea6924dd87bf8c027858ee7cd6c690733b427b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001782_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00145:0.0250982,GCF_005280335_1_GCF_005280335.1_00239:0.241402)n1:0.00226463,(GCF_003691675_1_GCF_003691675.1_02159:0.0147817,GCF_023573625_1_GCF_023573625.1_00153:0.0167213)n2:0.00226463)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001785_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001785_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8260ac40e996042b9ca858b71fd7a99708d4c6c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001785_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00177:0.0257512,GCF_003691675_1_GCF_003691675.1_02170:0.0151837)n1:0.0166446,(GCF_005280335_1_GCF_005280335.1_00225:0.169271,GCF_023573625_1_GCF_023573625.1_00169:0.0457533)n2:0.0166446)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001794_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001794_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..901087d7630adcf60cb915b5f22e259185fd4d9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001794_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00252:0.00080825,GCF_005280335_1_GCF_005280335.1_00118:0.0249718)n1:0.000664875,(GCF_003691675_1_GCF_003691675.1_02264:0.00316259,GCF_002008305_4_GCF_002008305.4_00252:0.0193844)n2:0.000664875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001795_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001795_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcf2378596d7753740f497b1e3c7a52ecb1c2c4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001795_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00253:0.0067025,GCF_005280335_1_GCF_005280335.1_00116:0.0105195)n1:0.00046575,(GCF_003691675_1_GCF_003691675.1_02265:0,GCF_023573625_1_GCF_023573625.1_00253:0)n2:0.00046575)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001796_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001796_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65a49dd70289361f8af0138739465fc939fd9fa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001796_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02287:0,GCF_002008305_4_GCF_002008305.4_00272:0)n1:0,(GCF_005280335_1_GCF_005280335.1_00084:0.45316,GCF_023573625_1_GCF_023573625.1_00270:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001802_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001802_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee1e69aedbb398681ce8f4aa6624f9f4be0bb69f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001802_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00327:0,GCF_003691675_1_GCF_003691675.1_00043:0)n1:0.001679,(GCF_005280335_1_GCF_005280335.1_00008:0.119485,GCF_023573625_1_GCF_023573625.1_00334:0.008043)n2:0.001679)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001803_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001803_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbec5eec9b2a7bd664d891ffbd7004891b5695ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001803_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00335:0.005669,GCF_005280335_1_GCF_005280335.1_00007:0.126148)n1:0.0056245,(GCF_003691675_1_GCF_003691675.1_00044:0,GCF_002008305_4_GCF_002008305.4_00328:0)n2:0.0056245)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001806_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001806_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..374d476bea8d214fddf012ea0f7a5afffe9d902e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001806_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00369:0.030218,GCF_005280335_1_GCF_005280335.1_02394:1.74452)n1:0.0237095,(GCF_023573625_1_GCF_023573625.1_00376:0,GCF_003691675_1_GCF_003691675.1_00085:0)n2:0.0237095)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001807_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001807_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4b458f2901af49bfcb227662d6f52dc4f638f36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001807_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00393:0.0291575,GCF_003691675_1_GCF_003691675.1_00111:0.0454005)n1:0.002751,(GCF_002008305_4_GCF_002008305.4_00387:0.0124685,GCF_020097155_1_GCF_020097155.1_02441:0.0168495)n2:0.002751)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001808_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001808_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a229bb09dabaf19e59ff3e8c4829a1667debf839
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001808_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_02566:0.464514,GCF_002008305_4_GCF_002008305.4_00390:4.73232e-07)n1:0.000957625,(GCF_003691675_1_GCF_003691675.1_00114:0,GCF_023573625_1_GCF_023573625.1_00396:0.008718)n2:0.000957625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001812_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001812_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a973a3d1c50bc043e2d72fa58ebeead3a82d7a02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001812_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00476:0,GCF_002008305_4_GCF_002008305.4_00476:0)n1:0,(GCF_003691675_1_GCF_003691675.1_00194:0,GCF_020097155_1_GCF_020097155.1_02355:0.271425)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001813_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001813_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e790fb03e55e6204996281660df2abe0865de3c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001813_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00509:0.0385947,GCF_020097155_1_GCF_020097155.1_02324:0.721322)n1:0.00204012,(GCF_002008305_4_GCF_002008305.4_00510:0.0395957,GCF_003691675_1_GCF_003691675.1_00230:0.0445152)n2:0.00204012)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001816_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001816_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5828d5d0e605a67caeb2374a1a51484f051ffe11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001816_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_02259:0.231418,GCF_002008305_4_GCF_002008305.4_00569:0.075382)n1:0.0108245,(GCF_003691675_1_GCF_003691675.1_00293:0.032947,GCF_023573625_1_GCF_023573625.1_00571:0.039492)n2:0.0108245)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001817_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001817_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b817de912ffd95eb6561c04d0dd8830d95cf025
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001817_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00308:4.815e-09,GCF_005280335_1_GCF_005280335.1_02357:0.001492)n1:8.35e-05,(GCF_002008305_4_GCF_002008305.4_00576:0,GCF_023573625_1_GCF_023573625.1_00577:0.003323)n2:8.35e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001819_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001819_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a1fabe8a3cead7e8abadf4d70cc74ca29b7e228
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001819_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00579:0.004504,GCF_002008305_4_GCF_002008305.4_00578:1.4304e-08)n1:3e-06,(GCF_003691675_1_GCF_003691675.1_00310:0,GCF_005280335_1_GCF_005280335.1_02355:0.0098)n2:3e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001821_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001821_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57f8be7543d25cb486afa997f83b56e9fb72842b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001821_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00593:0,(GCF_002008305_4_GCF_002008305.4_00624:5.34483e-07,GCF_002008305_4_GCF_002008305.4_00638:0)n2:0)n1:0.0178463,GCF_005280335_1_GCF_005280335.1_00752:0.516888)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001825_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001825_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2a99a51d864973e7ce23d404b84c3fb277c401b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001825_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_00632:0,((GCF_005280335_1_GCF_005280335.1_00404:0,GCF_020097155_1_GCF_020097155.1_02197:0)n2:0,GCF_023573625_1_GCF_023573625.1_00599:0)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001826_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001826_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95ed91d000dd0587f939da4c66097f288fa2830f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001826_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_00635:0.00448138,(GCF_005280335_1_GCF_005280335.1_00407:1.92087e-08,(GCF_020097155_1_GCF_020097155.1_02194:0.007326,GCF_023573625_1_GCF_023573625.1_00596:0.002931)n2:0.00018975)n1:0.00448138)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001830_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001830_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdaab7d6ea3fd4513990e6ebe6ceeafedaa451f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001830_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00400:0,GCF_023573625_1_GCF_023573625.1_00633:0)n1:0.001323,(GCF_002008305_4_GCF_002008305.4_00663:0.00213,GCF_005280335_1_GCF_005280335.1_02300:0.039167)n2:0.001323)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001832_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001832_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e331e13a08b36a522488e3cbb4154ec055c8a29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001832_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00403:0,GCF_002008305_4_GCF_002008305.4_00666:0)n1:0.0026225,(GCF_005280335_1_GCF_005280335.1_02296:0.157599,GCF_023573625_1_GCF_023573625.1_00636:0.002058)n2:0.0026225)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001835_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001835_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e5442f1f4a71481bac6de9ad9dfedc184724c1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001835_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00668:0.0151895,GCF_003691675_1_GCF_003691675.1_00435:0.0071025)n1:0.00130775,(GCF_005280335_1_GCF_005280335.1_02256:0.352739,GCF_002008305_4_GCF_002008305.4_00698:0.0124656)n2:0.00130775)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001840_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001840_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92cf9683b8be084603b9faeddfb001ae0e6eeca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001840_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_1_GCF_005280335.1_01991:0.0419712,(GCF_002008305_4_GCF_002008305.4_00946:0.00846525,(GCF_003691675_1_GCF_003691675.1_01109:0.96884,GCF_003691675_1_GCF_003691675.1_00665:0.00610898)n2:0.000678775)n1:0.0991973)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001843_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001843_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d99c9d23ec8623ff7608d825b546b35279e43804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001843_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01010:0,GCF_003691675_1_GCF_003691675.1_00724:0)n1:0.0238425,(GCF_005280335_1_GCF_005280335.1_01879:0.031042,GCF_023573625_1_GCF_023573625.1_00953:0.019751)n2:0.0238425)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001845_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001845_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16aa794263933be0e5a7967f5f9528a087a66b3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001845_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00960:0.00223575,GCF_005280335_1_GCF_005280335.1_01872:0.00848225)n1:3.875e-06,(GCF_003691675_1_GCF_003691675.1_00730:0.00224852,GCF_002008305_4_GCF_002008305.4_01016:0.00394648)n2:3.875e-06)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001847_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001847_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c1304a4fe10f0fe143cc135da56ad8726635cde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001847_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_02229:0.082969,GCF_003691675_1_GCF_003691675.1_00786:0.001791)n1:0.0064535,(GCF_002008305_4_GCF_002008305.4_01067:0.0155645,GCF_023573625_1_GCF_023573625.1_01014:1.1219e-07)n2:0.0064535)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001848_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001848_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de16ee15ec6d28b461d5f55b31976e61de312080
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001848_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01025:0,GCF_002008305_4_GCF_002008305.4_01076:0)n1:0,(GCF_003691675_1_GCF_003691675.1_00795:0,GCF_005280335_1_GCF_005280335.1_02322:0.400685)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001849_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001849_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b325916cd07a4a59ed44820538b6c56fa1d5146
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001849_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01026:-0,GCF_005280335_1_GCF_005280335.1_02323:0.3675)n1:0,(GCF_002008305_4_GCF_002008305.4_01077:0,GCF_003691675_1_GCF_003691675.1_00796:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001850_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001850_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f17fc96e81ba885eea427ffce0ded6531151520e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001850_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_01674:0.297631,GCF_023573625_1_GCF_023573625.1_01061:0.0644663)n1:0.0891056,(GCF_003691675_1_GCF_003691675.1_00830:0.00406801,GCF_002008305_4_GCF_002008305.4_01111:0.00718899)n2:0.0891056)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001852_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001852_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04890e471dbc0857c9cf469bac0ae215a6586854
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001852_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00864:0,GCF_023573625_1_GCF_023573625.1_01095:0)n1:0.0232923,(GCF_020097155_1_GCF_020097155.1_01641:0.623008,GCF_002008305_4_GCF_002008305.4_01145:0.0462775)n2:0.0232923)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001854_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001854_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c73baf4fd02613407597b21f3bbdd8a7badd8ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001854_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00879:0,GCF_023573625_1_GCF_023573625.1_01110:0)n1:0.0022705,(GCF_020097155_1_GCF_020097155.1_01627:0.881817,GCF_002008305_4_GCF_002008305.4_01160:0.00349)n2:0.0022705)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001856_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001856_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0325ca3f062e63043dc1a4a44e16d6f56d6f1231
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001856_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01223:0.00338225,GCF_005280335_1_GCF_005280335.1_01665:0.112838)n1:0.00311037,(GCF_003691675_1_GCF_003691675.1_00942:0.00839369,GCF_023573625_1_GCF_023573625.1_01181:0.00358231)n2:0.00311037)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001860_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001860_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..265b88e9520966d8197e47270623017dae29d778
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001860_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_01315:0.000774125,(GCF_020097155_1_GCF_020097155.1_01473:1.96476e-06,(GCF_005280335_1_GCF_005280335.1_01577:0.00451975,GCF_005280335_1_GCF_005280335.1_02666:1.33694)n2:0.148549)n1:0.941407)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001862_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001862_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee6541b3761a3234bac347a26339bd79f44d3b57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001862_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_01893:0.540251,GCF_003691675_1_GCF_003691675.1_01102:0.013929)n1:0.00561475,(GCF_023573625_1_GCF_023573625.1_01337:5e-07,GCF_002008305_4_GCF_002008305.4_01382:5e-07)n2:0.00561475)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001866_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001866_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..495cd9a28c79abbef2faccacc7a2408b7dc887a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001866_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01411:0.0045655,GCF_023573625_1_GCF_023573625.1_01361:0.0011375)n1:0.03252,(GCF_020097155_1_GCF_020097155.1_01395:0.391095,GCF_003691675_1_GCF_003691675.1_01141:0.216553)n2:0.03252)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001868_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001868_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b307a7ce4f5c3648bdfb070af4772b08013e436
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001868_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01445:0.0143665,GCF_003691675_1_GCF_003691675.1_01177:0.0230315)n1:0.00055725,(GCF_020097155_1_GCF_020097155.1_01358:0.580463,GCF_023573625_1_GCF_023573625.1_01395:0.019383)n2:0.00055725)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001870_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001870_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..008f61d2327620a36ab8c4f8b50ee99c4724ea4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001870_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01420:0.0198898,GCF_002008305_4_GCF_002008305.4_01470:0.0242422)n1:0.0117506,(GCF_003691675_1_GCF_003691675.1_01202:0.0401341,GCF_020097155_1_GCF_020097155.1_01332:0.385035)n2:0.0117506)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001872_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001872_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f00d2d114b09faf96eb35d9b135a87bc1a6e0b30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001872_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01427:5e-07,GCF_003691675_1_GCF_003691675.1_01209:5e-07)n1:0,(GCF_002008305_4_GCF_002008305.4_01477:5e-07,GCF_020097155_1_GCF_020097155.1_01325:0.0174215)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001873_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001873_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f55db172b8c2806f4baa57fff06266a356ed12a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001873_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_01506:0.0643782,((GCF_020097155_1_GCF_020097155.1_01746:0,GCF_020097155_1_GCF_020097155.1_02236:0)n2:0.0810405,GCF_020097155_1_GCF_020097155.1_00640:0.248333)n1:0.0643782)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001882_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001882_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6033ca156ca50afb630632f93cc8698b91bb06a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001882_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01374:0.0128678,GCF_005280335_1_GCF_005280335.1_01225:0.137613)n1:0.00370187,(GCF_002008305_4_GCF_002008305.4_01669:0.0202334,GCF_023573625_1_GCF_023573625.1_01599:0.0125396)n2:0.00370187)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001883_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001883_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8c3364d172603753e7adfcb2d2c866ad66eb997
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001883_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_01679:0.135004,(GCF_005280335_1_GCF_005280335.1_01199:0.270961,(GCF_020097155_1_GCF_020097155.1_01217:1.49068,GCF_020097155_1_GCF_020097155.1_02117:1.31849)n2:0.850826)n1:0.135004)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001888_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001888_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..137431ed07e56c0782b03a29be10c90d8e5d0129
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001888_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_01032:0.229771,GCF_002008305_4_GCF_002008305.4_01836:0.0323525)n1:0.00864175,(GCF_003691675_1_GCF_003691675.1_01533:0,GCF_023573625_1_GCF_023573625.1_01757:0)n2:0.00864175)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001890_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001890_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3426a732badfda123a3b39abe97932568918fc2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001890_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01877:0.00257825,GCF_003691675_1_GCF_003691675.1_01573:0.00635475)n1:0.0778559,(GCF_020097155_1_GCF_020097155.1_00920:0.849078,GCF_005280335_1_GCF_005280335.1_00982:0.0705412)n2:0.0778559)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001892_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001892_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f119f7afe821eccb77051693444cb347abfd956c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001892_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01879:0,GCF_003691675_1_GCF_003691675.1_01575:0)n1:0.0288085,(GCF_023573625_1_GCF_023573625.1_01799:0.011841,GCF_005280335_1_GCF_005280335.1_00980:0.346375)n2:0.0288085)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001896_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001896_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc14a9f14050e26f50c89b9e44386bacd29ce043
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001896_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01594:0.00451,GCF_002008305_4_GCF_002008305.4_01898:0.012204)n1:0.00224425,(GCF_005280335_1_GCF_005280335.1_00961:0.454486,GCF_023573625_1_GCF_023573625.1_01818:0.006046)n2:0.00224425)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001899_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001899_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90e57d71fa6f6484ef0b51a97c04dccd639335c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001899_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_1_GCF_020097155.1_00881:0.479684,GCF_002008305_4_GCF_002008305.4_01914:0.021714)n1:0.014482,(GCF_023573625_1_GCF_023573625.1_01834:0.00189,GCF_003691675_1_GCF_003691675.1_01610:0.001528)n2:0.014482)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001907_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001907_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..445d347b825066e11c9eb2f555df5b8dd1000191
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001907_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01987:0,GCF_003691675_1_GCF_003691675.1_01681:0)n1:0,(GCF_005280335_1_GCF_005280335.1_00870:0.006509,GCF_023573625_1_GCF_023573625.1_01913:0)n2:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001910_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001910_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76509100b0a7aa9256b3df26cedbbcb63e3dccac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001910_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00856:0.241133,GCF_002008305_4_GCF_002008305.4_02001:0.026574)n1:0.00557425,(GCF_003691675_1_GCF_003691675.1_01695:0.0075081,GCF_023573625_1_GCF_023573625.1_01927:0.0084389)n2:0.00557425)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001920_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001920_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..713cef871e501fdebac9cdddaa648cbbcee2ba99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001920_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02091:0.0426443,GCF_020097155_1_GCF_020097155.1_00603:0.0268817)n1:0.00153513,(GCF_005280335_1_GCF_005280335.1_00687:0.00496756,GCF_003691675_1_GCF_003691675.1_01799:0.0224314)n2:0.00153513)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001924_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001924_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccc42a9de2b278086651425dc439983736bc7d92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001924_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02108:9.46657e-08,GCF_023573625_1_GCF_023573625.1_02048:0.0269307)n1:0.00196687,(GCF_005280335_1_GCF_005280335.1_00670:0.064232,GCF_003691675_1_GCF_003691675.1_01815:9.46657e-08)n2:0.00196687)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001925_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001925_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..851b13dfd95a4d8513d848d96b4b6ddb33a1ec82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001925_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01824:0.0317335,GCF_005280335_1_GCF_005280335.1_00664:0.246457)n1:0.00855575,(GCF_023573625_1_GCF_023573625.1_02054:0.013992,GCF_002008305_4_GCF_002008305.4_02116:0.02537)n2:0.00855575)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001928_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001928_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08b32978aa9a7f9e2a717c17b507d6437f9d018a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001928_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02155:0.037156,GCF_003691675_1_GCF_003691675.1_01868:0.018649)n1:0.00582175,(GCF_023573625_1_GCF_023573625.1_02098:1.6456e-06,GCF_005280335_1_GCF_005280335.1_00602:1.58007)n2:0.00582175)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001930_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001930_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6189254f37058da47adca7ae1211deeebd939879
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001930_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02171:0.00192842,GCF_023573625_1_GCF_023573625.1_02116:0.00565058)n1:0.0541119,(GCF_020097155_1_GCF_020097155.1_00507:1.381,GCF_003691675_1_GCF_003691675.1_01885:0.0388162)n2:0.0541119)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001931_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001931_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d26da130c472180ae640ff87d0c00c9efecd5e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001931_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02172:0.00118975,GCF_003691675_1_GCF_003691675.1_01886:0.00211125)n1:0.00366937,(GCF_005280335_1_GCF_005280335.1_00580:0.485104,GCF_023573625_1_GCF_023573625.1_02117:0.0219618)n2:0.00366937)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001932_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001932_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4fe1757174f37473faa381f1599a15fd35e5760
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001932_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02132:0.00929275,GCF_003691675_1_GCF_003691675.1_01901:0.00814925)n1:0.00612562,(GCF_002008305_4_GCF_002008305.4_02187:0.0426602,GCF_005280335_1_GCF_005280335.1_00562:0.372974)n2:0.00612562)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001934_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001934_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59cbf8c9bd6ee25a1147140cc654f7763fb0aac6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001934_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02192:0.0179085,GCF_023573625_1_GCF_023573625.1_02136:0.0408515)n1:0.0143625,(GCF_005280335_1_GCF_005280335.1_00550:0.0644078,GCF_003691675_1_GCF_003691675.1_01905:1.50639e-07)n2:0.0143625)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001935_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001935_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cfb81ac53bf3a97c4681709feb8a3d47b87bfb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001935_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02137:0.0087985,GCF_002008305_4_GCF_002008305.4_02193:0.0097865)n1:0.003081,(GCF_003691675_1_GCF_003691675.1_01906:0.0535754,GCF_005280335_1_GCF_005280335.1_00553:0.566552)n2:0.003081)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001937_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001937_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9be8f2fff54172e123c643abbf9cc894ddabb995
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001937_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01920:0.0161193,GCF_005280335_1_GCF_005280335.1_00538:0.0509397)n1:0.0135681,(GCF_002008305_4_GCF_002008305.4_02207:0.0252892,GCF_023573625_1_GCF_023573625.1_02151:0.00365475)n2:0.0135681)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001938_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001938_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a7bdf52b95fff83b25e09bc048c5d5e0375eb98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001938_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02209:0,GCF_003691675_1_GCF_003691675.1_01922:0)n1:0.0228495,(GCF_005280335_1_GCF_005280335.1_00535:0.074514,GCF_005280335_1_GCF_005280335.1_02645:1.77901)n2:0.0228495)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001939_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001939_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f9524c23a1b53bb83e322fc8aa045b8c5f2ee43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001939_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01926:0.002217,GCF_002008305_4_GCF_002008305.4_02213:0.002026)n1:0.026504,(GCF_005280335_1_GCF_005280335.1_00531:0.0414494,GCF_005280335_1_GCF_005280335.1_02650:0.91224)n2:0.026504)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001943_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001943_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbfb14e5d3a56106d8268b98cb084f4e0bcfc28c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001943_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02222:0.00038625,GCF_020097155_1_GCF_020097155.1_00461:0.129598)n1:0.000391875,(GCF_023573625_1_GCF_023573625.1_02161:0.00299448,GCF_003691675_1_GCF_003691675.1_01938:0.0113515)n2:0.000391875)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001944_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001944_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87688e22626178fd1edc08792b5f4b4f89fb5408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001944_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02224:0.0131985,GCF_020097155_1_GCF_020097155.1_01229:0.435267)n1:0.001158,(GCF_023573625_1_GCF_023573625.1_02162:0.00727402,GCF_003691675_1_GCF_003691675.1_01939:0.00463098)n2:0.001158)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001947_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001947_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16c082870634bc5389e50e492a6fa40a78c4e8d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001947_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01964:0.168978,GCF_005280335_1_GCF_005280335.1_00460:0.0595613)n1:0.130226,(GCF_020097155_1_GCF_020097155.1_00410:0.99526,GCF_002008305_4_GCF_002008305.4_02272:0.0491268)n2:0.130226)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001949_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001949_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b9ec55a0b9287da17df740f558acca6f3eef8cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001949_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_02222:0.00787775,GCF_003691675_1_GCF_003691675.1_01974:0.00710125)n1:0.00107212,(GCF_005280335_1_GCF_005280335.1_00808:0.804358,GCF_002008305_4_GCF_002008305.4_02283:0.00315017)n2:0.00107212)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001950_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001950_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6adf7a4281551e8ef940d09d88d426f26b93cd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001950_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_1_GCF_005280335.1_00453:0.0319748,GCF_023573625_1_GCF_023573625.1_02223:3.74892e-08)n1:0.00171813,(GCF_002008305_4_GCF_002008305.4_02284:0.00247075,GCF_003691675_1_GCF_003691675.1_01975:3.74892e-08)n2:0.00171813)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001951_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001951_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2db52efa4d001d6faf55d4f7a486405bc9dbf05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001951_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01991:7.05275e-07,GCF_005280335_1_GCF_005280335.1_00945:0.489416)n1:0.0243705,(GCF_002008305_4_GCF_002008305.4_02298:7.05275e-07,GCF_023573625_1_GCF_023573625.1_02239:0.203501)n2:0.0243705)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001954_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001954_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6df7a65ff8e98ff72c3b0832a7b0069e9a7fed5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001954_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_00238:0.0914504,(GCF_023573625_1_GCF_023573625.1_00844:0.257766,(GCF_005280335_1_GCF_005280335.1_02437:0.221591,GCF_005280335_1_GCF_005280335.1_01224:2.00426)n2:0.222695)n1:0.419343)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001955_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001955_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d16b35246be304f10caf3ccde0d91173619d1733
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001955_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_00255:0.02357,((GCF_023573625_1_GCF_023573625.1_00534:0.0246665,GCF_020097155_1_GCF_020097155.1_02300:0.0907395)n2:0.02753,GCF_005280335_1_GCF_005280335.1_02418:0.798463)n1:0.02357)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001963_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001963_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e071f01a6fc3bea3e3d9cdb11e33eb867bc7e255
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001963_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01697:0.0737088,((GCF_005280335_1_GCF_005280335.1_00854:2.06428e-06,GCF_023573625_1_GCF_023573625.1_00736:1.42231)n2:0.343581,GCF_020097155_1_GCF_020097155.1_00791:0.463245)n1:0.0737088)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001965_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001965_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4594536a2d87b19a3357e48523b21ffbfca0f713
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001965_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01700:0,(GCF_023573625_1_GCF_023573625.1_01928:0,(GCF_005280335_1_GCF_005280335.1_00851:0.019725,GCF_020097155_1_GCF_020097155.1_00788:0.129528)n2:0.014444)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001967_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001967_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31ef730c075992f24707e1eed1a1e95cfa22a86f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001967_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01702:0,(GCF_023573625_1_GCF_023573625.1_01930:0,(GCF_020097155_1_GCF_020097155.1_00786:0.0625435,GCF_005280335_1_GCF_005280335.1_00849:0.0593505)n2:0.0489025)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001970_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001970_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dae8392b3df70165dd6a7fb5d9264ff128b9eb21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001970_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01707:0,(GCF_023573625_1_GCF_023573625.1_01935:0,(GCF_005280335_1_GCF_005280335.1_00845:0.180286,GCF_020097155_1_GCF_020097155.1_00778:0.165953)n2:0.0811885)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001971_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001971_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b35d4bdab221d0e9f29a4d8c64191bef06c8a553
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001971_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01708:0.0343881,(GCF_023573625_1_GCF_023573625.1_01936:0.0543698,(GCF_020097155_1_GCF_020097155.1_00777:0.335659,GCF_005280335_1_GCF_005280335.1_00844:0.206842)n2:0.0932768)n1:0.0343881)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001978_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001978_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a24bff4d317c47c734d269755e18a520ca401f92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001978_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_1_GCF_020097155.1_00415:0.0683035,((GCF_005280335_1_GCF_005280335.1_00733:0,GCF_005280335_1_GCF_005280335.1_00750:0)n2:0.190257,GCF_005280335_1_GCF_005280335.1_02328:0.067477)n1:0.0683035)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001983_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001983_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc6c3443a778d1c32468c7c6aa89ebc4e96a03ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001983_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_1_GCF_020097155.1_00644:0.454029,(GCF_020097155_1_GCF_020097155.1_00423:0.498852,(GCF_020097155_1_GCF_020097155.1_01822:0.156351,GCF_020097155_1_GCF_020097155.1_01784:0.467803)n2:0.8943)n1:0.454029)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001984_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001984_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ce058274b00c05e88153d71f65f93c3614d81cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001984_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_1_GCF_020097155.1_01398:1.16184,((GCF_020097155_1_GCF_020097155.1_00698:2.61957e-06,GCF_020097155_1_GCF_020097155.1_00722:0.0385245)n2:0.163786,GCF_020097155_1_GCF_020097155.1_00661:0.0961175)n1:1.16184)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000003_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000003_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58a28158c000be008a8ad5d333cad1ceb8a6cc01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000003_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2280:0.00000050,(1_1283:0.00000050,2_740:0.00000050):0.00000000):0.00000000,((((((2_1292:0.01201103,(2_1287:0.00000050,2_1256:0.00000050):0.00596747):0.00680981,(2_1279:0.00500704,(2_2572:0.01675969,2_2296:0.00125131):0.01323346):0.00549544):0.00247950,(0_1023:0.01334462,3_608:0.01073738):0.00120444):0.00414823,((3_1759:0.00000050,(3_1797:0.00000050,3_2155:0.00000050):0.00000000):0.00834597,(((((4_1825:0.01545768,4_109:0.00172532):0.00229961,1_1609:0.01243489):0.00205871,0_1338:0.00608304):0.03082399,0_2219:0.33871238):0.04719626,3_303:0.05677330):0.01405212):0.00538523):0.00188907,(1_752:0.00155310,(1_2209:0.00000000,1_303:0.00000000):0.01040690):0.00699543):0.00165557,(2_2556:0.03771600,1_1077:0.01163900):0.00519576):0.00045824,4_1485:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000005_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000005_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ca5956a1e20f4bdd8c32f3233335c1a94097b43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000005_tree_id.txt
@@ -0,0 +1,2 @@
+((((((2_2224:0.01977058,(((((3_733:0.00000000,3_1757:0.00000000):0.00010659,(3_614:0.00000000,3_2111:0.00000000):0.00285841):0.00068751,3_610:0.00079899):0.00179948,(((3_212:0.00008503,3_1796:0.00216597):0.00412963,3_298:0.00488987):0.00407000,3_1847:0.00760725):0.00215033):0.00719922,(3_301:0.00000000,3_628:0.00000000):0.02760206):0.00075433):0.04214498,(3_431:0.02401900,3_2154:0.04516500):0.05191919):0.22252734,((3_661:1.30711747,1_1728:0.96327753):0.89546681,3_213:0.48469869):0.36414287):0.17695922,(3_624:0.05238479,(3_1335:0.04708632,3_1793:0.17256668):0.01893871):0.05481080):0.04613514,2_1257:0.05515765):0.00967885,3_635:0.03817470,3_1781:0.04802730);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000012_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000012_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be2372eb370dd15e7c65a5235579d7c9dd617003
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000012_tree_id.txt
@@ -0,0 +1,2 @@
+(((((1_329:-0.00388253,((0_151:0.10536729,2_704:0.11735971):0.30441380,((3_2171:0.00000000,0_2002:0.00000000):0.34562663,1_282:0.22476437):0.11141320):0.05608328):0.00388253,1_322:-0.00388253):0.00388253,1_758:-0.00388253):0.02282178,0_1030:-0.00855844):0.19296344,(2_702:0.00000000,4_979:0.00000000):0.10182563,0_148:0.04648637);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000027_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000027_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee079db646582aae5db67152d52316b4dc33daa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000027_tree_id.txt
@@ -0,0 +1,2 @@
+((1_320:0.00000000,(2_706:0.00000000,(1_331:0.00000000,0_1028:0.00000000):0.00000000):0.00000000):0.00000000,(1_756:0.00000000,4_977:0.00000000):0.02016800,0_153:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000037_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000037_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e17968befa680986e8f68b62f32cff8180e4ab78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000037_tree_id.txt
@@ -0,0 +1,2 @@
+(0_722:0.00959819,(((3_2026:0.73087094,(3_668:0.77847450,3_669:0.94980450):0.40074156):0.27913606,2_2132:0.54098144):0.40820531,1_461:0.01044031):0.01586819,4_686:0.03364081);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000048_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000048_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06ba929e7ae7008548071cec9690c597a1adc16a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000048_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_981:0.15989219,(2_382:0.21050756,2_2584:0.73428844):0.07262231):0.08636306,(1_1457:0.00000050,0_1749:0.00000050):0.04485594):0.01823306,2_1045:0.00580594,4_1671:0.00437206);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000056_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000056_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1a9ba2912b05693401e456b7ccd83f83fca965a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000056_tree_id.txt
@@ -0,0 +1,2 @@
+((4_22:0.01099227,(1_1991:0.01884131,(3_338:0.43686212,2_354:0.24056788):0.08569158):0.00733491):0.01738548,0_22:0.00328129,2_355:0.40449971);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000063_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000063_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f26a76569c1d63cec7fb5178acf6b3a251be6da8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000063_tree_id.txt
@@ -0,0 +1,2 @@
+(4_96:0.00300130,(0_101:0.00218716,(2_270:0.00792683,(3_217:-1.01211388,2_31:1.72518988):1.08985804):0.01746755):0.00085434,1_2065:-0.00023630);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000064_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000064_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44ab4707b16e1d7cf252d99e27445d3d53296cdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000064_tree_id.txt
@@ -0,0 +1,2 @@
+((2_252:0.06071859,((2_79:0.62484050,3_127:0.44056450):0.37841674,0_114:0.35703815):0.02038335):0.02359941,4_122:0.00000000,1_2081:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000090_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000090_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1881b265bebfaab40b08fb1aa07f95e8f68c51b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000090_tree_id.txt
@@ -0,0 +1,2 @@
+((((3_2257:0.00494850,0_498:0.04807450):0.00434688,2_2375:0.00382862):0.02005987,1_229:-0.01375462):0.06745212,4_498:-0.04193412,2_1194:2.47311712);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000096_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000096_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6458c64876aa138408600f92268191c6b61db4c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000096_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1724:0.06294675,0_589:0.03695225):0.18344875,(3_527:0.23325125,3_685:0.21623575):0.07965475):0.28784675,1_310:0.01880125,4_1947:0.02298075);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000108_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000108_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b9ed43a7b082a591e66933e24b915abe9b676e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000108_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_748:0.00000000,4_967:0.00000000):0.00147494,0_1020:0.00689306):0.08468339,(3_1678:0.11351650,0_808:1.45797350):0.09485865,2_1790:0.08475330);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000112_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000112_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3900ab60e660f8be6640ddbe95670c4018963b04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000112_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1841:0.37223750,(1_694:0.00000000,0_971:0.00000000):0.02342550):0.04889320,(2_1840:0.61457213,3_1727:0.80865188):0.10873278,4_914:-0.01953970);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000141_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000141_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..167eac9483ca634e38203675cf0200340ee36980
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000141_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1234:0.01920937,((4_1511:0.01802900,0_1582:0.02470500):0.01983701,3_1144:0.01248202):0.02538510):0.00798613,3_1186:0.71586578,1_1297:0.00776422);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000153_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000153_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ace2f7ec282b6c9a7cec7e3a1410fee3f89f8a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000153_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1841:0.00436273,(2_863:0.10563018,1_1619:0.00015482):0.00685351):0.01972306,(3_799:0.08448463,0_1914:0.09782337):0.44573764,0_1915:0.07809454);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000158_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000158_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d08c336cc55d85b8a9dfe7d40aad6d77e56bb740
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000158_tree_id.txt
@@ -0,0 +1,2 @@
+((3_732:0.29889721,(0_1968:0.33353800,(2_771:0.34486937,4_1906:-0.01767737):0.12469038):0.07257050):0.08599729,0_1970:0.20198750,1_1688:-0.01166750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000171_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000171_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08abf008a40a3d91de1452279f5e1f65ff02ccc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000171_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2186:-0.00475425,(0_2244:0.00000000,1_1948:0.00000000):0.00728425):0.07691100,(2_1906:2.30841250,3_367:0.28618050):0.05306950,2_414:0.18820950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000178_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000178_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a4ee9c3d9d9e266cf706dbea666f4778a66e31b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000178_tree_id.txt
@@ -0,0 +1,2 @@
+((0_4:0.00412192,(1_1960:0.00000000,4_4:0.00000000):0.00158208):0.03846881,3_354:0.08937217,2_401:0.03235983);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000191_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000191_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..193bc4e140fc2ce4de8f3ba420bcd6b096bfd98a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000191_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1988:0.00057120,(4_19:0.00156202,(3_341:0.16268933,2_358:0.01613367):0.00680201):0.00181848,0_19:0.00224180);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000194_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000194_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..605f624cd290528e764e0c3fffa331b2d8277404
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000194_tree_id.txt
@@ -0,0 +1,2 @@
+((4_27:0.00236134,1_1996:0.00397766):0.00243291,(3_290:0.13780333,2_351:0.01672067):0.00964019,0_28:0.00015293);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000195_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000195_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51d96f33b34c52d694240dc258f93a19d6c8f9f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000195_tree_id.txt
@@ -0,0 +1,2 @@
+((4_28:0.00323862,(1_1997:0.00134563,0_29:0.00232437):0.00166137):0.10268938,2_350:0.08319787,3_446:0.18224413);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000204_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000204_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b421513b0bd21b78b8f626e513be61bad2e28948
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000204_tree_id.txt
@@ -0,0 +1,2 @@
+((2_334:0.16120675,3_280:0.37932725):0.07390475,(1_2006:0.00000000,0_42:0.00000000):0.00432275,4_37:0.00524525);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000206_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000206_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42f0ae61f30e3c7b5b6820c2c8b5d9c76ca870f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000206_tree_id.txt
@@ -0,0 +1,2 @@
+((0_46:0.00881750,(1_2010:0.02492950,4_41:0.00499150):0.01511350):0.12147600,2_338:0.08699675,3_1194:2.13568725);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000214_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000214_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b43a260a7212880b2e5171c787575e17163726e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000214_tree_id.txt
@@ -0,0 +1,2 @@
+((3_260:0.09457250,2_318:0.19578950):0.25124950,(1_2022:0.00758600,4_53:0.00401300):0.00474350,0_58:0.00399300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000216_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000216_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..213abd393e0b3b77dee18dec89ad3e8b920be702
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000216_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2026:0.00359182,(4_56:0.00792154,0_62:-0.00018454):0.00722372):0.06502239,2_314:0.11246417,3_254:0.07780483);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000219_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000219_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccc4c115a674d678759152d3732c906c6c3f6636
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000219_tree_id.txt
@@ -0,0 +1,2 @@
+((4_60:0.01171688,0_66:0.00943012):0.00376912,(2_307:0.17958812,3_250:0.15220787):0.12625863,1_2030:0.05044237);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000229_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000229_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48d80bb6ff63a7e59517649267255cb5366653a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000229_tree_id.txt
@@ -0,0 +1,2 @@
+((0_78:0.00697782,(1_2042:0.00000000,4_72:0.00000000):0.00469318):0.09427661,2_296:0.10004733,3_238:0.11981867);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000238_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000238_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d6cbdd225e3a94636499b2ec400ae00130ba0ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000238_tree_id.txt
@@ -0,0 +1,2 @@
+(0_89:0.00071485,((2_283:0.04615250,3_229:0.20762250):0.03231487,1_2053:0.00896211):0.00818489,4_84:0.00000915);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000253_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000253_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4668f3f568eb278246a532b7350db1848f9486a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000253_tree_id.txt
@@ -0,0 +1,2 @@
+((2_265:0.00950767,3_207:0.01999333):0.03989866,(1_2070:0.00000000,0_106:0.00000000):0.00121301,4_101:0.00364799);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000265_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000265_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d109e52e0fd76657aa59518957fb6768fcbae5d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000265_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_179:0.10618367,2_245:0.04651433):0.06619971,4_130:0.00148713):0.00411137,0_122:-0.00000857,1_2087:0.01114057);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000266_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000266_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38f22fdebaf4afd159b301eab3563c5c48e27486
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000266_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2088:0.00687553,0_123:-0.00035453):0.00346935,4_131:0.02570818):0.05214202,2_244:0.22657600,3_634:2.01153900);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000280_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000280_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7b078ac8a71a86918498f3c77723318b767a9dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000280_tree_id.txt
@@ -0,0 +1,2 @@
+((0_140:0.00000000,(3_802:0.11355350,2_225:0.01301750):0.00331650):0.00000000,4_148:0.00000000,1_2105:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000285_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000285_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49e99d5d3251750fa910f54ed4666164746d6340
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000285_tree_id.txt
@@ -0,0 +1,2 @@
+(0_146:0.01437096,(4_159:0.02296757,(3_403:0.17688650,2_452:0.08949650):0.16140002):0.01304193,1_2111:0.01219204);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000295_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000295_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d28a5dbd532b4290c2c0e2296e0e23b798df45e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000295_tree_id.txt
@@ -0,0 +1,2 @@
+(2_205:0.00641973,((0_178:0.00191583,1_2125:0.00262517):0.01119165,3_150:0.05449346):0.00269354,4_175:0.01186727);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000310_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000310_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c30cc09d4bff127c23f53f379c02e0c6bea8193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000310_tree_id.txt
@@ -0,0 +1,2 @@
+(0_204:0.00322720,((2_164:0.04598767,3_113:0.07332133):0.01923860,4_204:0.00524280):0.00370770,1_2148:-0.00041120);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000318_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000318_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..240568baeb650a3b4f6f4b03cb3341a3f741bcc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000318_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_145:0.00185150,3_103:0.04003950):0.00587050,0_217:0.00000000):0.00000000,4_218:0.00000000,1_2181:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000323_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000323_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8e9771bafabd38a544220b9d59f8863b78bc326
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000323_tree_id.txt
@@ -0,0 +1,2 @@
+((4_224:0.00759775,(0_223:0.00151600,1_2187:0.00776200):0.01536875):0.13015175,3_96:0.09441400,2_138:0.09901500);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000332_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000332_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5890680edeb2687e4ac3dac691204eea22b97e5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000332_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2198:0.00143411,(4_235:0.00536202,(3_85:0.58952233,2_116:0.11642767):0.11139934):0.00927148,0_235:0.00826089);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000333_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000333_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..915e26ee582ef273c968c60f2e46929cd241380c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000333_tree_id.txt
@@ -0,0 +1,2 @@
+((4_237:0.00147058,(0_237:0.00235987,1_2200:0.00026613):0.00436137):0.02325476,2_114:0.39628117,3_83:0.35206483);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000361_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000361_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..894cbadd857aa6eaecb3a86d6e8731ee258be06b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000361_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_290:0.00000050,0_283:0.00000050):0.00000000,1_0:0.00000050):0.01359600,3_32:0.11056950,2_53:0.02610350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000377_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000377_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea3e71d3717f4f77df15440bef8a6d20e0f27f0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000377_tree_id.txt
@@ -0,0 +1,2 @@
+((0_302:0.00544271,(4_309:0.00000000,1_26:0.00000000):0.02094429):0.08425074,3_13:0.54465550,2_17:0.08439650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000381_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000381_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f80504afe432ba241566df49c2d9901b4d218fc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000381_tree_id.txt
@@ -0,0 +1,2 @@
+((1_31:0.00000000,0_307:0.00000000):0.00000000,(3_8:0.06519050,2_12:0.00916150):0.03189550,4_314:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000400_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000400_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7daa5a6b876455f0f28a335bd3cc79825cfd36af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000400_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2413:0.32285675,2_2554:0.14744325):0.05684550,0_330:0.10107450):0.09831950,4_337:0.02262050,1_55:0.02412950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000403_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000403_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd2529b8ad0b409fe3482bc3ca0e43cb01b0c4be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000403_tree_id.txt
@@ -0,0 +1,2 @@
+((0_333:-0.00107995,(3_2410:0.36916383,2_2551:0.16225617):0.18074452):0.01229395,1_58:0.00000000,4_340:0.00000000);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000405_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000405_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c08bcaae2d2f0590c3ebf5aad4b86275217ed62a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000405_tree_id.txt
@@ -0,0 +1,2 @@
+(1_61:0.00253078,((3_2407:0.33966450,2_2548:0.09355450):0.10188644,0_336:0.00741382):0.00358168,4_343:-0.00000078);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000408_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000408_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0b1a04613f5bfbad3f359cdbd4fd3a175da25a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000408_tree_id.txt
@@ -0,0 +1,2 @@
+(4_347:0.00000000,((2_2544:0.14718200,3_2403:0.61855500):0.29644350,0_340:0.00724550):0.12926550,1_65:0.00000000);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000409_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000409_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7544a4a58a13bb44558acdc79af68817004c067
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000409_tree_id.txt
@@ -0,0 +1,2 @@
+((1_66:-0.00011416,(3_2402:0.12556850,2_2543:0.19297650):0.03340211):0.00011416,4_348:0.00000000,0_341:0.00813000);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000413_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000413_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34ed3ee344d08784155015771ad729d364b6cc0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000413_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_70:0.00000000,0_345:0.00000000):0.00000000,4_352:0.00000000):0.00241450,2_2539:0.01995350,3_2398:0.14658550);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000420_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000420_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ace47697e5b33f849b5278ee037604e5701a2ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000420_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2530:0.00470350,(0_356:0.00000000,4_362:0.00000000):0.00122050):0.46210683,3_1156:0.76966300,2_7:1.34439500);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000425_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000425_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c79aea677ab31f782f57e9a7b2aac852dec27ca0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000425_tree_id.txt
@@ -0,0 +1,2 @@
+(1_95:0.01380525,(0_362:0.00431500,(2_2516:-0.00230025,1_86:2.36171325):0.01175750):0.00674950,4_368:0.06165775);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000427_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000427_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72139770ebb9f48fc27eb8e9fb090a2c8f75df97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000427_tree_id.txt
@@ -0,0 +1,2 @@
+(2_2514:0.01627485,(4_370:0.00664925,(0_364:0.00000000,1_97:0.00000000):0.00619475):0.00550825,3_1718:0.02978115);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000436_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000436_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d286e7c00ebdad9592420b2a6180d34b806a2ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000436_tree_id.txt
@@ -0,0 +1,2 @@
+((4_383:0.00171026,(3_2374:0.61766267,2_2503:0.19066233):0.11243075):0.00575274,0_377:0.00000000,1_110:0.00000000);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000441_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000441_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f69aacf50bee6d0d364e7422f6364d8d2c43910
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000441_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2496:0.03448133,3_2364:0.29957167):0.02388154,(4_389:0.00665795,0_383:0.04686705):0.00373267,1_115:0.01399923);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000444_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000444_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..643c3589c25fccae01ccd3c01adbd107444d149f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000444_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000451_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000451_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7f639a136d80309c01881bc6bee8c82df524175
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000451_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2483:0.03605600,1_129:-0.00001600):0.00001600,0_399:-0.00001600):0.00001600,4_402:-0.00001600,3_2352:0.00356400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000456_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000456_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..349ccf232a8a1390c40183f0910f55727cbe0e9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000456_tree_id.txt
@@ -0,0 +1,2 @@
+((1_135:0.00380271,(0_405:-0.00009260,4_408:0.00327260):0.00026889):0.04232310,3_2345:0.16653567,2_2475:0.03608033);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000459_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000459_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..836274514da94863ccfd63204e423a636ad4d04f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000459_tree_id.txt
@@ -0,0 +1,2 @@
+(4_411:0.00113125,((3_2342:0.23172175,2_2472:0.13961825):0.21668825,1_138:0.00469725):0.00309825,0_408:0.00275275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000468_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000468_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c781c9d6ece0e8c28d16c144ec49da2fa6f9fd90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000468_tree_id.txt
@@ -0,0 +1,2 @@
+(4_421:0.00269594,((3_2333:0.17171967,2_2462:0.22450633):0.09775755,1_148:0.00632764):0.02819086,0_418:0.00271306);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000477_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000477_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..673ccf3913882095ca144969b092739c667acb3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000477_tree_id.txt
@@ -0,0 +1,2 @@
+((0_428:0.06958162,(4_431:0.01634138,1_158:0.03968862):0.08942687):0.29686238,2_2451:0.14349713,3_2323:0.45916488);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000480_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000480_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40f598d89e461eece126f70a8158aa6947ceff75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000480_tree_id.txt
@@ -0,0 +1,2 @@
+(1_161:0.00000000,((3_2320:0.26154250,0_434:0.00961050):0.02946300,2_2436:0.00545100):0.00102100,4_434:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000483_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000483_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..047f36101198d8d36e92f63acd07655a286005c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000483_tree_id.txt
@@ -0,0 +1,2 @@
+((1_164:0.00502287,(4_437:0.00002337,0_437:0.00301462):0.00260713):0.07399463,3_2317:0.19613538,2_2433:0.07406062);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000490_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000490_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f14a8ba6603c3ad503ccdb049a8f8dc35303d54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000490_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_445:0.00000000,0_445:0.00000000):0.01261083,1_172:0.00475617):0.10305956,2_2426:0.16579783,3_2309:0.30404117);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000491_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000491_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0b6d2616ab4143fdc78a14c50e5e9322a596b89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000491_tree_id.txt
@@ -0,0 +1,2 @@
+((1_173:0.00173250,(4_446:0.00341875,0_446:0.00525325):0.00151950):0.07881900,3_2308:0.15173575,2_2425:0.10497125);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000493_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000493_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c78b10e1dde23313187b659e6ebfae9239e6ee4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000493_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_448:0.00000000,0_448:0.00000000):0.00000000,1_175:0.00000000):0.01837900,3_2306:0.05402400,2_2423:0.01944600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000494_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000494_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b245e1ca8b8007fd63407c2c4d9ca556fa92868f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000494_tree_id.txt
@@ -0,0 +1,2 @@
+(1_176:-0.00017200,((2_2422:0.13074750,3_2305:0.08570450):0.13679850,0_449:-0.00017200):0.00017200,4_449:0.00247300);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000496_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000496_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64f425edf54a2e8bb171334593d9e4bd146b99ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000496_tree_id.txt
@@ -0,0 +1,2 @@
+(4_451:0.00552606,(0_451:0.00186909,(2_2420:0.05297200,3_2303:0.04457300):0.01032803):0.00229591,1_178:0.00054394);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000524_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000524_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b65ad22013a9c16a6b151adc925d73e5bcb9ec10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000524_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2269:0.58049289,(1_217:0.03453891,4_487:0.03556909):0.00718648):0.01951464,2_2387:0.02661150,0_488:0.01539350);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000530_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000530_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf3a9a84fa7e7af5b0b6864a068f9777cd87f18b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000530_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2253:0.09618963,((1_234:0.00761638,0_504:0.00555862):0.00472388,4_504:0.00722562):0.00252887,2_2371:0.02851837);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000531_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000531_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ba245f0947c73a7157a46f8f3e1da30c023c400
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000531_tree_id.txt
@@ -0,0 +1,2 @@
+(1_236:0.00932437,((3_2251:0.37897912,2_2370:0.06966388):0.08823637,4_506:0.01486663):0.00227388,0_506:0.00463763);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000543_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000543_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5958465788a9c8fa4edb3c1d51adc048cea2e09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000543_tree_id.txt
@@ -0,0 +1,2 @@
+((0_520:0.01688840,(1_254:0.00569396,4_523:0.01603404):0.01360773):0.20974880,2_2351:0.14324950,3_2234:0.36176750);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000544_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000544_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b6ae66bc6065c75584b330fc5b6403e869ac0bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000544_tree_id.txt
@@ -0,0 +1,2 @@
+(1_255:0.00628733,(0_521:0.00577008,(2_2350:0.03571517,3_2233:0.10458683):0.03226286):0.00274442,4_524:0.00800467);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000561_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000561_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2dac21d4d07ae8742a4d00c99ea08bdeb45bb1b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000561_tree_id.txt
@@ -0,0 +1,2 @@
+((1_274:0.00364675,(0_540:0.00502575,4_543:0.00429625):0.02065775):0.16555075,3_2210:0.21785225,2_2327:0.10044175);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000565_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000565_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f50457b57d2aee7895e82acd35e08dd35e75b997
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000565_tree_id.txt
@@ -0,0 +1,2 @@
+((4_549:0.00570150,0_548:0.00756950):0.05296025,(1_281:0.05960775,2_2321:0.10028625):0.08701925,3_2200:0.10500375);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000566_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000566_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d63282f4010b5edcf5804b71c54a42b01758bda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000566_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000581_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000581_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27f58b9433a9954d7708fabb32358ce685a07441
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000581_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000593_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000593_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec659a2f4bee4e9cd73f242c6e173b82fdfb2c56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000593_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2252:0.08543800,3_2107:0.19705200):0.02130235,(0_635:0.05708987,1_381:0.00652313):0.00094838,4_605:-0.00115919);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000598_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000598_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed22a40ee443e55cffbb76f1b4cee4e3f768ec00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000598_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2242:0.07023950,3_2103:0.14091750):0.08545325,1_390:0.00945475):0.00481875,0_644:0.00599275,4_614:0.00094125);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000601_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000601_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81304cfc698d3a1888d0c950328b89b63b9bd211
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000601_tree_id.txt
@@ -0,0 +1,2 @@
+((0_647:0.00290691,1_393:-0.00042691):0.00986158,(3_2100:0.55293717,2_2239:0.07435383):0.05226473,4_617:0.00897034);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000620_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000620_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06167188135635b683622eb29b050a94532494e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000620_tree_id.txt
@@ -0,0 +1,2 @@
+((3_447:0.52350312,2_2210:0.00609087):0.00783862,(1_414:0.00043513,0_668:0.00047887):0.00103462,4_638:0.00445938);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000640_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000640_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d43c30e011c3d4dc032221517e9b6a70f3b65062
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000640_tree_id.txt
@@ -0,0 +1,2 @@
+((1_435:0.00000000,0_695:0.00000000):0.00000000,(3_2058:0.11484550,2_2187:0.01822950):0.01855850,4_659:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000647_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000647_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af4c81ac714829646007d2d3d9476d24900549b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000647_tree_id.txt
@@ -0,0 +1,2 @@
+(4_666:0.00000000,((3_2051:0.30153333,2_2179:0.06503967):0.09926812,1_442:0.00584837):0.00863363,0_702:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000657_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000657_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f24efe2f5151598b8d83ff50c659f58ac77b027
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000657_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_714:0.00000000,4_679:0.00000000):0.00258300,1_454:-0.00041500):0.02109350,2_2139:0.01799850,3_2036:0.04578150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000661_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000661_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78bd8d886d04a3042023de8a05cca7de76cfed0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000661_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2032:0.00120117,0_718:0.01278483):0.00554108,4_683:0.00376873):0.00388827,2_2135:0.04114422,1_458:0.00293678);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000663_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000663_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2aa9ae022384f959da97391a4480f893de747c63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000663_tree_id.txt
@@ -0,0 +1,2 @@
+((1_462:0.00626751,4_687:0.00203849):0.00375656,(2_2131:0.02780750,3_2025:0.09248050):0.02134578,0_723:0.00516865);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000673_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000673_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea37f2947cb16cf42f00d97b84b14cd2727402cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000673_tree_id.txt
@@ -0,0 +1,2 @@
+((0_733:0.01510259,1_472:0.01494641):0.00689989,(3_2015:0.25588650,2_2121:0.30476750):0.18694032,4_697:0.01674799);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000678_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000678_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7dc5b2867ffa9d2f92fc03c33a70fa8ee7edd4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000678_tree_id.txt
@@ -0,0 +1,2 @@
+(0_739:0.00708923,((2_2114:0.06179783,3_2009:0.14584517):0.05132121,4_703:0.00545513):0.00475187,1_478:0.00440477);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000685_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000685_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d54597da77a53945dbe1b093c07f62996fdd3bb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000685_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2106:0.01478105,(4_715:0.00595323,3_2000:0.14328977):0.00292748):0.00619731,1_488:0.00127333,0_748:0.00080067);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000694_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000694_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46f70757cb1e77ad8359cf0b95f183a18087f65f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000694_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2097:0.11123417,3_1990:0.23994983):0.03832515,0_757:0.03355496):0.03357204,4_724:0.01916463,1_497:0.02782337);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000716_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000716_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81d983f30f9ecc7696d9517cb57021c6b65b743d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000716_tree_id.txt
@@ -0,0 +1,2 @@
+(2_2073:0.03389509,((1_522:0.00000000,4_750:0.00000000):0.00381950,0_781:0.00187550):0.00263450,3_1963:0.42876291);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000717_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000717_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d309a9105b90ab5db2db25e09f2e3a730434a6b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000717_tree_id.txt
@@ -0,0 +1,2 @@
+((4_751:0.00000000,0_782:0.00000000):0.00000000,(2_2072:0.01509100,3_1962:0.18830100):0.00612400,1_523:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000724_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000724_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b4430e5f41de180fd52b6d8f2ea1714dc0f92e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000724_tree_id.txt
@@ -0,0 +1,2 @@
+((4_758:0.00069175,0_789:0.04354525):0.00532475,(3_1955:0.34790225,2_2065:0.12571975):0.07694475,1_530:0.00332225);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000731_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000731_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5b96b012330d6ce1e0175680855373354650ca9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000731_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2050:0.01725500,3_1948:0.10739900):0.04399477,1_537:-0.00040869):0.00040869,0_796:0.00000000,4_765:0.00300800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000762_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000762_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8c6e5fec551c0457eddd426d485ee0fb0f0fd50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000762_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_573:0.00837300,0_842:-0.00014300):0.00236300,4_801:0.00093500):0.04947750,2_2017:0.04693300,3_1910:0.18226000);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000764_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000764_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad6c265a4893bcdc8ad324b66f048cbe16f8208f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000764_tree_id.txt
@@ -0,0 +1,2 @@
+((1_575:-0.00050187,4_803:0.00684488):0.00050187,(3_1908:0.25308038,2_2015:0.02817963):0.03505838,0_844:-0.00050187);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000770_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000770_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7ab2a163970201979d4af68f5ffc37925c2b87f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000770_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2008:0.00519950,4_810:0.00646050):0.08540625,3_1901:0.11576875):0.11408275,1_583:0.00117825,0_852:0.00005075);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000775_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000775_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc5c5c5646aa4435454ab68c0e60aedd87bf3a9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000775_tree_id.txt
@@ -0,0 +1,2 @@
+(0_869:0.01985332,((1_597:0.00478483,4_817:0.00504417):0.05917149,3_1894:0.18230396):0.04214154,2_1997:0.04183368);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000792_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000792_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbc44c3cf97d33724a53247086d1b3fba28b15ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000792_tree_id.txt
@@ -0,0 +1,2 @@
+(0_886:0.00021338,(1_614:0.00243963,(3_1877:0.11921513,2_1979:0.02204987):0.02623637):0.00163837,4_834:0.00228663);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000801_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000801_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..241f2855bc3fd0982658e6b1ed5915afe7b1f893
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000801_tree_id.txt
@@ -0,0 +1,2 @@
+(0_895:0.01729162,(4_843:0.00220090,(2_1969:0.06834500,3_1867:0.26892300):0.07181630):0.00447860,1_623:0.00124538);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000802_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000802_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99d9c938534054494e692e803539cbb4ae0fc2ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000802_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_896:0.01089065,1_624:0.01480235):0.01661212,4_844:0.04325927):0.11801140,2_1968:0.31329850,3_1865:0.44310050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000816_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000816_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81fba8214ce40c4b347feff861bffd9d6603812c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000816_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_861:0.00665333,1_641:-0.00186833):0.00054117,0_913:0.00611216):0.00634061,2_1948:0.09840300,3_1848:0.03137900);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000820_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000820_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed0e640cdb9b02ef421d4965bec3ec1d06ef63a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000820_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1837:0.17866925,2_1887:0.09689875):0.07434200,(4_871:0.00453400,1_647:0.00282700):0.00185250,0_925:0.00526650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000821_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000821_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8620e863ffbe9b02958a44fcb0c9480640ebc62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000821_tree_id.txt
@@ -0,0 +1,2 @@
+((1_648:0.03344358,(4_872:0.01426238,0_926:0.01900662):0.03170083):0.14590765,2_1886:0.24310233,3_1836:0.24570167);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000832_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000832_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdd11fbc011765e465be9a1f2604aa2e3e66e7c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000832_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_941:0.00000000,1_664:0.00000000):0.00000000,4_884:0.00000000):0.33496750,2_1872:0.09108050,3_1818:0.07228450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000837_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000837_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60f469e3a3e76a55379183e464b3c72912a9b52f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000837_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_946:0.00000000,4_889:0.00000000):0.00370750,1_669:0.00107550):0.00022850,2_1866:0.43962376,3_1812:0.00120124);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000843_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000843_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b5d8688fee87ccdf71ef001066c0ac0d621d50a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000843_tree_id.txt
@@ -0,0 +1,2 @@
+((0_952:0.00468800,3_1806:0.00675400):0.00296425,(2_1860:0.00532075,4_895:0.00801625):0.00168275,1_675:0.00499825);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000885_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000885_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e001830885a648b9bdd93c5f3156396bf11e5ad9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000885_tree_id.txt
@@ -0,0 +1,2 @@
+((1_733:0.00169076,(4_952:0.00144727,0_1011:0.00216373):0.00047479):0.05193735,2_1798:0.06855617,3_1687:0.08961583);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000904_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000904_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd4b45d7ac8a22f599cf490beab037e09f8481bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000904_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1776:0.25107483,3_1664:0.10677817):0.07675995,(1_771:0.00000000,4_992:0.00000000):0.00321165,0_1043:0.01307335);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000911_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000911_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff6c581ff57ccac5f8cf825e886d9500a29605f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000911_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1050:0.00109894,4_999:-0.00012794):0.00012794,1_778:0.00000000):0.09894141,2_1768:0.14274233,3_1657:0.19587767);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000920_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000920_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c42a5819d783d0321e05b61e5dcf35758e333bbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000920_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1010:0.00000000,0_1061:0.00000000):0.00000000,1_789:0.00000000):0.04347000,2_1755:0.06552900,3_1646:0.27173600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000921_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000921_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a44fa59e7b67a32059358036c20ee1b141fd8824
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000921_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1062:0.00342682,(1_790:0.00000000,4_1011:0.00000000):0.00469118):0.00787777,3_1645:0.05288950,2_1754:0.02051550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000924_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000924_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..caf1d528a5795879d825b32e3110165dfbb66cdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000924_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1067:0.00000000,((3_1641:0.27141725,2_1749:0.12069375):0.09309025,1_795:0.00637025):0.00081075,4_1017:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000933_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000933_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7854f35d43467650f39c4c44dbcf477f88b8bd5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000933_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1028:-0.00005975,0_1078:0.00153875):0.00206625,1_806:0.00386625):0.02807575,3_1630:0.09982850,2_1738:0.03190950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000955_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000955_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8dcf09c010160b19d0bcc4700fdd9d8b0b243cab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000955_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1102:0.01106700,(4_1052:0.00000000,1_830:0.00000000):0.00946200):0.02540150,2_1713:0.04326650,3_1606:0.05363350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000964_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000964_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc066f7d4cd910f042e474ebb3de5e262b946fba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000964_tree_id.txt
@@ -0,0 +1,2 @@
+(1_841:0.00000050,((3_1596:0.18156250,2_1699:0.05906850):0.06662534,4_1063:-0.00003147):0.00003197,0_1113:0.00145550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000967_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000967_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13022d238633b6b8a9046072e0d9e4afe7287c8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000967_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1696:0.12370100,3_1592:0.38414400):0.10750332,(1_845:0.01505634,0_1117:0.00853366):0.00888380,4_1067:0.00634795);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000975_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000975_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a5851417d8cfd01438008cb6e061cc523d1c246
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000975_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1075:0.02619812,(1_853:0.01373188,0_1125:0.02173512):0.00419337):0.13368588,2_1687:0.15738263,3_1584:0.20324637);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000978_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000978_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66a7768224c9c14fedcf3d67f3aa10196bea7120
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000978_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1128:-0.00000888,4_1078:0.00465388):0.00014662,1_856:0.00542887):0.01756662,3_1581:0.24523087,2_1684:0.02276712);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000997_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000997_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7d597a9c74101d07fc2c199fdc1d30fb11698d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000997_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1148:0.02139290,((2_1662:0.26874067,3_1559:0.55690233):0.18815623,4_1102:0.02170269):0.00719581,1_877:0.01896210);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001009_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001009_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a30b8d8855dc7d252c1828bdd6cc68ca0ccd5cf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001009_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1649:0.20523850,3_1546:0.27016350):0.04890011,1_889:0.02439884):0.01424516,4_1118:0.00000000,0_1161:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001029_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001029_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7397950a58bdb385ad78d5839c99c7d4b52fb92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001029_tree_id.txt
@@ -0,0 +1,2 @@
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+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001036_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001036_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0ebfa487260aab60f5af0fef75754060553655e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001036_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001043_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001043_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06f5caf6237683088451449b2dad1a2a41fe8ca0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001043_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1197:0.00000000,(4_1155:0.00633600,(3_1510:0.18540600,2_1613:0.03432900):0.01191500):0.00166800,1_925:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001062_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001062_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7df5f3599c96ee77d66cd4d9fc744009ffecd7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001062_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1174:0.00000000,(0_1217:0.00457276,(2_1592:0.03014233,3_1487:0.10620667):0.02894625):0.00792524,1_945:0.00000000);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001074_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001074_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9bc1efe0fe243c6ecf51d51b3b074ef8579ea85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001074_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1579:0.11344100,3_1474:0.16780900):0.09714100,0_1230:0.00000000):-0.00000000,4_1187:0.00000000,1_958:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001079_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001079_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03f9a4993aa46d25b3214a42e35d6c9bbf81b493
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001079_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1468:0.36925550,2_1572:0.15881050):0.09575121,(4_1192:0.00000000,1_963:0.00000000):0.03314887,0_1235:0.00718313);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001136_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001136_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d16ef39f7117ee12ec78d9b90a6ca6668127b61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001136_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1260:0.00720737,(1_1035:0.00085687,(3_1404:0.20695262,2_1508:0.04316738):0.05662562):0.00162812,0_1306:0.00055762);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001152_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001152_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea8894a722d347043c90a04704bf568f22144407
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001152_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1324:0.00000000,(1_1053:0.00279050,(2_1490:0.11038550,3_1386:0.33114750):0.15527350):0.00391350,4_1278:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001162_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001162_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31e7c959bfcf4869efa6de6aaea6049df1ba9b09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001162_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1354:0.02502674,(1_1093:0.00000000,4_1303:0.00000000):0.08874426):0.12392425,2_1463:0.45950933,3_1375:1.15466467);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001173_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001173_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0b503fdca7fe41fa5528d7c9ae0b4c6bf9abc66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001173_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1371:0.04090642,((2_1450:0.05808867,3_1358:0.18795033):0.03282989,4_1320:0.00523768):0.01044532,1_1111:0.00309158);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001176_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001176_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d0528f29a153f90c65ef02c70660c1c01c42902
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001176_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1323:0.00000000,1_1114:0.00000000):0.00673410,(2_1447:0.09854567,3_1355:0.30275833):0.12270263,0_1374:0.02394690);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001178_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001178_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e3524bbe0a5ee64954bd0bf07e4811f943a47b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001178_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1116:0.00653587,(0_1376:-0.00024038,4_1325:0.00193438):0.00339062):0.02950613,3_1352:0.13641012,2_1445:0.05356988);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001181_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001181_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebc550cb78b38a5b201f882bd44a7387e61c3def
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001181_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1328:0.00004900,0_1379:0.00302100):0.00255150,(3_1349:0.03041475,2_1442:0.01619325):0.00589950,1_1120:0.00268850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001189_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001189_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6415c2f8e37aef795c97325058333287ef5b7158
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001189_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1336:0.00115538,((3_1341:0.23900837,2_1433:0.08824563):0.06943187,1_1128:0.00737512):0.00402788,0_1387:0.00118463);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001193_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001193_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4926d10b25533d8f05f83c4dc7140ffe2ea1265e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001193_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1133:-0.00030220,4_1341:0.00171720):0.00282440,0_1392:0.00101980):0.01882367,2_1428:0.02286500,3_1336:0.13920200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001196_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001196_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15e08bc3d5a4ba99405624a6e6e78482fa3b26dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001196_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1425:0.05498750,3_1329:0.30149250):0.04539650,0_1396:0.00000000):-0.00000000,4_1345:0.00000000,1_1137:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001212_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001212_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..409a0e75136006e83c01d22a77568879e6b4d131
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001212_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1155:0.00638763,(0_1414:0.00294888,4_1363:0.00339512):0.00214138):0.02011188,2_1408:0.02966538,3_1311:0.11235362);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001214_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001214_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12ccd358c06edda55dff152be227485d996441e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001214_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1406:0.18814500,3_1308:0.38876900):0.17796013,1_1157:0.01071838):0.01020062,4_1365:0.01747507,0_1416:0.00061593);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001215_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001215_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cb45cf6b06a45ad089c555f0101f19c1e34fa19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001215_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1307:0.51346238,2_1405:0.08992662):0.10371762,4_1366:0.01997888):0.00791713,0_1417:0.02214563,1_1158:0.01603837);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001218_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001218_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efd194fa7fe49f94ce94c7ce2bbcd2e1eb6173fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001218_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1370:0.01207875,(1_1162:0.00000000,0_1421:0.00000000):0.01420825):0.09722075,2_1401:0.16090625,3_1303:0.20688875);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001222_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001222_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3635deee624355c606f99546a7980d5829cce65f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001222_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1427:0.00000000,1_1168:0.00000000):0.00000000,(2_1397:0.24429700,3_1297:0.19975600):0.37471200,4_1376:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001235_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001235_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..367be691ff012819391b3ebf34d6c4179c5790fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001235_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1283:0.13918300,2_1383:0.03943300):0.01916457,4_1390:0.00179071):0.00111429,1_1182:0.00000000,0_1463:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001247_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001247_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d9dfda8f5468ee2d27f6afe9b01a25106a03332
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001247_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1475:0.00005184,1_1195:0.00391216):0.01044692,4_1402:0.02035852):0.01165825,2_1371:0.01538500,3_1263:1.05726100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001255_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001255_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4eeba590a78f47571403d3db5a2f7e20ba2704ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001255_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1483:0.00837100,((2_1363:0.05016475,3_1255:0.14501625):0.03768325,4_1410:0.00549375):0.00518275,1_1203:0.00227400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001256_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001256_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9da946cdd8a0ad4076389ff8097ba68b5daeacd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001256_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1411:0.00036025,(1_1204:0.01552867,(2_1362:0.09936917,3_1254:0.28752483):0.11776139):0.01062233,0_1484:0.02792475);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001258_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001258_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a547b4d056bcd04e780a6c2aec72def427e029f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001258_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1414:0.01259336,(0_1487:0.00161657,1_1207:0.00177743):0.00468346):0.04579437,3_1251:0.12893967,2_1359:0.04878633);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001262_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001262_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31526ed80579e1eb6e867ebe9cd5e4541109158c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001262_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1211:0.00000000,((2_1355:0.10364425,3_1247:0.27928275):0.13366225,4_1418:0.04100375):0.04831125,0_1491:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001266_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001266_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a25d789d2445c12434c42c77507dacf1ce007ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001266_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1496:-0.00065613,(3_1242:0.05521513,4_1423:-0.00065613):0.00065613):0.00065613,1_1216:-0.00065613,2_1350:0.01394113);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001269_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001269_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e50476e7d793a2c52b836b68c106517c687d9499
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001269_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1499:0.00044650,(1_1219:0.00367450,(2_1347:0.02972300,3_1239:0.15738300):0.05153050):0.00054800,4_1426:0.00142450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001280_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001280_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19550a4050f008990d8cb08ec1d4e71c6e33e801
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001280_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1439:0.00270911,(0_1512:0.01022026,1_1232:0.00367674):0.00223480):0.06310683,3_1227:0.23485567,2_1335:0.07012233);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001283_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001283_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce5ef4b539595a18130641daa8b4fa5d96f5edf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001283_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1516:0.00292941,(1_1236:0.02922822,(2_1329:0.12623817,3_1223:0.76407183):0.08545224):0.01879428,4_1443:0.00571659);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001284_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001284_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87682968530d44f938266e79d447d23f66c69640
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001284_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1237:0.01350700,(0_1517:0.00298275,4_1444:0.00174825):0.00660850):0.10230350,2_1328:0.14522125,3_1222:0.40288975);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001292_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001292_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f65c0ef3841f1e1b84605e8ccf93fe7182b11653
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001292_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1452:-0.00017662,(0_1525:0.00132062,1_1245:-0.00017662):0.00017662):0.00193162,2_1319:0.09432312,3_1213:0.01490787);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001295_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001295_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb224e6e122109355893cbb3ccf91631b8084deb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001295_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1462:0.00133500,0_1535:0.00133500):0.01236614,(2_1308:0.03087000,3_1207:0.42643300):0.02420395,1_1256:0.01555686);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001307_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001307_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c48056634b9c15309c1dd740520da39bf238647b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001307_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1261:0.02289467,0_1558:0.03111933):0.00930018,(4_1484:0.02453592,1_1279:0.03016208):0.00603058,3_1167:0.04065671);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001323_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001323_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01266842fc672ddcdc6c1bc42b81b2e981acc0a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001323_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1303:0.05899662,0_1588:0.01426037):0.02086037,4_1518:0.02553462):0.20041388,3_1138:0.99197837,2_1226:0.24092963);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001328_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001328_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47a78109840b0a977c6eeb8f5d7a188b51efbd24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001328_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1523:0.05511255,(0_1593:0.01697686,1_1308:0.04180514):0.02257460):0.33601165,2_1221:0.30506633,3_1133:0.68781167);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001405_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001405_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ede063986104cd6ecb3a51c074145774d3642dec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001405_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1678:0.00000000,4_1607:0.00000000):0.00000000,1_1395:0.00000000):0.01011700,2_1121:0.01019400,3_1051:0.03267700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001412_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001412_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c3730d10eaedd7371752807b3aafe578ac3cb0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001412_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1113:0.03116725,3_1043:0.04730475):0.02488375,1_1402:0.00049125):0.00279975,4_1614:0.00234050,0_1685:0.00058550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001417_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001417_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f3e475660ac2bcd1d5a1c8fcf640800fe97fd2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001417_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1038:0.38127046,((1_1407:0.00000000,0_1690:0.00000000):0.05294625,4_1619:0.00292075):0.05029625,2_1108:0.08426554);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001425_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001425_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af4be9489a67185a5e5657802be2a0620c701bd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001425_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1415:0.00000000,((2_1100:0.07950017,3_1026:0.19658383):0.06721665,4_1627:0.00832946):0.00673754,0_1698:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001435_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001435_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..149e24fd98b1d97e8176b07f7b35f1d1209506b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001435_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1425:0.02347462,((3_1016:0.85479512,2_1090:0.10587387):0.12733038,0_1708:0.00054063):0.00570637,4_1637:0.00856038);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001453_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001453_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24ed3cae56f9b9f02ca8c15ab2128e923310bb61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001453_tree_id.txt
@@ -0,0 +1,2 @@
+(3_989:0.00548131,((2_1052:0.00491633,1_1449:0.01042267):0.00515286,0_1741:0.01054059):0.00137291,4_1663:0.00610969);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001454_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001454_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a5a4cf11c5daf743611fa25f6e60e9427c1e92d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001454_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1450:0.01051633,2_1051:0.01815867):0.04091671,(4_1664:0.01796579,3_988:0.00599421):0.00393217,0_1742:0.01247540);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001457_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001457_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b30d79cb21f27d393990c04afb2b64c9f8295bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001457_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1453:0.00780179,(3_985:0.47500459,(4_1667:0.04463517,0_1745:0.00991583):0.20712003):0.12779591,2_1048:0.02214821);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001460_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001460_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..041691291c169e7c4b69fbdddecad3d8a0063eb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001460_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1752:0.00970098,(1_1460:0.00065570,4_1674:0.01624630):0.02064884):0.03222740,3_978:0.19629617,2_1042:0.08769083);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001469_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001469_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..697776a6908c7fc5528981841509f8a065c178a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001469_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1469:0.01848063,(0_1761:0.00835912,4_1683:0.00528488):0.00288137):0.09927887,3_968:0.13041212,2_1028:0.14088387);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001477_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001477_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3db6fa0bfa8e6ca1dea58f760773c6e845be9f07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001477_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1020:0.09472150,3_960:0.44593550):0.14056553,(0_1769:0.01848364,1_1477:0.01080336):0.00712377,4_1691:0.02193927);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001481_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001481_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..235c29b95214be94f0eeff7d62176da63373329c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001481_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1032:1.16895567,2_1014:0.11990233):0.04860314,(4_1696:0.06897420,0_1774:0.05572780):0.00331738,1_1482:0.04310635);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001502_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001502_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d47a1101e393bae886c9498c9ed0dd8b0b443d30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001502_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1800:0.00220025,(4_1721:0.00378600,1_1507:0.00015800):0.00293375):0.05318425,3_927:0.17090250,2_983:0.05520850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001510_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001510_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd792c38ca41dcb667e524ec7d9eafbf2692401a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001510_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1729:0.00350315,0_1808:0.00038085):0.00048590,(3_911:0.12651200,2_972:0.05651300):0.05006688,1_1515:0.00008192);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001511_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001511_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3f82eaaac19f9d6b45f959c92d8c5244ad46bb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001511_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1809:-0.00081974,((2_971:0.06923317,3_910:0.13774783):0.07683375,1_1516:0.00421676):0.00651524,4_1730:0.01235574);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001518_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001518_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4fe72c45696c40e766b04ae60e49e744e2cb98e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001518_tree_id.txt
@@ -0,0 +1,2 @@
+((3_902:0.37561150,2_963:0.01889550):0.00660950,(4_1737:0.01474450,0_1816:0.00119650):0.00790650,1_1523:0.01937650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001534_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001534_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..460450a80e56031218d8e5c45f7d71b0276691b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001534_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1547:0.00105099,4_1761:0.00253101):0.00901136,(2_938:0.03787767,3_879:0.18069133):0.07921113,0_1840:0.00393572);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001549_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001549_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ee333040be50aa64b75995a770eed052a73d591
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001549_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1783:0.00000000,0_1862:0.00000000):0.00198728,(2_918:0.07404050,3_854:0.11656750):0.05915874,1_1569:0.00462172);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001583_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001583_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43cca214bbc7d53ca4df4efa562ccbcb52e13afc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001583_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1848:-0.00023225,(2_857:0.57097125,1_1626:-0.00023225):0.00023225):0.00023225,3_793:0.01153225,0_1921:-0.00023225);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001585_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001585_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0b605f5dda05ff35bfee2a65a8faf5721ab73f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001585_tree_id.txt
@@ -0,0 +1,2 @@
+((3_789:0.02653250,(2_852:0.00000000,0_1925:0.00000000):0.00017350):0.00282050,1_1630:0.00277200,4_1852:0.00234300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001602_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001602_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a29b3dfb09f44bdf5c0c7ea29dce5077e614ab8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001602_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1887:0.00000000,1_1669:0.00000000):0.00000000,0_1948:0.00000000):0.03743050,3_752:0.04928550,2_814:0.01397350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001603_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001603_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1496789ebcf2866324dcaa002ecb44e6604eafc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001603_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1888:0.00304764,0_1949:0.01180036):0.00284629,1_1670:0.00165053):0.05050042,3_751:0.11414200,2_813:0.03604100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001605_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001605_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3862b4137d82e4a7977243c658a5e7e7b2f5eb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001605_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1951:0.00788526,((3_749:0.10217500,2_811:0.03116300):0.02538756,4_1890:0.00402369):0.00391831,1_1672:0.00265474);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001609_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001609_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ce8c5cf2e54edf8d3b8ba37ab42537ddbd51fa1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001609_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1896:0.01435075,3_743:0.00913425):0.50025375,2_2481:0.12950602):0.55979798,0_1958:0.00000000,1_1678:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001610_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001610_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfe06ed2579fe1ea9bf622f91d3dbea8e9da929e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001610_tree_id.txt
@@ -0,0 +1,2 @@
+((3_742:0.03764784,(4_1897:0.02988937,2_784:0.47181163):0.00562152):0.01615231,0_1959:0.01586583,1_1679:0.01879117);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001616_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001616_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b4ae645cb181103ae45aa7db0af33f58bc7ef74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001616_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1965:0.01129961,(1_1685:0.00000050,4_1903:0.00000050):0.00685889):0.04451570,3_736:0.02482550,2_775:0.21716650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001618_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001618_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f00c9ebf71c83a543767c8cdc66cd72dab61e173
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001618_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1905:0.00000000,1_1687:0.00000000):0.00000000,(3_734:0.12365450,2_773:0.16307650):0.03080250,0_1967:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001622_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001622_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..329d5b621680a002ac75f83be7b6f523befacb3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001622_tree_id.txt
@@ -0,0 +1,2 @@
+((2_762:0.21967425,0_1975:0.01129575):0.00619975,(4_1911:0.00000000,1_1693:0.00000000):0.01119888,3_729:0.00693212);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001623_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001623_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53c0e25cee43f874b89361d52f28153c0a269456
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001623_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1694:0.00000050,4_1912:0.00000050):0.00377125,0_1979:0.00271325):0.01107575,2_760:0.09866275,3_728:0.07157425);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001647_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001647_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8029fa5f47d030c6278359b046f13c89d04ee824
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001647_tree_id.txt
@@ -0,0 +1,2 @@
+((3_573:0.31264033,2_656:0.13843767):0.07606299,(0_2044:0.00000000,1_1762:0.00000000):0.00160502,4_1985:0.00150198);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001674_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001674_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a97fa32cdcbc71bac8d8fd7ac8a673d7a67d0e77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001674_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2078:0.00000000,4_2017:0.00000000):0.00000000,1_1797:0.00000000):0.08118550,2_615:0.09941650,3_540:0.29889050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001681_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001681_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bc9e1c2238ceb39aa2e6a6adb5594f5a8ea7aeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001681_tree_id.txt
@@ -0,0 +1,2 @@
+(4_2025:0.00494663,((2_604:0.10026863,3_530:0.06576538):0.06330213,0_2086:0.02154337):0.04556462,1_1805:0.00047137);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001692_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001692_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bda4e6d15c149a9c563f8e50463e85b43ac14c95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001692_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2048:0.00000000,(0_2102:0.01211266,1_1827:-0.00045266):0.00045266):0.09844912,2_576:0.11789367,3_500:0.23518833);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001705_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001705_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae768fbefaf279ca42d6b23066be358be495a27c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001705_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1846:0.01841838,(3_478:0.17415587,2_550:0.25066212):0.18590963):0.01377512,4_2067:0.01628488,0_2121:0.01675313);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001711_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001711_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afb866b5473b609528dc570c436997f69787c42b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001711_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_2078:0.00141150,1_1857:0.00433550):0.00762225,0_2133:0.01263125):0.12612225,3_465:0.81085125,2_528:0.24667575);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001734_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001734_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97a1ac42231ae28109fa5a349049c1e4b03f5c24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001734_tree_id.txt
@@ -0,0 +1,2 @@
+(4_2140:0.00557818,((0_2207:0.00738317,3_476:0.32425383):0.00071547,2_444:0.04019990):0.00159410,1_1911:0.01666982);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001739_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001739_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e382676f205e283b4343ed336b7a26c4e40e61fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001739_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_2166:0.00741662,0_2226:0.00491238):0.00565987,1_1928:0.01334562):0.01931088,3_386:0.22643512,2_432:0.03095187);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001750_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001750_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4723d6a302b44f353ac666cece77e634960f2088
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001750_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1945:0.03278275,4_2183:0.04329325):0.03517800,(2_417:0.68491925,3_370:0.66509075):0.04429900,0_2241:0.07831700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001754_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001754_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af05c1b6c6af98cbf3e372780165ceff215ea4a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001754_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2247:0.00520710,4_2189:0.00877890):0.00551377,(3_364:0.28369033,2_410:0.15606767):0.10969350,1_1951:0.00598015);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001756_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001756_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26a242fc07265b548b784aab42f6ad3de33084ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001756_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2249:0.00000000,1_1953:0.00000000):0.00507975,4_2191:0.00255425):0.00567525,3_362:0.15774475,2_408:0.02151325);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001778_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001778_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fba97689f343736b094f7a23d16a2e2131a72440
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001778_tree_id.txt
@@ -0,0 +1,2 @@
+(0_81:0.00644884,(4_76:0.01343400,1_2045:0.00593700):0.00382250,2_291:0.12638516);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001782_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001782_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4db9362c3b7492e651782a4ea57d791d19d7de33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001782_tree_id.txt
@@ -0,0 +1,2 @@
+((0_137:0.02509825,2_229:0.24140175):0.00452925,1_2102:0.01478175,4_145:0.01672125);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001788_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001788_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7328390b021336f7b96089cd3dd389cee6c4da17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001788_tree_id.txt
@@ -0,0 +1,2 @@
+((0_193:0.00930050,4_195:0.02090250):0.00106050,2_195:0.25557463,1_2139:0.01365637);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001809_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001809_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f51c4e05ee86764d48c4acb32fd449a2ab0c129c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001809_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2377:0.35973800,(1_107:-0.00094900,0_374:0.00459800):0.00423500,4_380:0.00328600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001838_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001838_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8bdd829db1c44cdfb5fbf8e904e06d20c17e87aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001838_tree_id.txt
@@ -0,0 +1,2 @@
+(0_816:0.04515400,(4_775:-0.00549525,2_2043:0.47995425):0.11479525,1_547:0.12559500);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001841_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001841_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51a65101797f14d04a8d2555fca20a53cda53ede
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001841_tree_id.txt
@@ -0,0 +1,2 @@
+(0_923:0.00298453,(3_1839:0.44735525,4_869:0.01415675):0.00167725,1_645:0.00385347);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001853_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001853_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91f40b81aa3450e2ec7773dd975191f9c54fa8ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001853_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1703:1.06452300,(1_837:0.00000000,4_1059:0.00000000):0.00000000,0_1109:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001854_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001854_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..734bf5919f66a03c1b2694eea312e6f72e1f6144
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001854_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1595:0.88181700,(1_842:0.00000000,4_1064:0.00000000):0.00454100,0_1114:0.00349000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001871_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001871_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c977e6e88e87cbabf9498a249da21bc4feb98646
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001871_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1300:0.00995200,1_1165:0.00000000):-0.00000000,0_1424:0.00000000,4_1373:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001872_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001872_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58515fa431d7476f94e023a7acfd310bb4948e06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001872_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1374:0.00000050,1_1166:0.00000050):0.00000000,0_1425:0.00000050,3_1299:0.01742150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001877_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001877_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f79f6098a0b816bc2bd28a571d1b23960a479765
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001877_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1255:0.00053950,(4_1461:0.00000000,0_1534:0.00000000):0.00110950,2_1309:0.02213950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001882_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001882_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6905b6a22eedccb64db1f0d1a2a13381b9156da2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001882_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1615:0.02023336,(1_1330:0.01286775,2_1200:0.13761325):0.00740375,4_1545:0.01253964);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001886_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001886_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d22e1ba1cd56d69e0b93295ced272a36c5471783
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001886_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1439:-0.00134875,(3_1001:0.39050275,4_1651:0.00898425):0.03213125,0_1722:0.00663675);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001898_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001898_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37fbd87786ba23054731176f89bdc9d08dfa6882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001898_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1560:0.00778900,(4_1774:0.00000000,0_1853:0.00000000):0.00437700,3_863:0.13550500);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001903_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001903_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a50de26f9a51614ef88fd08b63026faef2410fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001903_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1800:0.00000050,(2_899:0.98341700,1_1587:0.00680700):0.04540950,0_1880:0.00000050);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001926_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001926_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10793e8cf739526fd38a3cd8cd67611425f8cce7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001926_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1782:0.00475950,(3_556:0.02309900,0_2063:-0.00020400):0.01837400,4_2002:0.00837450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001928_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001928_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61d21834c632bdb77a806f9d0671ed44b5d2a5e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001928_tree_id.txt
@@ -0,0 +1,2 @@
+(4_2038:-0.00191450,(0_2094:0.03715600,1_1818:0.01864900):0.01164350,2_584:1.58006550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001939_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001939_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dabc1604df152d272b6039949f1f04fb7cb70402
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001939_tree_id.txt
@@ -0,0 +1,2 @@
+(2_513:0.04144935,(1_1876:0.00221700,0_2152:0.00202600):0.05300800,2_2591:0.91223965);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001966_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001966_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1dd5b3ce8bea256f40f17b70cb81419321ce4b66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001966_tree_id.txt
@@ -0,0 +1,2 @@
+(2_831:0.02645750,(1_1651:0.00527450,4_1869:-0.00019650):0.03883600,3_769:0.07241450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001979_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001979_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52d76f2aa872dc9394cf6bdc408f5a812e8be10f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001979_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2038:0.21805655,(2_2525:1.97236025,2_2610:0.53980275):0.28629425,2_2140:0.18329045);
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001980_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001980_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77e3b6e8a01020e36cb01bee7bb37ba90265d152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001980_tree_id.txt
@@ -0,0 +1,2 @@
+((3_697:1.27565525,3_385:1.03725775):1.20744025,2_2197:0.19363775,3_2069:0.23404125);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001981_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001981_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd5dac31af0f15e1ac269405f7d12aa37773b801
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001981_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2592:0.00000000,2_2286:0.00000000):0.00000000,2_2291:0.00000000,2_2581:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001983_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001983_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93c1843d99533ed652db63e37d30a0bbf6034d80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001983_tree_id.txt
@@ -0,0 +1,2 @@
+((3_627:0.90805900,3_406:0.49885200):0.89429950,3_1783:0.15635090,3_1747:0.46780310);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.phy b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.phy
new file mode 100644
index 0000000000000000000000000000000000000000..2bce1d2022c64bb4d7c6a9772dcfb45a345a732d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.phy
@@ -0,0 +1,5 @@
+4
+1_1 0 0 0.2 0.25
+0_2 0 0 0.21 0.28
+3_1 0.2 0.21 0 0
+4_1 0.25 0.28 0 0
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.phy_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.phy_fastme_stat.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39b61a82a9fa3184971b7344579e00bed1cc8829
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.phy_fastme_stat.txt
@@ -0,0 +1,25 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  no              
+  S                                   SPR postprocessing  no              
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Tree length is 0.23500000	Explained variance : 0.97082530
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.tre b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.tre
new file mode 100644
index 0000000000000000000000000000000000000000..f5cbe5b87adf2d90a46bc4cdbfe6105022745ae9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/SimpleTest.tre
@@ -0,0 +1,2 @@
+((0_2:0.01000000,1_1:-0.01000000):0.23500000,3_1:-0.03000000,4_1:0.03000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/Species0.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/Species0.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa078c95afc7aba6db8a431ffc7c122d7df1233a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/Species0.fa
@@ -0,0 +1,16 @@
+>0_0
+MNINSPNDKEIALKSYTETFLDILRQELGDQMLYKNFFANFEIKDVSKIGHITIGTTNVTPNSQYVIRAY
+ESSIQKSLDETFERKCTFSFVLLDSAVKKKVKRERKEAAIENIELSNREVDKTKTFENYVEGNFNKEAIR
+IAKLIVEGEEDYNPIFIYGKSGIGKTHLLNAICNELLKKEVSVKYINANSFTRDISYFLQENDQRKLKQI
+RNHFDNADIVMFDDFQSYGIGNKKATIELIFNILDSRINQKRTTIICSDRPIYSLQNSFDARLISRLSMG
+LQLSIDEPQKADLLKILDYMIDINKMTPELWEDDAKNFIVKNYANSIRSLIGAVNRLRFYNSEIVKTNSR
+YTLAIVNSILKDIQQVKEKVTPDVIIEYVAKYYKLSRSEILGKSRRKDVVLARHIAIWIVKKQLDLSLEQ
+IGRFFGNRDHSTIINAVRKIEKETEQSDITFKRTISEISNEIFKKN
+>1_2
+MKTKLKRFLEEISVHFNEANSELLDAFVHSIDFVFEENDNIYIYFESPYFFNEFKNKLNHLINVENAVVF
+NDYLSLEWKKIIKENKRVNLLNKKEADTLKEKLATLKKQEKYKINPLSKGIKEKYNFGNYLVFEFNKEAV
+YLAKQIANKTTHSNWNPIIIEGKPGYGKSHLLQAIANERQKLFPEEKICVLSSDDFGSEFLKSVIAPDPT
+HIESFKSKYKDYDLLMIDDVQIISNRPKTNETFFTIFNSLVDQKKTIVITLDCKIEEIQDKLTARMISRF
+QKGINVRINQPNKNEIIQIFKQKFKENNLEKYMDDHVIEEISDFDEGDIRKIEGSVSTLVFMNQMYGSTK
+TKDQILKSFIEKVTNRKNLILSKDPKYVFDKIKYHFNVSEDVLKSSKRKKEIVQARHICMYVLKNVYNKN
+LSQIGKLLRKDHTTVRHGIDKVEEELENDPNLKSFLDLFKN
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/diamondDBSpecies0.dmnd b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/diamondDBSpecies0.dmnd
new file mode 100644
index 0000000000000000000000000000000000000000..ba6d89f3f3a0b51535c60cabbf49be309e60dafd
Binary files /dev/null and b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/dependencies/diamondDBSpecies0.dmnd differ