diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000078_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000078_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24f26adba25b6c2a586e7fdc2cb7bee18e373f99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000078_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00025:0.00509109,GCF_023573625_1_GCF_023573625.1_00317:7.591e-05)n1:0.00392913,(GCF_002008305_4_GCF_002008305.4_00310:0.0061578,(GCF_005280335_1_GCF_005280335.1_00027:0.233312,(GCF_020097155_1_GCF_020097155.1_00654:1.70175,GCF_020097155_1_GCF_020097155.1_00023:0.169007)n4:0.0187786)n3:0.0146682)n2:0.00392913)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000287_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000287_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77d2ebff14abfade9f794f81f530dfdd2bb6ad5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000287_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02174:0.00119425,GCF_020097155_1_GCF_020097155.1_00169:1.25933)n1:0.0104705,(GCF_002008305_4_GCF_002008305.4_00178:0.0062685,(GCF_023573625_1_GCF_023573625.1_00175:0.0945343,GCF_005280335_1_GCF_005280335.1_00223:0.0729267)n3:0.040686)n2:0.0104705)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000719_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000719_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..746c4fcd14d197f1856a32c5d465ed966e011e2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0000719_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_02118:0.139987,GCF_020097155_1_GCF_020097155.1_02009:0.416477)n2:0.144601,GCF_002008305_4_GCF_002008305.4_00812:0.0030803)n1:0.0026881,(GCF_003691675_1_GCF_003691675.1_00544:0.00419902,GCF_023573625_1_GCF_023573625.1_00781:1.198e-05)n3:0.0026881)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001070_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001070_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dff57963c5fe0cf8e3ab2182f8fc2e788bb517bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001070_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00993:0,GCF_023573625_1_GCF_023573625.1_01232:0)n1:0.00172759,(GCF_002008305_4_GCF_002008305.4_01274:0.00429683,(GCF_020097155_1_GCF_020097155.1_01508:0.251225,GCF_005280335_1_GCF_005280335.1_01613:0.0978223)n3:0.0400059)n2:0.00172759)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001101_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001101_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be05f9dca740137b7e96155a7d46e15d5302f140
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001101_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01037:0.001181,GCF_023573625_1_GCF_023573625.1_01272:0.00031)n1:0.0420361,(GCF_020097155_1_GCF_020097155.1_01472:0.11189,(GCF_005280335_1_GCF_005280335.1_01576:0.001628,GCF_002008305_4_GCF_002008305.4_01316:2.69522e-07)n3:0.0705772)n2:0.0420361)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001198_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001198_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a110c44fc35a64b81c3b5027501af9cfb2839f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001198_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01401:0.0221468,GCF_002008305_4_GCF_002008305.4_01451:0.0297062)n1:0.137059,((GCF_003691675_1_GCF_003691675.1_01183:0.302676,GCF_020097155_1_GCF_020097155.1_01352:0.159531)n3:0.0258844,GCF_005280335_1_GCF_005280335.1_01448:0.0879168)n2:0.137059)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001264_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001264_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e37c83c73b296e2a24d9b807ac890dd3cd8b3d81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001264_tree.txt
@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_01269:0.544278,GCF_023573625_1_GCF_023573625.1_01474:0.028221)n2:0.0145785,GCF_003691675_1_GCF_003691675.1_01257:0.0346676)n1:0.0114194,(GCF_002008305_4_GCF_002008305.4_01547:1.26654e-06,GCF_005280335_1_GCF_005280335.1_01378:0.630409)n3:0.0114194)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001757_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001757_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b823df3b287ff23fa9363e7b8c7d8aa60a8d83eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001757_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00425:0.0801053,GCF_020097155_1_GCF_020097155.1_00378:0.54123)n2:0.0249441,GCF_002008305_4_GCF_002008305.4_02311:0.0269024)n1:0.00937531,(GCF_003691675_1_GCF_003691675.1_02004:0,GCF_023573625_1_GCF_023573625.1_02252:0)n3:0.00937531)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001822_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001822_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e5bb610ba504f93d3396ea29d5274b74751c063
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Resolved_Gene_Trees/OG0001822_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_4_GCF_002008305.4_00625:0.0363891,(GCF_005280335_1_GCF_005280335.1_00734:4.33571e-07,(GCF_005280335_1_GCF_005280335.1_00746:0.0049975,GCF_005280335_1_GCF_005280335.1_00749:0.0847985)n2:0.272297)n1:0.0363891)n0;
\ No 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/OG0000000_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000000_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3252f4b80c61e3b61f1d49e29d2c4ade86bfe18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000000_tree_id.txt
@@ -0,0 +1,2 @@
+(((((((4_265:0.00000050,4_1492:0.00000050):0.01546769,1_2024:0.01878281):0.00500793,0_60:0.01136257):0.00648969,((((((((2_37:0.01647713,((1_1918:0.02961679,2_2573:0.04008821):0.00582069,1_1079:0.01872531):0.00790387):0.01896625,((2_1475:0.34198608,2_2288:0.32166692):0.22782524,2_137:0.17716976):0.01922553):0.17896753,(2_674:-0.00000051,2_538:0.00145251):0.05347808):0.01713073,((((2_2418:-0.00003350,(2_1469:-0.00003350,2_2555:0.00221750):0.00003350):0.00451981,2_761:0.09288719):0.00932183,((2_2578:0.00157093,2_2285:-0.00011593):0.00011593,2_1737:-0.00011593):0.02903030):0.01249768,1_36:0.03458926):0.01524779):0.01254458,(((4_2046:0.05466563,4_2042:0.00211837):0.02735514,1_336:0.05194536):0.00857689,((2_1706:0.00000000,2_2499:0.00000000):0.00249019,2_217:0.00116081):0.04036186):0.00611815):0.00575053,(1_1921:0.01662750,1_125:0.00854050):0.01673339):0.00757110,1_10:0.01659136):0.00713079,(((((4_1516:0.00278280,((4_770:0.00041057,4_1128:0.00179143):0.00611915,4_845:0.00197085):0.00089645):0.00300558,1_1117:0.00419467):0.00466130,0_1289:0.02312795):0.00340532,1_297:0.00959290):0.00323066,1_1192:0.01176556):0.00452211):0.00466332):0.00539598,((0_2050:0.00090440,0_2217:0.00216260):0.01086990,1_1768:0.01171010):0.01486565):0.01170238,((4_495:0.01148278,4_1937:0.01102322):0.01319317,0_1892:0.01153583):0.01120845):0.03179405,0_2007:0.00628150,1_1771:0.00994150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44b751a438e33594d71e399f738b4d583e0cb176
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt
@@ -0,0 +1,2 @@
+(((((((((((0_1025:0.00000000,0_2210:0.00000000):0.00000000,0_577:0.00000000):0.00337008,2_2445:0.00026392):0.00114750,2_703:0.00340150):0.02635533,(0_578:0.00326081,2_2612:0.00526519):0.03380717):0.00788706,(((0_1969:0.00000050,0_1155:0.00000050):0.00046683,(4_2137:0.00000050,4_2154:0.00000050):0.00074617):0.03187404,2_673:0.02471196):0.00619406):0.02887453,(((1_1087:0.31742073,(0_2171:0.24689482,0_2003:0.10455618):0.04899627):0.18600090,0_1451:0.18399885):0.07857963,2_876:0.18610125):0.09456086):0.04109445,((0_2165:0.00349121,((0_564:0.00000000,(0_687:0.00000000,(0_1351:0.00000000,0_166:0.00000000):0.00000000):0.00000000):0.00016443,((((0_2004:0.03110246,0_1452:0.52640554):0.06102341,0_2170:0.02169909):0.11691813,0_2168:0.00128162):0.00811785,0_2205:-0.00203685):0.01256939):0.00129351):0.02190863,0_598:0.02425093):0.06665167):0.35285918,4_1295:-0.02098121):0.02442171,0_1346:-0.02082854):0.02449054,1_1088:0.20261045,4_1936:-0.02437645);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de9bc32777ed1722dd4fe1ba86f0cdc40f790d5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt
@@ -0,0 +1,2 @@
+(((((1_751:0.00123687,(((((3_604:0.00000000,3_609:0.00000000):0.00250577,(4_108:0.00000000,4_1824:0.00000000):0.00507023):0.00882327,3_302:0.04967373):0.00139610,1_1610:0.00804765):0.00487737,((1_316:0.00000000,3_2179:0.00000000):0.00696494,4_974:0.00622306):0.01543675):0.00526825):0.00217197,((((((2_2571:0.00000000,2_2297:0.00000000):0.02652277,1_304:-0.00001277):0.00001277,1_1284:-0.00001277):0.00001277,0_1339:-0.00001277):0.00001277,1_2208:-0.00001277):0.00136415,1_1078:0.00997735):0.00200872):0.00372999,((2_1288:0.00000000,2_1293:0.00000000):0.00353253,2_1255:0.00212247):0.02689702):0.00138189,(4_1486:0.00040598,(((0_1024:0.02079803,2_1278:-0.00002603):0.00002603,2_739:-0.00002603):0.00002603,2_2281:-0.00002603):0.00147652):0.00161499):0.00403270,(3_1758:0.00000000,3_1798:0.00000000):0.00000000,3_2156:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000004_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000004_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9349594fe6241d570878fcc5a8697230cbf01bd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000004_tree_id.txt
@@ -0,0 +1,2 @@
+((((((((1_1086:-0.00000974,(1_1696:-0.00000974,(0_2216:-0.00000974,(1_1769:-0.00000974,(4_1914:-0.00000974,(0_2051:-0.00000974,(4_111:-0.00000974,(0_1345:-0.00000974,((1_339:-0.00000974,(((2_875:0.00000000,2_218:0.00000000):0.26129373,1_973:0.03290927):0.09412338,2_2052:0.00437312):0.00521224):0.00000974,0_355:-0.00000974):0.00000974):0.00000974):0.00000974):0.00000974):0.00000974):0.00000974):0.00000974):0.00000974):0.00000974,1_1964:-0.00000974):0.00074121,(4_1821:0.00000000,(4_1493:0.00000000,4_1495:0.00000000):0.00000000):0.00038011):0.00319271,2_1476:-0.00010439):0.00010439,2_625:-0.00010439):0.05404883,(2_879:0.58612287,3_1790:0.60731813):0.35642841):0.35100772,2_219:-0.02010541):0.11852441,1_976:0.08856469,0_2008:0.00598831);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000006_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000006_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c6c1dd6952cb2f6fc6f08c2bc548eba88566f76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000006_tree_id.txt
@@ -0,0 +1,2 @@
+((0_149:-0.00009953,((4_1201:-0.00009953,(((4_563:0.00000000,4_2145:0.00000000):0.00189142,0_1244:-0.00008342):0.00002009,((((1_1075:0.01017937,1_972:0.11610363):0.00153869,2_1189:0.00131131):0.00056055,1_1065:-0.00011055):0.00011055,0_993:-0.00011055):0.00007434):0.00005231):0.00009953,0_2016:-0.00009953):0.00009953):0.00136053,(((4_1826:0.00900793,4_565:0.16364407):0.01933747,4_1290:0.00250603):0.01820729,(0_1336:0.00089900,1_1971:0.00272400):0.00276396):0.00224471,1_1073:0.00138604);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5b4a94c461cced5e831b6b50b3c588fd0084cf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1450:0.21983549,((4_582:-0.00000549,(1_2225:-0.00000549,(4_972:-0.00000549,(1_975:-0.00000549,(1_328:-0.00000549,(4_2103:-0.00000549,(4_1110:-0.00000549,(1_1349:-0.00000549,((0_2167:0.11810349,0_1352:-0.00000549):0.00000549,1_79:-0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549,0_686:-0.00000549):0.00000549,4_1301:-0.00000549);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48d132bb68ee1a1ff87252c7b1b99e9e7c14ad55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt
@@ -0,0 +1,2 @@
+(((((3_621:0.00000000,3_613:0.00000000):0.00000000,3_820:0.00000000):0.33667149,((0_432:0.26129447,0_815:0.16719453):0.06313377,((4_1294:-0.00262205,0_1344:0.00638105):0.00500683,1_1085:0.00513422):0.52658948):0.62525320):0.17754245,((2_1070:0.00000000,2_491:0.00000000):0.51747797,2_99:-0.09934097):0.15045989):0.11184455,2_1071:0.13421859,2_490:0.02647741);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e2d090d202f1585019c5aee494753b128cb6c4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_323:0.00000000,1_1729:0.00000000):0.00000000,0_591:0.00000000):0.01062291,(((((1_753:0.01135805,1_334:0.00684395):0.62638223,4_1945:0.71690827):0.02924489,(1_1719:0.02965334,0_584:0.01836466):0.13164373):0.03865239,(2_709:0.04496850,2_2314:0.07097450):0.03310580):0.06241858,(0_2013:0.01805192,4_1942:0.04409708):0.13257427):0.07869023,2_701:0.01093009);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000014_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000014_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c44c45593d725666a9eaa70906b64c83ba88dbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000014_tree_id.txt
@@ -0,0 +1,2 @@
+(((((0_1029:0.00000000,1_330:0.00000000):0.00000000,0_152:0.00000000):0.00096904,(1_321:0.00121875,1_757:0.00149425):0.00301701):0.00106070,((3_2168:0.00753556,0_1999:-0.00155956):0.18403313,1_283:0.18707043):0.21499430):0.00014071,2_705:0.00166318,4_978:0.00214782);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000015_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000015_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ef2ccf9c9e7a2abcde3ae806f4375344ca827c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000015_tree_id.txt
@@ -0,0 +1,2 @@
+(((((((0_335:0.00086601,(1_60:0.00361936,4_342:-0.00007436):0.00065449):0.00444025,2_2549:0.00817400):0.00845650,3_2408:0.01210162):0.42151019,3_1125:0.03015568):0.00724594,2_1213:0.00968165):0.01644085,0_1602:0.00653071):0.00153679,1_1317:0.00317510,4_1532:0.00186290);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000016_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000016_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb823aa3fce2ece37ebbf2aa2dba11d72ff95edc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000016_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1859:0.03393412,((0_953:0.01250644,3_1805:0.01188556):0.00231212,(4_896:0.00377569,1_676:0.00465431):0.00501738):0.00301887):0.01071425,((1_1430:0.00000000,0_1713:0.00000000):0.00351475,4_1642:0.00446625):0.01285687):0.00598188,2_1085:0.03042850,3_1012:0.09388650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000019_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000019_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4291eccab1ef0d7da511bb7375d9ebdb9bf02b4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000019_tree_id.txt
@@ -0,0 +1,2 @@
+(((((2_2225:0.00604717,2_2575:-0.00069917):0.01153047,(2_2558:0.00000000,2_2442:0.00000000):0.00247070):0.01767701,1_1716:0.04967698):0.14093497,(4_865:0.06802764,3_1843:0.01029236):0.18790151):0.04749702,1_326:0.12605278,4_1489:0.21603122);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000020_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000020_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a46abd812cb506918d05dc58ad886c128ef6bfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000020_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2364:0.08921680,((((4_501:0.00675058,0_501:0.00442542):0.00956661,1_231:0.01304829):0.37293559,2_1186:1.04887880):0.25178440,3_2245:0.39441187):0.05735580):0.07807089,4_512:0.01134396,1_242:0.00593104);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2ab8111471640e37c910fad017cc75bb6f47a2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt
@@ -0,0 +1,2 @@
+(((((0_546:0.02915833,1_279:0.00112167):0.27921589,4_548:-0.01415217):0.27080449,(0_547:0.01019928,1_280:0.00689172):0.13001756):0.08839560,2_2322:0.53822125):0.21660881,2_2323:0.33192837,3_2201:0.43306663);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed961783c6ff134ae03a2f5de58e5912d4bbbd37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2144:0.00219647,2_389:0.00492553):0.01029034,4_573:0.00369116):0.00751134,((4_1198:0.00251147,(1_969:0.00000000,0_1241:0.00000000):0.00094753):0.08331847,3_693:0.07509703):0.49036109,0_608:0.01370766);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000026_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000026_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f806576a5df88bae7ae07d37cc8004933f0591a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000026_tree_id.txt
@@ -0,0 +1,2 @@
+((((1_2091:0.00000000,(4_134:0.00280964,0_126:-0.00012864):0.00012864):0.01962869,2_241:0.01751978):0.06917324,3_176:0.09369415):0.09832679,3_177:0.23171330,3_2128:0.45444670);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000028_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000028_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d64c24f74c7e9985cc3398323527cae3209f17c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000028_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_755:0.00413650,(2_707:0.00307510,0_154:0.02093190):0.00013460):0.00038950,(0_1027:0.00000000,4_976:0.00000000):0.00000000):-0.00000000,1_319:0.00000000,1_332:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000029_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000029_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cf50883e86f909292d37de2842516eb2f125c59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000029_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_155:-0.00001406,(0_1026:-0.00001406,1_333:0.01479306):0.00001456):0.00001456,1_318:-0.00001406):0.00631431,(4_975:-0.00002819,2_708:0.00841419):0.00002819,1_754:-0.00002819);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a2d8503491f66ab45137c0959ca4662f97ccc01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1950:0.00188381,(1_344:-0.00027381,((2_2167:0.85778456,2_181:1.29451344):0.31294919,2_161:0.52549931):0.69657606):0.00112606):0.00381069,2_2283:0.00266569,0_161:0.00704631);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05ae21e27ded3f1a100f79e14429257bb8a7ca10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_84:0.64215019,1_88:0.96025081):0.33458081,3_84:0.18483869):0.17312881,((4_236:0.01456513,2_115:0.01158787):0.01153969,1_2199:0.00155281):0.00141406,0_236:0.00111569);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99b9d254e69e1b3047d2df5700541df0ca52dc99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt
@@ -0,0 +1,2 @@
+((((4_1943:0.16990516,2_700:0.01777684):0.00107886,(3_2162:0.00000000,1_324:0.00000000):0.01088379):0.00699889,1_1730:0.00283550):0.00418850,0_592:0.00000000,0_2014:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..291b508551c8b498dcd0fce8bde7dc4fd8ac980e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_579:0.00000000,1_356:0.00000000):0.00116114,(0_602:0.00758284,3_2137:0.04633916):0.00165752):0.00100654,(2_373:0.00090960,2_377:0.04208040):0.01706028,2_394:0.00046546);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000038_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000038_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b50c0203caacb7bafd04bf8906ee7b847682e7ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000038_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1003:0.05988475,((1_1437:0.00726013,(0_1720:0.00569369,4_1649:0.00439331):0.00177587):0.06023988,2_1078:0.07905762):0.00863038):0.66502275,0_806:0.44481738,0_807:0.13195263);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7967e59e83f91a2664c42cdd55c0916d38d95092
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_918:0.09708395,(2_1837:0.00352750,1_697:0.00112550):0.00052400):0.00899222,0_974:-0.00694217):1.19028617,(4_917:-0.68772370,3_2203:1.31174070):0.03769970,2_804:1.30472800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000041_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000041_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d2af91ffb3b7b2f3a356824c49efdb12866cfe7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000041_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1134:-0.01789897,((2_1678:0.66886616,1_862:-0.01859916):0.03596197,4_1084:-0.02181497):0.02542697):0.38494822,3_1575:0.46061678):0.07313222,3_300:0.93003472,2_1677:0.27866528);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000042_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000042_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b719c6f4d35818d9d942ff84b10a2adff8a06652
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000042_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1240:0.00000000,((((0_1573:0.01725019,4_1502:0.00237081):0.27317431,2_602:0.25932919):0.12537306,3_694:0.19311619):0.13524031,4_1197:0.01048381):0.00914119,1_968:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000043_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000043_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdc0794b8b133617e1ac19e06d53ab217058e17f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000043_tree_id.txt
@@ -0,0 +1,2 @@
+((((3_2164:0.00000000,3_631:0.00000000):0.01171738,(2_396:0.03020512,3_311:0.02041888):0.00376613):0.00558413,4_1298:0.00511887):0.00439462,1_1091:0.01393088,0_1349:0.00028712);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15f7a0f7e65acc809427dce2ae019ecf5020b7f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt
@@ -0,0 +1,2 @@
+((3_312:0.08377256,3_2165:-0.00373256):0.00373256,((1_1092:0.00071144,(0_1353:0.13095931,4_1302:0.36028569):0.04558656):0.01033281,2_397:0.01965469):0.00575931,3_632:-0.00373256);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..458bb009b93680883de8383fbad3287bb5259aac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt
@@ -0,0 +1,2 @@
+((((3_645:1.81551912,4_1968:-0.17046712):0.19431437,2_676:-0.13629337):0.15651787,(1_1744:0.01053269,0_2028:0.01525831):0.03120325):0.30734975,2_1283:0.00842769,3_2185:0.03767031);
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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/OG0000051_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000051_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b18764dd20ac557c2e23a76d6ad0041cfcd118de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000051_tree_id.txt
@@ -0,0 +1,2 @@
+(((((2_666:0.05828863,0_2033:0.03951137):0.00386081,1_1752:0.01924019):0.02766956,3_582:0.33358244):0.28745206,3_583:0.29333481):0.15742419,4_1971:0.76443844,3_2050:0.70680156);
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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/OG0000052_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000052_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..976e62ce5b678dacb9ab5d00a9fd40a99faade9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000052_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_2044:0.00158944,(0_2099:0.00000000,1_1823:0.00000000):0.00916856):0.03637194,2_580:0.03779156):0.04152094,(2_2524:1.60355419,2_571:0.37239781):0.39913194,3_503:0.07621006);
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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/OG0000053_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000053_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccd01a49f93f31ab111a058f9205ba19af5820c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000053_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2132:0.01101675,((1_1898:0.01185187,(4_2118:0.00688531,0_2185:-0.00064731):0.00196763):0.19826725,3_405:1.64472925):0.09859525):0.00460275,0_2200:0.03587081,3_401:0.04619419);
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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/OG0000054_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000054_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..997b10deb1b502db95c2224ca81efdc0b96339ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000054_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_470:0.01530531,(4_2124:0.00430931,3_417:0.00631569):0.00174669):0.00470219,(1_1902:0.00431900,0_2192:0.00831700):0.00616081):0.12850119,2_475:0.13837944,0_2214:0.72640956);
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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/OG0000055_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000055_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eef22a26393221327b3cb8cec3b8a6b3bbe30644
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000055_tree_id.txt
@@ -0,0 +1,2 @@
+(2_989:0.88488431,((((2_836:0.06745370,1_1646:0.20090630):0.06452505,3_774:0.12521059):0.16959534,4_708:0.26459935):0.29607888,3_851:0.79018170):0.02650430,3_923:0.56945369);
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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/OG0000057_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000057_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13d5308314f6ab49106161d6f42f751cae7ba03f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000057_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_446:1.44313107,3_410:1.57250193):0.09227583,(4_2148:0.19384638,0_2213:0.25098762):0.53974128):0.08640290,0_544:1.44500744,0_33:1.24672156);
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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/OG0000059_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000059_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57b3a5f4eaeed9b45624ecb3d8867e8c2e834884
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000059_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2013:0.01009569,(4_44:0.01313569,0_49:0.01309531):0.04873081):0.10272481,3_279:0.18316219):0.10450031,2_331:0.01886881,3_270:0.04642919);
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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/OG0000060_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000060_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de6e004189d9a78c4c1b296fcdd880feef7a143e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000060_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_59:0.01029091,1_2023:0.02548309):0.01065043,4_54:0.01943298):0.11405682,3_259:0.12408396):0.06457935,2_317:0.03592237,2_191:1.90909163);
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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/OG0000061_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000061_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4f0b74682d26d8532c228d63bf5388a34cf98c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000061_tree_id.txt
@@ -0,0 +1,2 @@
+((2_311:0.05624506,((1_2028:0.00378656,0_64:0.00132244):0.01840394,4_58:0.01560856):0.01871144):0.02724744,3_252:0.04386931,3_667:0.71686069);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000062_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000062_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..443a44de3ef80090de6c5dd30b8a8f6bd6120ce4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000062_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2036:0.00795127,(4_66:0.00000000,0_72:0.00000000):0.00241173):0.00309078,2_302:0.01884497):0.25774774,3_244:0.14167525,2_2287:1.34913975);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e95f37d6e89d630036d5da1c4175e5ffa830476
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt
@@ -0,0 +1,2 @@
+((3_139:-0.07142019,((1_1974:1.14174644,4_190:-0.05792844):0.07503194,1_2137:-0.05750094):0.07318719):0.07590019,2_187:0.51692156,0_190:-0.07330556);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000070_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000070_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0c6c115bbbda31f937d156daa947aa39f5d4393
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000070_tree_id.txt
@@ -0,0 +1,2 @@
+((((1_2179:0.00000000,0_215:0.00000000):0.00430212,4_216:0.00279487):0.13498288,2_147:0.11807963):0.04799588,2_570:1.38933087,3_105:0.19680412);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000071_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000071_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..865845c2f2e39d71b4d404bba15e255a5af143c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000071_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/OG0000074_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000074_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69d8f755f461b4a2548c0fa9abc45641c2034dde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000074_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/OG0000075_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000075_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de3e76f6ebb939e1573075b0edc957251dece0c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000075_tree_id.txt
@@ -0,0 +1,2 @@
+((4_272:0.00455281,0_273:0.00810519):0.00200369,((3_48:0.16764269,3_433:2.04507731):0.10153319,2_62:0.06938881):0.09773944,1_2239:0.00368381);
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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/OG0000077_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000077_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fff40c30d1c05311011622e3cf910453258241fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000077_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/OG0000078_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000078_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc04ceb49f92d218445c2fe627230baeff5b1548
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000078_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/OG0000080_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000080_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b7757b1df2fb6daa9170d298db9f4f9376bf2f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000080_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2545:0.00604444,2_1227:1.02832456):0.00440931,3_2404:0.04615369):0.00641581,(0_339:0.00218344,1_64:0.00437356):0.00178681,4_346:0.01081769);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000082_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000082_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67fca6e0cba875aec9062610ecae25d7b868ccb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000082_tree_id.txt
@@ -0,0 +1,2 @@
+((4_371:0.00424781,(0_365:-0.00018119,1_98:0.00382219):0.00306019):0.00628444,(2_2513:0.02984794,3_1719:0.12329806):0.00326944,3_2388:0.15727656);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000083_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000083_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfd71ddae9b582a358e45e9cefc6bb720cdf2519
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000083_tree_id.txt
@@ -0,0 +1,2 @@
+((4_394:0.00000000,0_391:0.00000000):0.00065750,((3_2359:0.04314975,2_2491:0.01966025):0.01322550,2_2587:1.91983200):0.00757650,1_120:0.00258950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c31daf6a91dbe9d7e4d3ccb74ab2d397f842b6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_127:0.08089881,(0_397:-0.00152869,4_400:0.00305769):0.12554269):1.11298344,2_2486:1.06994906):0.13904644,3_2354:1.39196694,2_2485:0.06404906);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e9f5954bd906a04a8bd652349f35944a0b04b1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt
@@ -0,0 +1,2 @@
+((0_402:-0.00902969,(4_405:-0.01355869,(1_132:-0.01751519,2_2478:0.45422019):0.03622469):0.05000619):0.11230669,2_2479:0.42698531,3_2349:0.05456069);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..633df9f09c66a84f354adb2355f4bbe6d06dac31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_430:0.00279306,(0_427:-0.00022944,1_157:0.00144544):0.00024344):0.02777794,3_666:0.87925356):0.01640494,3_2324:0.04906444,2_2453:0.04054856);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee72911691bf63d46104c411d952e76478332539
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt
@@ -0,0 +1,2 @@
+((1_197:0.00000000,0_467:0.00000000):0.00104686,((3_2287:0.04973900,4_1499:1.12797100):0.05788387,2_2404:0.00170325):0.00143446,4_466:0.00104314);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000088_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000088_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75e5d2e09d0e8794d776c3e1982f5b882aacaef4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000088_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2398:0.02347656,((0_473:0.01016619,1_203:0.01089681):0.00415844,4_472:0.01335306):0.00238419):0.09330994,2_1196:1.79847494,3_2281:0.12364106);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da993cf5e5249fbc559ed95853136999802b8f7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1193:2.48045050,3_2271:0.02622050):0.03396572,((4_485:0.02194197,0_486:0.00744403):0.01830022,1_215:0.04154268):0.00283560,2_2388:0.04570912);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fcd96e672260a17cebca5924e12e6ce2733a94f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt
@@ -0,0 +1,2 @@
+((1_258:0.00895888,4_527:0.00985112):0.00207375,(3_2230:0.49947350,(2_2346:0.32474400,2_2347:0.29526900):0.10283450):0.12939350,0_524:0.00547575);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000093_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000093_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47e5abfa4a5ce2098e30829359d9a649540ceb1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000093_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2059:0.00000050,0_2113:0.00000050):0.00000000,((3_488:0.07951750,0_579:1.63863050):0.06457550,2_560:0.08344900):0.12777250,1_1838:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000094_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000094_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7ad6d6ab247264cf27ae4663ea27e08d881f009
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000094_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2583:0.54854425,4_1944:0.11480575):0.01563000,(0_585:0.01324187,1_1720:0.00425513):0.07770425):0.10023575,3_2150:0.00437363,2_383:0.00293637);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34c0814714eb431986f6f6f0c9c515480bdef591
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2293:0.18683579,((3_1166:1.83428617,1_1721:0.20649983):0.05785398,0_586:0.13885244):0.03246256):0.11027621,1_311:0.00000000,4_1948:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000098_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000098_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ba6aa7e43bb072c04af952d7488ffa4627d4950
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000098_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2136:0.04231225,(1_355:0.00375637,4_580:0.00745362):0.00211225):0.00502325,(2_395:0.13646063,0_601:0.11164837):0.15216025,2_376:0.00909975);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69756d0e65b5ccc471f889904e86bd6851e1ba47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_2268:0.06920556,3_2126:0.06060044):0.03695269,3_567:1.03720181):0.03707369,4_589:0.00455506):0.00864944,0_619:0.01276406,1_365:0.00997494);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000101_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000101_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..130f077eeddac010ca2a5971caec050a9682327b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000101_tree_id.txt
@@ -0,0 +1,2 @@
+((0_624:0.02986694,(1_370:0.00714744,4_594:0.00460756):0.02321137):0.04820963,(3_2119:0.09988825,0_811:2.72110575):0.16614472,2_2263:0.08152794);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc9218b2733631f4082e51343cb8317a0ec8dc17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_376:-0.00040181,(4_600:0.00215956,0_630:-0.00026056):0.00087831):0.05560231,2_2257:0.07936869):0.04671181,3_2113:0.13249981,2_152:1.50019419);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e4f09dfd45bcee5664513db46632b211caa9ad4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt
@@ -0,0 +1,2 @@
+(0_666:0.00000877,(4_636:0.01459090,((2_2213:0.11430212,3_2387:0.88280888):0.61325802,2_2212:0.24171930):0.27770467):0.01650460,1_412:0.00258823);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000107_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000107_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45f76d14ee9ec5ab90e652acb1dd622e17be042a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000107_tree_id.txt
@@ -0,0 +1,2 @@
+((0_742:0.01357581,(2_788:0.75117906,(3_2007:0.07827731,2_2112:0.03121969):0.00871644):0.02216869):0.00493469,1_481:0.25135031,4_706:0.00067469);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000111_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000111_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15393d3c4abca1e3a39d07e74d89e47ab9c69f45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000111_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_897:0.01467531,(0_954:0.01229656,1_677:0.01566844):0.00293419):0.01268444,2_1858:0.02850231):0.04125069,3_1804:0.14430256,2_1785:1.43444144);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000113_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000113_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f35641677a8b97c1776d6b09a3652c5f3dd2df41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000113_tree_id.txt
@@ -0,0 +1,2 @@
+((0_987:0.00000000,1_711:0.00000000):0.00000000,(3_1707:0.07289100,(2_175:0.97280300,2_1816:0.86234100):0.98459350):0.01517700,4_931:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000115_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000115_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9505ef8105e692ddd18766f46f9d2b4839d9ad4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000115_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_989:-0.00016156,3_1705:0.01198156):0.00016206,1_713:-0.00016156):0.00016206,4_933:-0.00016156):0.70446406,2_1817:0.48871881,2_176:0.41517519);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000116_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000116_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c478fdbc22cd8dff3d6bf15829dc4444199b6a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000116_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1698:0.68129008,(2_316:0.00377650,2_526:0.00900350):0.26807829):0.14239481,(1_723:0.02065220,0_1001:0.00613980):0.01599492,4_942:0.01051821);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000119_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000119_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b93380c05fc830784ab509d86ef687e8812414b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000119_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1071:0.00130106,(((1_357:1.00686169,3_1637:0.06379331):0.04474094,2_1745:0.02402206):0.02080894,1_799:0.00231856):0.00113144,4_1021:0.00099494);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000121_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000121_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a971c36df6f187b8e5a6903bce9219744916130
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000121_tree_id.txt
@@ -0,0 +1,2 @@
+(1_829:0.00000000,(0_1101:0.00354933,((2_753:1.43395513,3_1607:0.09451687):0.01467363,2_1714:0.01880700):0.03992777):0.00516567,4_1051:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000123_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000123_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ca8ee622920e83f338fc03c73189c1a169c5c57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000123_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_1224:0.00000000,4_1181:0.00000000):0.00000000,1_952:0.00000000):0.04556150,2_1585:0.03217350):0.01239650,4_1823:3.04938300,3_1480:0.07201000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000125_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000125_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5e9a2172681bd3e025f1bb92141acc477cd577f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000125_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_1286:0.00000000,4_1241:0.00000000):0.00186900,1_1016:0.00125400):0.06020175,2_1527:0.02307175):0.15596275,3_121:1.74033000,3_1423:0.08080900);
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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/OG0000126_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000126_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9af56327ec372f8c87053ba3f8b3b2f65b19c6a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000126_tree_id.txt
@@ -0,0 +1,2 @@
+((((4_1247:0.00000000,1_1022:0.00000000):0.00337400,0_1293:0.00979600):0.04411250,2_1521:0.05244750):0.24049350,3_1385:2.21555425,3_1417:0.01157075);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2eca185e3c9a3f18430356bb8e99d3cf6004497
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_1321:0.02063044,4_1275:0.01390156):0.00523794,1_1050:0.02795256):0.24634694,3_1389:0.35584806):0.14746544,0_1893:2.62664694,2_1494:0.14971206);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000128_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000128_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bc6cbe7e2ba562f7d50f7fd16f49b6f6b318b09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000128_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1129:0.00000000,4_1337:0.00000000):0.00094046,((3_1340:0.13635925,3_2386:0.80496675):0.04336073,2_1432:0.06971546):0.06892505,0_1388:0.00079054);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000130_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000130_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e5d3a4bf486ee08c797c1c6d5559e5e50f2793e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000130_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1485:0.02080256,(4_1412:0.01792707,1_1205:0.04072993):0.00928940):0.05250890,2_1361:0.12836767):0.03709559,3_1253:0.10160450,3_272:3.33823850);
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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/OG0000131_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000131_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..412f38190650b9c1044de55d1ef395948de2c629
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000131_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1272:1.82395038,3_1243:0.08982962):0.04181391,2_1351:0.03972657):0.04340667,(0_1495:0.00145993,4_1422:0.00242707):0.00446074,1_1215:0.00168778);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0233b905763132cd0a2d663a2afa9a768ed38876
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1442:0.01198300,(0_1515:0.00075565,1_1235:0.00286035):0.00429334):0.09481190,2_1330:0.09711531):0.04387141,3_1224:0.11629600,2_2521:0.28197600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33bcbfbdba4d2ed355dc690722a2b982ee662d2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1455:0.00712669,3_1210:0.00741931):0.00312781,(1_1249:0.20623269,(1_1248:0.03124669,2_1315:-0.00864969):0.26975231):0.11817906,0_1528:0.00093419);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000136_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000136_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d363466970d77584f2850862219e132b9f0a33c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000136_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1457:0.00000000,2_1313:0.00000000):0.00000000,((0_2188:0.04275675,3_441:0.16727925):1.47059617,1_1251:0.00279783):0.00174217,0_1530:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a7899b28047399b0c6a8910c5bf2127ccccd1d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_711:0.39173512,(0_1731:0.00000000,2_1065:0.00000000):0.99920087):0.18740838,1_1707:0.01137062):0.00529638,0_1990:0.00099388,4_1925:0.01487913);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000146_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000146_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f341ae5150452518449e4f7f4acc37e0d19ac3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000146_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1989:0.00683875,(1_1706:0.00409386,4_1924:0.00522114):0.00388031):0.20067067,3_712:0.13552683):0.54038617,0_1736:0.00000000,2_1060:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fb13f0a86b7f44320916b2db21bb01b79267274
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1500:0.01421431,(4_1714:0.01335269,0_1793:0.00120731):0.01337069):0.08074119,(3_938:0.19297756,2_1037:1.45413644):0.08160369,2_995:0.09983881);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000151_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000151_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f0d1b423e1ea8e1df3bcbdcf9441601e0a26e8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000151_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_1861:0.00325944,1_1568:0.00925356):0.00957146,4_1782:0.01332925):0.03619164,2_919:0.06688883):0.92573142,2_768:1.41367125,3_855:-0.33692725);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000152_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000152_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d86e35a22a4dc97a35c669dc110ef8dbe55a6b7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000152_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1586:0.00293450,(0_1879:0.00000000,4_1799:0.00000000):0.00696150):0.05811125,2_900:0.02884175):0.05963525,3_835:0.11409600,3_2083:1.32109800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c740a12f159a3ca460a3c081eb41ab543697242f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_542:0.22077262,2_725:0.20549737):0.02002725,(0_2009:0.00753475,4_1938:0.00941525):0.18450200):0.07065275,3_469:0.41506062,1_1068:0.85842637);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ab80287e55324f8657715975f4c165ae81f58ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt
@@ -0,0 +1,2 @@
+((2_718:0.49344838,(2_722:0.17712917,3_471:0.15479183):0.13921852):0.61433669,(4_1940:0.02406075,0_2011:0.03939325):0.14816145,2_723:0.18700690);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000162_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000162_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d459d213935895e5667d145edfe8909a8e17e6af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000162_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1750:0.40017710,(2_667:0.02266411,3_584:0.04575789):0.19146225):0.19908583,3_538:0.90740507):0.28487316,0_2032:0.12695662,1_1751:0.24614738);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000163_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000163_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..092461f6bd6f29d54472e7303ad9c19fd1f6cd68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000163_tree_id.txt
@@ -0,0 +1,2 @@
+((((1_1755:0.00000000,0_2037:0.00000000):0.00429658,4_1978:0.00060442):0.02811238,2_663:0.04625276):0.05846438,2_1470:3.11273725,3_578:0.16577875);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb662e314f5b6f955bfa459769a9c1741345dd6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_2061:0.01189923,4_2000:0.00899377):0.00210951,1_1780:0.01093832):0.01366134,3_558:0.03081033):0.12767116,2_640:0.18818400,3_700:0.63237200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000166_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000166_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..970bc91558435691a8b19ec984db4378aea42a9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000166_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1832:0.00062969,(4_2053:0.01808944,0_2107:0.01486756):0.00586681):0.08855706,2_566:0.16863769):0.04436081,3_493:0.15542481,3_1863:1.52305219);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..752b538331b76ef82de07e93c77aec62dfebbe40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt
@@ -0,0 +1,2 @@
+(2_471:0.03934138,((4_2123:0.00088025,1_1901:0.00349575):0.00602663,(0_2215:0.02361038,0_2191:0.00572863):0.00321437):0.00105238,3_418:0.00586862);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000169_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000169_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f073613655fd4f0a853e553ffc947973f696b9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000169_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2204:0.01464925,(2_451:0.01357675,(3_402:0.10815600,(2_623:0.14529987,4_2138:0.05272013):0.06977000):0.01548100):0.00377825,1_1910:0.24994075);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fda5f44f2c2371c96c28d172b3064af1ef4dad70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt
@@ -0,0 +1,2 @@
+((3_136:0.01247692,4_193:0.01313708):0.10611384,(2_84:0.78509765,(3_123:1.16084463,2_83:0.85863137):0.15572245):0.38237198,2_185:0.15742458);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..641855d1665f837cb7e310688bb2fde1ddba02ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1:0.00000000,4_1:0.00000000):0.00000000,1_1957:0.00000000):0.02145550,3_358:0.09552650,2_404:0.05310750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000176_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000176_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4cb78713f8a817ae96360f74bdc188d8fa26523
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000176_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2:0.00335525,(1_1958:0.00563850,0_2:0.00090650):0.00618325):0.06033825,2_403:0.05830350,3_357:0.09654850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000177_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000177_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfafa122ff0a4b622e3194464c59baac9e46b441
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000177_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_356:0.15793850,2_402:0.14478950):0.09826300,4_3:0.00368200):0.00457100,1_1959:0.00000000,0_3:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31f0317f1a977f99a24585ad24b6b86c798ffab4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1963:0.00000000,4_7:0.00000000):0.00299325,(2_398:0.05097375,3_351:0.73022625):0.07339575,0_7:0.02192175);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000183_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000183_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..233fc72aa66fdf01756c0b1f062201f79fae48b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000183_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_349:0.76476283,2_367:0.14013917):0.22951401,1_1980:0.04543253):0.01669297,0_11:0.00406444,4_11:0.00237656);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..642cc8a6c43130e20d00ca5709702b62d0889402
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_366:0.02708350,3_348:0.02001650):0.03393950,4_12:0.00000000):0.00000000,0_12:0.00000000,1_1981:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e982b8ae77d7850e4358007e4f10ede38dc1b88b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1982:0.01731737,(4_13:0.00604363,0_13:0.00656637):0.01075463):0.08043312,3_347:0.30265487,2_365:0.27206613);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03275d4c4d0e961911c6c2dcf4fc8ef812095ed0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt
@@ -0,0 +1,2 @@
+((0_17:0.01918265,(4_17:0.01847353,1_1986:0.01165447):0.01170078):0.05980097,3_343:0.33782900,2_360:0.08046000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91e5e5b0a0ee7004197a0de40e0c8530069682f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt
@@ -0,0 +1,2 @@
+(2_359:0.01900761,(4_18:0.00946850,(0_18:0.00017867,1_1987:-0.00017867):0.00783250):0.00253350,3_342:0.35010439);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c5cc35efbf521e1ae9d04864b7b32da33209091
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1989:0.04781418,(0_20:0.02596116,3_340:0.36106384):0.00245185):0.01777735,2_357:0.02761267,4_20:0.03462033);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0142cb087123ffe9717c6b8449fe9ee068f8a090
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt
@@ -0,0 +1,2 @@
+(2_356:0.00247450,(3_339:0.24990025,(0_21:0.00285875,1_1990:0.00010825):0.00481325):0.00041125,4_21:0.00346950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..280450151b3148429a76a1cc55c29d02b1eccd62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt
@@ -0,0 +1,2 @@
+((4_29:0.00409888,(0_30:0.00537062,1_1998:0.00163337):0.00575613):0.04146462,2_347:0.06984588,3_289:0.06975713);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f14d108f1bcbaaca9270213837f3c47cbff16d81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt
@@ -0,0 +1,2 @@
+(0_36:0.00925375,((3_287:0.25514700,2_345:0.14866200):0.17571225,4_31:0.00155925):0.01124125,1_2000:0.04673225);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000200_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000200_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b338ecec8332e5c50e7a10450079a90621fa74b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000200_tree_id.txt
@@ -0,0 +1,2 @@
+((0_38:0.00829239,(2_343:0.03163950,3_286:0.10536750):0.04415796):0.00533511,4_33:0.00140726,1_2002:-0.00020526);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37728bdc98591a792506e03779853b2bd12c907f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt
@@ -0,0 +1,2 @@
+(4_36:0.00000000,((2_340:0.13756717,3_283:0.24185283):0.15788589,0_41:0.01737416):0.00793884,1_2005:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84cbaa9987330b85a1b308ba80a00362c51d314a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt
@@ -0,0 +1,2 @@
+((0_43:0.00747350,(4_38:0.03943350,1_2007:0.00314150):0.01559750):0.20570750,2_333:0.17770825,3_281:0.53193275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000208_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000208_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..727ef0b41caf328722d54fdd60963754fec8426e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000208_tree_id.txt
@@ -0,0 +1,2 @@
+((0_51:0.00429225,(1_2015:0.00179475,4_46:0.00168425):0.00202975):0.03972425,3_267:0.09247775,2_327:0.02831825);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000210_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000210_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f00ebd79dcc532d83ed6115ac8ffdc9ca9f0098
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000210_tree_id.txt
@@ -0,0 +1,2 @@
+((0_53:0.00348725,4_48:0.00294775):0.00086750,(3_264:0.37743950,2_323:0.13407450):0.07292000,1_2017:0.00596050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000212_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000212_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe0b1193416164c12c8e0c5a906e399899cfb690
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000212_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_56:0.00401725,4_51:0.00375275):0.00892275,1_2020:0.01825475):0.13905275,2_320:0.09774200,3_262:0.27109200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000213_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000213_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e90627aca74057353932b9d908ddfe242067040a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000213_tree_id.txt
@@ -0,0 +1,2 @@
+((3_261:0.05684317,2_319:0.01827183):0.01551262,(0_57:0.00000000,4_52:0.00000000):0.00067765,1_2021:0.00841335);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0709fa4b5b1c374c43d1f552cf040eb062e6da25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2029:0.01741313,(4_59:0.01654163,0_65:0.02031037):0.00656937):0.19208538,3_251:0.29387887,2_308:0.37459713);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000220_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000220_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dea0e86bbd5349c6793ff72f5f93138784d02b70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000220_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_61:0.02207212,0_67:0.01869188):0.02383388,1_2031:0.02788913):0.21657437,2_306:0.38568887,3_249:0.25292912);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000221_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000221_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b0dd070ec712e257b8be4d1291a3310ac43b9e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000221_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2032:0.00000000,(4_62:0.00461356,(3_248:0.02025967,2_305:0.03159333):0.03325785):0.00103644,0_68:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f634c1b71e1636fc6583104081b361ec92c3cf3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_70:0.00028412,1_2034:0.00083888):0.00081462,4_64:0.00274287):0.03578412,2_304:0.01725762,3_246:0.12738637);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d251b6937e8d7e4a74d396e766edfe3fb0f3054
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_71:0.00000000,1_2035:0.00000000):0.00248450,4_65:0.00241750):0.03599150,2_303:0.08542200,3_245:0.12497000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000224_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000224_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..804b240ce0745eeb3c63f577724155b360cdf722
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000224_tree_id.txt
@@ -0,0 +1,2 @@
+((0_73:0.00353188,(1_2037:0.01058488,4_67:0.00990812):0.00463162):0.01822413,3_243:0.21525763,2_301:0.02988737);
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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/OG0000226_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000226_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28d5ab44c8668748dca2b9c8e10d1239d83355e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000226_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_299:0.08744333,3_241:0.46041167):0.09421819,0_75:0.01657158):0.03602742,1_2039:0.00000000,4_69:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000227_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000227_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efd56a6b2875199d288c1bf76d945be4a4a4b9bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000227_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2040:0.00000000,4_70:0.00000000):0.00583372,0_76:0.00021728):0.07148576,2_298:0.04651167,3_240:0.30717633);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000230_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000230_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a12d95366992fafa63a8a12acc4488953961ea9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000230_tree_id.txt
@@ -0,0 +1,2 @@
+((0_80:0.01326250,(4_75:0.00000000,1_2044:0.00000000):0.02029750):0.05300500,2_292:0.12045050,3_237:0.48668950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32fb019ccb99c184a1692fa0e667c7c8197bad8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_287:0.08692638,3_233:0.30054463):0.07564487,4_80:0.02709612):0.01805438,0_85:0.02446662,1_2049:0.00659638);
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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/OG0000236_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000236_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d849b053bfcd5dd04c03d51d2eedd6a71d1eab2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000236_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_87:0.00000000,4_82:0.00000000):0.00529921,1_2051:0.00471879):0.02997460,2_285:0.00766933,3_231:0.00921367);
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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/OG0000237_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000237_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8fb5b646689c3a540dc63c4688396e8abb2ef3da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000237_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2052:0.01006175,(2_284:0.01714425,(0_88:0.00000000,4_83:0.00000000):0.01554075):0.00388525,3_230:0.00534725);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000239_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000239_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c0dc11622b890c01d97e903bf64276ccb363cd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000239_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2054:0.01666875,(4_85:0.00720300,0_90:0.00236600):0.00983425):0.26076775,2_282:0.21075250,3_228:0.46807950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000240_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000240_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e1364b1a3afa5e61874bd857ceeb5af4b2a49eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000240_tree_id.txt
@@ -0,0 +1,2 @@
+((4_86:0.00696610,(1_2055:0.00176030,0_91:0.01145870):0.00322725):0.11906457,2_281:0.17155967,3_227:0.11693433);
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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/OG0000242_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000242_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b35c5c3aef4930112132a76fe5c9106a30dbbeea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000242_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2057:0.00372637,(4_88:0.00360812,0_93:0.00098188):0.00214113):0.01348313,2_279:0.03093638,3_225:0.09056662);
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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/OG0000243_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000243_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c1ae7b16a243c379626c414f1ad30f119f92fba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000243_tree_id.txt
@@ -0,0 +1,2 @@
+(0_94:0.00000000,((3_224:0.17180225,2_278:0.17140375):0.17081475,1_2058:0.01626975):0.00069725,4_89:0.00000000);
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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/OG0000244_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000244_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ccdcb1dc4c6167ce91bf27399307b215ac791c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000244_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2060:0.00175347,(0_96:0.00153069,4_91:0.00001831):0.00070772):0.00993389,3_223:0.06745233,2_276:0.01451567);
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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/OG0000245_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000245_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e78fa2890d468bbc2434f12a513185a0c75cf70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000245_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_274:0.10549175,4_92:0.06095125):0.07018975,3_221:0.49769725):0.03374975,1_2061:0.00000000,0_97:0.00000000);
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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/OG0000249_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000249_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c0795076a26f1733b3649210307bc9dcd355529
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000249_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2066:0.00419425,(0_102:0.00564125,4_97:0.00321775):0.00608925):0.08213375,2_269:0.07285175,3_211:0.18883425);
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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/OG0000250_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000250_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9644e54371a5ee204b26080044687f685be161c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000250_tree_id.txt
@@ -0,0 +1,2 @@
+(0_103:0.00010000,((2_268:0.09172025,3_210:0.34185175):0.13045650,4_98:0.03620250):0.01681450,1_2067:0.00222100);
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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/OG0000252_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000252_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2734364f80ea806cca7d3f8021332c5c564c1bb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000252_tree_id.txt
@@ -0,0 +1,2 @@
+((0_105:0.00000000,4_100:0.00000000):0.00000000,(2_266:0.16624250,3_208:0.09142450):0.23617650,1_2069:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e8247ad139a96300ec3a0ed5395ac22b5dcd3cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt
@@ -0,0 +1,2 @@
+((0_110:0.00000000,1_2074:0.00000000):0.00295974,(2_258:0.08292467,3_191:0.14220833):0.07405109,4_115:0.00519526);
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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/OG0000259_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000259_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bde632a2b81ac06e905938bf1c3ff20d164b772
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000259_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_188:0.17529700,2_256:0.05288300):0.04921900,0_112:0.00084150):0.00160650,1_2076:0.00000000,4_117:0.00000000);
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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/OG0000260_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000260_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a98376a8971c0b6ce3c23b90e66b9847eb7da655
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000260_tree_id.txt
@@ -0,0 +1,2 @@
+((2_250:0.05196050,0_117:0.04328750):0.00256775,(1_2082:0.01270450,4_125:0.00748750):0.03938675,3_184:0.08267625);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ad68b42785d4749eea613be5a793a1462b04b30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt
@@ -0,0 +1,2 @@
+((2_247:0.16059933,3_181:0.04740267):0.48311177,(1_2085:0.00534978,4_128:0.00306022):0.04006531,0_120:0.03502315);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000267_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000267_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..616166edb380de9082e05d787b88bebfcb7edf80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000267_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2090:0.00425296,(4_133:0.01974403,(2_242:0.08341417,3_178:0.12118283):0.08448218):0.01681847,0_125:0.00545404);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000269_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000269_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d39b879f266297056d0998e4f1685d431d25856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000269_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2093:0.00949525,4_136:-0.00112025):0.01312650,(3_172:0.33516725,2_238:0.11988075):0.08346650,0_128:0.00763750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000270_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000270_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e92fd6daf0f7c061010c243f568bf0efa7814a0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000270_tree_id.txt
@@ -0,0 +1,2 @@
+(4_137:0.00317750,(3_171:0.01001175,(2_237:0.05499075,0_129:0.00568625):0.00328425):0.00089775,1_2094:0.00029450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000272_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000272_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e0967f0b509606c84e31acfe1a7044eeb7848ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000272_tree_id.txt
@@ -0,0 +1,2 @@
+(2_235:0.01863359,((0_131:0.00000000,4_139:0.00000000):0.01371050,3_169:0.39521950):0.01078550,1_2096:0.01884041);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000273_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000273_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98e26115e8b79575334861e44705e309bbaab148
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000273_tree_id.txt
@@ -0,0 +1,2 @@
+((4_140:0.00000000,0_132:0.00000000):0.02353900,(3_168:0.07523050,2_234:0.02761850):0.02411150,1_2097:0.00744000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb41b5c2483ba84a4d70ce93d7d7869a08c6e1b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt
@@ -0,0 +1,2 @@
+((0_134:-0.00034687,1_2099:0.01988687):0.00034687,(3_166:0.23583038,2_232:0.04815462):0.04959538,4_142:-0.00034687);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ff68167aeebc0457d432f56d643286349c1d9a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2101:0.00174638,4_144:0.00404563):0.00443362,0_136:0.00180838):0.04238213,2_230:0.02579762,3_164:0.18314038);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000278_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000278_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31f372344e41a93c510e7fdfbb5e71aa453704db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000278_tree_id.txt
@@ -0,0 +1,2 @@
+((3_163:0.03127750,2_228:0.02712850):0.02990775,(4_146:0.00479950,1_2103:0.00128450):0.00277125,0_138:0.00947775);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ee01212fd6a72dfc27b3e3c537e8a5567b1c0f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt
@@ -0,0 +1,2 @@
+((2_226:0.05571800,3_803:0.47649800):0.02437000,(1_2104:0.00000000,4_147:0.00000000):0.00024150,0_139:0.03265950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000281_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000281_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc13c57259e6702e088bea1771031af100402193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000281_tree_id.txt
@@ -0,0 +1,2 @@
+((0_141:0.00119554,(1_2106:0.00098251,4_149:0.00029049):0.00224511):0.06357415,3_801:0.33287517,2_224:0.09071783);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000284_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000284_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86a1b305f83e7dfc32ef843b932f8c5a9c7bae88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000284_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_160:0.11367300,2_221:0.02898600):0.02664600,1_2109:0.00000000):0.00000000,4_152:0.00000000,0_144:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42b0a4a1a6defb4a0f0adab12e0fbccd1e2d693a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2282:-0.00093712,0_160:0.01591012):0.00403638,(3_659:1.52720013,4_1951:0.00334887):0.00550087,1_343:-0.00266288);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000287_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000287_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..391b1d4eedfc87872bd1d99e5f5ebe101db8b4d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000287_tree_id.txt
@@ -0,0 +1,2 @@
+((0_170:0.00626850,(1_2117:0.00119425,3_159:1.25933475):0.02094100):0.04068600,4_167:0.09453425,2_213:0.07292675);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..949b76b98fcdb474873e8449aae4a89f59b87677
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt
@@ -0,0 +1,2 @@
+((4_168:0.00231150,(1_2118:0.00350675,0_171:-0.00002675):0.00117350):0.00583100,2_212:0.01407925,3_158:0.01649175);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a3363e61b92f09a80e48fddcfe1b20ecd16b456
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_153:0.44881333,2_208:0.00673267):0.00228314,1_2122:0.00349919):0.00337179,0_175:0.00737417,4_172:0.00165483);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000297_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000297_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b2c64e0f97a19c29608bdf2e2b6a285a0e9051b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000297_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_145:0.11710400,0_184:0.00746700):0.00476418,4_184:0.00078954):0.00377146,1_2131:0.00068729,2_198:0.03504471);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000298_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000298_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd882b5f722f32b784843d3254559dbde8bb856e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000298_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2132:0.00000000,((3_144:-0.00005950,2_197:0.02246350):0.00228000,0_185:0.00666850):0.00073350,4_185:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000301_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000301_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3a3ddac3ee6a5ac0d7017cd8c8254093b1a27d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000301_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2135:0.00000000,4_188:0.00000000):0.03480400,0_188:0.02694900):0.01180650,2_193:0.15003750,3_141:0.02286750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000302_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000302_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40a5f9b5f4cdb2566e49a7b97a817f1bf45b3efb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000302_tree_id.txt
@@ -0,0 +1,2 @@
+((4_189:0.03469793,(0_189:0.02613777,1_2136:0.01483023):0.01780200):0.16340457,3_140:0.20798250,2_192:0.20484950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..998e91725194da6cba0136b864e78bb1ab7aa1cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt
@@ -0,0 +1,2 @@
+((4_197:0.00201322,(1_2141:0.00249862,0_195:0.00000138):0.00425141):0.01094689,3_133:0.01144200,2_178:0.26616200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000306_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000306_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa197ac0730906cadbec3ede0c273897d203b59e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000306_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2144:0.01502125,(2_173:0.19525850,3_119:0.59496950):0.04637575):0.05065225,0_200:0.01015450,4_200:0.00099650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000307_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000307_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5700baf38331f5fc304efe83a007d8599ef9a27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000307_tree_id.txt
@@ -0,0 +1,2 @@
+((0_201:0.01807000,(1_2145:0.00308325,4_201:0.00757775):0.01163350):0.12390800,2_172:0.16888250,3_118:0.76893250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000311_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000311_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4558df1244e99a9fce9cc1a790469fe26ea699d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000311_tree_id.txt
@@ -0,0 +1,2 @@
+(2_163:0.05190975,((3_112:0.07002600,0_205:-0.00062500):0.00062500,4_205:-0.00062500):0.00046900,1_2149:0.00945925);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000312_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000312_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6fb68994839b4597e9fb9498083f00401d5db56d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000312_tree_id.txt
@@ -0,0 +1,2 @@
+((3_110:0.24411575,2_159:0.26187325):0.26516600,(1_2150:0.02954850,4_206:0.02582650):0.00555450,0_206:0.02592100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000314_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000314_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba25f29adabd11e0f82a74045da9c5990c7b848f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000314_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2155:0.00000000,((2_1574:0.26374133,3_599:1.07248067):0.32721472,0_210:0.01286315):0.01793185,4_211:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000315_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000315_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5941c42047a8baa2cd921a958552c4d0399f03cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000315_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2176:0.15195365,(3_108:0.12161833,2_150:0.24190567):0.12896122):0.01544385,0_212:0.04758162,4_213:0.01369338);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000316_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000316_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92e8e9a7798588400e9d0783d8de52fe158d4666
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000316_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_148:0.00915050,3_106:0.10738850):0.01999325,4_215:0.00027925):0.00281325,0_214:0.00000050,1_2178:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3056a594fadc35023cf7c2aa5bf232a4ce23dc7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2180:0.00832750,((2_146:0.15677500,3_104:0.50539600):0.18955400,0_216:0.01111700):0.01982250,4_217:0.03260050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000319_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000319_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a80403da5f42b0bab56b3bb77c35cebbd8a56fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000319_tree_id.txt
@@ -0,0 +1,2 @@
+((4_219:0.05256144,(1_2182:0.05993289,0_218:0.04711311):0.01578361):0.15642841,2_144:0.22691267,3_102:0.37368433);
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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/OG0000322_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000322_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e604a40ab5a705d4f3b02b905a66cd030f88dd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000322_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_98:0.10913867,2_141:0.03889733):0.02989635,4_223:0.00374306):0.00306094,1_2186:0.00000000,0_222:0.00000000);
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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/OG0000325_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000325_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97e82dc306fc66d65d73466ca2a330e52d2b2751
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000325_tree_id.txt
@@ -0,0 +1,2 @@
+(0_225:0.03919214,((2_128:0.23211533,3_93:1.03918867):0.20111987,1_2189:0.02403961):0.02084989,4_226:0.00762686);
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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/OG0000329_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000329_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b4e8281df69ed33628d025f4c755e5d6d03eb12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000329_tree_id.txt
@@ -0,0 +1,2 @@
+(4_231:0.00000000,((3_88:0.48227317,2_123:0.05038783):0.05595276,0_230:0.00539179):0.00267921,1_2194:0.00000000);
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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/OG0000330_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000330_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b60455e71179aac5c942196586cfd5f5a0af153
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000330_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_122:0.23006850,3_87:0.57881050):0.18146500,0_231:0.03831750):0.02175100,4_232:0.00516825,1_2195:0.02538175);
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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/OG0000334_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000334_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec9f2986c9d245078f5c3613138abc9130dc5812
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000334_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2202:0.00132912,(0_239:0.01374693,4_239:0.00031407):0.00156916):0.02362850,2_113:0.04623583,3_81:0.10129317);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000337_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000337_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3242af32392be65e8970ed56ca32568da312008
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000337_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2211:0.00012840,(4_245:0.00255982,0_246:0.00164818):0.00111420):0.00368633,3_73:0.16461433,2_105:0.00198767);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000338_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000338_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19e83901fa9bc68e0c37a6d09c17d030e56bea72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000338_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2212:0.00169869,((3_72:0.14138783,2_104:0.03789617):0.03238002,0_247:0.00194757):0.00103343,4_246:0.00359631);
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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/OG0000339_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000339_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b24593790e2d5d0049728ced9574a9d5d001c797
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000339_tree_id.txt
@@ -0,0 +1,2 @@
+((4_247:0.00214821,0_248:0.00276379):0.00615419,(3_71:0.47388867,2_103:0.06068433):0.10572246,1_2213:0.00456628);
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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/OG0000341_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000341_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d1e9d0f39261d19d5970f65b3e82939e721f2ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000341_tree_id.txt
@@ -0,0 +1,2 @@
+((4_251:0.01876920,(1_2217:0.00609193,0_253:0.00478607):0.02013750):0.29243513,2_96:0.25711900,3_66:0.77519400);
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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/OG0000342_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000342_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82e938b7748c76c9ec1ebfa139c79fd9e18b77a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000342_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/OG0000343_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000343_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1090a73a253298fe78447caaadd447c4f597f594
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000343_tree_id.txt
@@ -0,0 +1,2 @@
+((4_253:0.01881550,(0_255:0.00000000,1_2219:0.00000000):0.01016150):0.33790950,3_61:0.49599200,2_90:-0.01673200);
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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/OG0000344_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000344_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58886329a9f38ed7baa0ee8c6c8f33eb7692dc96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000344_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_89:0.06622900,3_60:0.08901300):0.00705100,4_254:0.00000000):-0.00000000,0_256:0.00000000,1_2220:0.00000000);
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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/OG0000346_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000346_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b7653eb6e126ae06f25621650fded3b7385c623
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000346_tree_id.txt
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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/OG0000351_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000351_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..115989468262bd775b678f598657595988230719
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000351_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/OG0000356_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000356_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5a9531283c0b611674f058828860073fca2eb14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000356_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2248:0.00281449,((3_40:0.13237300,2_60:0.55289000):0.14587453,0_275:0.04320159):0.03031991,4_281:0.00277351);
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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/OG0000358_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000358_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..406070274e713a4613250513ac4bc1d785e0d821
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000358_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2253:0.00000000,4_286:0.00000000):0.01258525,0_280:0.01449875):0.10246875,3_35:0.41801375,2_56:0.15221925);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000362_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000362_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7408c26fa3f327cdfdd519c3262c94ae3bef9188
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000362_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/OG0000363_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000363_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96e3e0e99bc7cb2a1816b2e5ecb7cb5c2ce90c31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000363_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2:0.00196638,((3_29:0.02898387,2_51:0.04313713):0.00611387,0_285:0.00577812):0.00385288,4_292:0.00002963);
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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/OG0000365_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000365_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d161cf6678e839287b7ca5d6644957fb724eecd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000365_tree_id.txt
@@ -0,0 +1,2 @@
+((3_26:0.13447875,2_48:0.05238025):0.03015925,(1_5:0.00534700,0_288:0.00135300):0.00072225,4_295:0.00492825);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000366_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000366_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb5d6702696c925f4beea791968f2141a3c93ef1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000366_tree_id.txt
@@ -0,0 +1,2 @@
+(0_289:0.00000839,((2_47:0.03550867,3_25:0.15305733):0.03327946,1_6:0.00096938):0.00279012,4_296:0.00588161);
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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/OG0000370_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000370_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dac81d8e526c2eddbc20cef4d39645ac7fd98cf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000370_tree_id.txt
@@ -0,0 +1,2 @@
+(1_18:0.00430325,((3_21:0.41160100,2_25:0.04788400):0.03021156,0_294:0.01074968):0.00421882,4_301:0.00039575);
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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/OG0000373_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000373_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8f41e7bcc609fd59739f73dcc826f85a9c7432e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000373_tree_id.txt
@@ -0,0 +1,2 @@
+(0_298:0.01114777,((3_17:0.29854650,2_21:0.07310050):0.07160280,4_305:0.00463789):0.00474161,1_22:0.00757323);
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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/OG0000379_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000379_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8668de246fe5ef999ca76763d8cb1e5ffaa41b43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000379_tree_id.txt
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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/OG0000382_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000382_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..615e6149233fe1a365ccd30ead01c59d23f379ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000382_tree_id.txt
@@ -0,0 +1,2 @@
+((1_32:0.00000000,4_315:0.00000000):0.00000000,(3_7:0.60008250,2_11:0.12641050):0.08837250,0_308:0.00000000);
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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/OG0000383_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000383_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a83f3098eb259343840ebb5534b3dc8737cad2cb
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000383_tree_id.txt
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+(0_309:0.00000000,((2_10:0.03022717,3_6:0.10265383):0.02118805,4_316:-0.00010436):0.00341036,1_33:0.00000000);
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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/OG0000387_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000387_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7c86d3c16eff2141236552049cfae18a863d00f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000387_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/OG0000393_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000393_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02e33bc02fabf12b5ec880a2d33dbe72cf1ff9e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000393_tree_id.txt
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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/OG0000394_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000394_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8fd325519d3fac54eb959d2235ed5ea38447b34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000394_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/OG0000397_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000397_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28aec81829c172d0409229b4b4bd1d5c191ec9bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000397_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/OG0000401_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000401_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdec570f1f0460ecdd23697ae4c1ab66d4af6a9e
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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/OG0000402_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000402_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32e2dc1eb4487113157e751faf0bff27ff9485d6
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+(4_339:0.00523535,(1_57:0.00721621,(3_2411:0.13251817,2_2552:0.05982083):0.02176724):0.00173379,0_332:0.01145665);
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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/OG0000404_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000404_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..670dd355a1f503161899bbe72d71eff829852ab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000404_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/OG0000410_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000410_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58a8cb8d4b63fa79bd8b02405f8b798c4a121606
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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/OG0000414_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000414_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd46cb0698a9d819ba4ae09a0e66127ac947de0d
--- /dev/null
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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/OG0000415_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000415_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff9a13f9a36b56c02aa6cfbc713afb351f8f8648
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000415_tree_id.txt
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+(4_356:0.00214871,(0_349:0.00558050,(2_2536:0.04665933,3_2395:0.12875467):0.03423283):0.00145300,1_74:0.00333529);
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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/OG0000417_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000417_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb031685271f5e6ca506ce6d72e3ef118e63924f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000417_tree_id.txt
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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/OG0000418_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000418_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9682a1a5196ed8a1f897c11e555ed35f9612d9b8
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000418_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/OG0000423_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000423_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7cb6925164d0224d57ce89f6db0d8b488f4a0db0
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000423_tree_id.txt
@@ -0,0 +1,2 @@
+(0_360:0.00665300,((2_2518:0.08774775,3_2390:0.00829425):0.01120675,1_93:0.00642875):0.00227025,4_366:0.00077600);
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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/OG0000428_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000428_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c7bf8871b3def66804b5f6bb62e625fb227816e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000428_tree_id.txt
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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/OG0000429_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000429_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30c603857221520491f06edc1f3cf742e058c581
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000429_tree_id.txt
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+(1_101:0.00364562,(4_374:0.00999337,(3_2382:0.51136613,2_2511:0.08124287):0.08510513):0.00496213,0_368:0.00332038);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000430_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000430_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ac52ec6fec98088947a97fd63a7c438c4cf68e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000430_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2509:0.09169350,3_2380:0.14667750):0.07801672,0_370:0.00610967):0.00246533,1_103:0.00842013,4_376:0.00009487);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000431_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000431_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1719e22630c24156c7e174de1f8058ae2c2f76a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000431_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_371:0.00000000,1_104:0.00000000):0.00000000,4_377:0.00000000):0.02055350,3_2379:0.22404050,2_2508:0.03225850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000432_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000432_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b93e55268ca02570f8a49db3cb80d8772f7495e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000432_tree_id.txt
@@ -0,0 +1,2 @@
+((1_105:0.02130962,(2_2507:0.24400563,2_162:0.69008837):0.19894488):0.00826837,4_378:0.01315563,0_372:0.04072937);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000434_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000434_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15a5fed3d5e2398e0fde3c6ac6df8ee993281336
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000434_tree_id.txt
@@ -0,0 +1,2 @@
+(1_108:0.00093490,((3_2376:0.09931083,2_2505:0.06544517):0.02977091,4_381:0.00015823):0.00264527,0_375:0.00031010);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000437_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000437_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..142788bd64ae6a45574cc0d007922285635a824a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000437_tree_id.txt
@@ -0,0 +1,2 @@
+((4_384:0.00029780,(0_378:0.00000000,1_111:0.00000000):0.00665920):0.01697110,2_2502:0.02281617,3_2373:0.18793383);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000439_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000439_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11fff9b61a035ce4a73aa72c7fe12c29417b5fb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000439_tree_id.txt
@@ -0,0 +1,2 @@
+((1_113:0.00080500,4_386:0.00392900):0.01296501,(3_2369:0.09197073,2_2500:0.02322027):0.00742050,0_380:0.02294566);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000440_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000440_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c938755e9df74830bfa37eefa8db8671268e8b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000440_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2366:0.10317475,2_2497:0.02433725):0.00971500,1_114:0.00794200):0.00733250,0_382:0.00206725,4_388:0.00992975);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000443_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000443_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5e96c2ac599dbe72489f0be63a137b313529877
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000443_tree_id.txt
@@ -0,0 +1,2 @@
+((1_117:0.00346400,(0_385:0.00251325,4_391:0.00558375):0.00164250):0.00596100,2_2494:0.00703525,3_2362:0.41017675);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000445_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000445_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90fc23600836e12264880bce00aeda5e8f7a14a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000445_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2492:0.01403375,(0_390:0.00000000,1_119:0.00000000):0.00702025):0.01281575,3_2360:0.01322275,4_393:0.01155325);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000447_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000447_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10dc1a263151e588a29c9ced80ec142740eaad73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000447_tree_id.txt
@@ -0,0 +1,2 @@
+((0_393:0.00002593,(1_122:0.00000000,4_396:0.00000000):0.00538407):0.02380814,2_2489:0.01804517,3_2357:0.10673683);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000448_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000448_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad46ac20e26bc5a70303ebe9c40956f20016bcd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000448_tree_id.txt
@@ -0,0 +1,2 @@
+((4_398:0.01428800,1_124:-0.00104300):0.00104300,(2_2488:0.03666100,3_2356:0.27097200):0.04111800,0_395:-0.00104300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000449_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000449_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..132d4092d921c18eb42da0027febaa62d0982b75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000449_tree_id.txt
@@ -0,0 +1,2 @@
+(0_396:0.00074325,(1_126:0.00755325,(3_2355:0.22136150,2_2487:0.04852850):0.02923775):0.01381925,4_399:0.00431475);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000452_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000452_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b6905ff92cdfc5f7ed7c2ac7dcfa669cb38ed88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000452_tree_id.txt
@@ -0,0 +1,2 @@
+((1_130:0.01135035,(0_400:0.00329475,2_2482:0.05573225):0.00096517):0.00424476,4_403:0.02141667,3_2351:0.01897233);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000453_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000453_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e5d79504dcf419b0d7237a91a0d1f0da2ddf408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000453_tree_id.txt
@@ -0,0 +1,2 @@
+((0_401:0.00538649,1_131:0.00083951):0.00433535,(2_2480:0.04700750,3_2350:0.15418550):0.03857474,4_404:0.01825596);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..870f3c4188faeaeb65e1c6065af22dee469bae1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt
@@ -0,0 +1,2 @@
+((4_407:0.03625456,(1_134:0.00000000,0_404:0.00000000):0.01076544):0.08397385,2_2476:0.10800300,3_2346:0.31463100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000457_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000457_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..800d9de2492ce63788122dc0bdc8ae61b71db96c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000457_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2344:0.02158250,2_2474:0.07702950):0.00908925,0_406:0.00128726):0.00231224,1_136:0.01004835,4_409:0.00221965);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa72deec8389d83f78e61b1aadbb36e7d332d5d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt
@@ -0,0 +1,2 @@
+((4_412:0.09007546,(0_409:0.02020965,1_139:0.02140735):0.02339315):0.31058118,3_2341:0.51406183,2_2471:0.53734017);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000463_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000463_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f0e94c9dbcffd6b923b3d09ee0f61e2224f532e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000463_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2467:0.01016300,3_2338:0.02214200):0.00654420,(4_416:0.00000000,0_413:0.00000000):0.00135141,1_143:0.00333059);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000465_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000465_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2717e205971038d9d809c5f7f629de6007bac69d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000465_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_145:0.00000000,0_415:0.00000000):0.00000000,4_418:0.00000000):0.03111050,3_2336:0.06420150,2_2465:0.01523650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000466_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000466_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05552d4bde4ebe0025712fe33dbb9b97725d6788
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000466_tree_id.txt
@@ -0,0 +1,2 @@
+(1_146:0.00251683,((3_2335:0.15290250,2_2464:0.03501150):0.02112957,4_419:0.00392820):0.00529980,0_416:0.00499317);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000467_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000467_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df3345126cd206333dfcb3cdacd654e797969f46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000467_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_147:0.00000000,4_420:0.00000000):0.00148775,0_417:0.00156125):0.04369525,2_2463:0.05753975,3_2334:0.11974625);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ee4d11c5e59ce39382fe9e003d064b98880c9b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2461:0.11351650,3_2332:0.05765250):0.06381075,(4_422:0.00219900,1_149:0.00179700):0.00319625,0_419:0.00759325);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000470_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000470_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adfb55d6b0ea86d0f02e86f5f241bf9de0709811
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000470_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2331:0.14172500,2_2460:0.25487600):0.14823725,(4_423:0.00489250,0_420:0.00741350):0.02871075,1_150:0.01447475);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000473_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000473_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ffd4e7ccf4cda192d5c8b68bd54b5a17f2742f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000473_tree_id.txt
@@ -0,0 +1,2 @@
+((4_426:0.00573550,0_423:0.00294450):0.00144300,(2_2457:0.02805225,3_2328:0.12505675):0.06765550,1_153:0.00722700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000474_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000474_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a10830ea74e885ff66f7e06ee27a76a8c7bd7911
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000474_tree_id.txt
@@ -0,0 +1,2 @@
+((4_427:0.00047596,(0_424:0.00440923,1_154:-0.00076723):0.01003527):0.07464601,2_2456:0.10421600,3_2327:0.35657800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000475_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000475_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6bc611da0822151f59fe1e936e4e9c29dfa64bab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000475_tree_id.txt
@@ -0,0 +1,2 @@
+((0_425:0.01108130,(4_428:0.00203879,1_155:0.00646521):0.00072526):0.02179236,3_2326:0.14090967,2_2455:0.02678433);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9fe07512fbe1eda1507bf400dd9a74aa778ed27e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt
@@ -0,0 +1,2 @@
+(4_432:0.00490290,((2_2450:0.03157683,3_2322:0.25726317):0.00806603,0_429:0.00793660):0.00703290,1_159:0.00104310);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000479_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000479_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05e242d4230d5b88494113019d3f2d0ca41d8aba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000479_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_430:0.02729263,2_2449:0.03836038):0.06172487,3_2321:0.10949412):0.09449588,4_433:0.00248713,1_160:0.00076487);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000482_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000482_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a8842f513df770c3f5e7b2a1c9da29d4c2ed819
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000482_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2318:0.52248500,2_2434:0.10651700):0.07804484,(0_436:0.00872938,1_163:0.00538262):0.00539376,4_436:0.01183248);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000484_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000484_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de575fc292c6949154e51ca18a71d1e8b079c90b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000484_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_165:0.01633396,4_438:0.00579704):0.01001738,0_438:0.01324056):0.11168342,2_2432:0.12234717,3_2316:0.50444083);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000485_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000485_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb1bbb3af222580e7ba2556c881318ab8baf9541
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000485_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_439:0.00000000,1_166:0.00000000):0.00658425,4_439:-0.00029525):0.01775925,2_2431:0.02375175,3_2315:0.12522025);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000486_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000486_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d97e61cc81d0b3835ef0a359bbd20c0e7abb3f1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000486_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2430:0.10305217,3_2314:0.75464783):0.09123725,(0_440:-0.00102094,4_440:0.00775494):0.00102094,1_167:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000489_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000489_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e0edc133ab2e69210b2f38f7a61a26e4d6fc98a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000489_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_171:0.00000000,4_444:0.00000000):0.00000000,0_444:0.00000000):0.10370900,2_2427:0.08082400,3_2310:0.14453200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000495_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000495_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46ec060e57ba563503425c6c76c95703b340a924
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000495_tree_id.txt
@@ -0,0 +1,2 @@
+(1_177:0.00000000,(4_450:0.00697889,(3_2304:0.45429433,2_2421:0.16775667):0.07749930):0.00949911,0_450:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000498_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000498_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a12a23ed1928489ae9d0deeeb939ef2d3bb6cb21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000498_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2417:0.10235825,3_2301:0.35072075):0.08151925,(4_453:0.00000000,0_453:0.00000000):0.00566425,1_180:0.00671675);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000499_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000499_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ecc737ecafe42895a19092a908fe684dca1b05b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000499_tree_id.txt
@@ -0,0 +1,2 @@
+(0_455:0.00000050,((3_2299:0.15445300,2_2416:0.22135500):0.05734850,1_182:0.00525750):0.00293900,4_455:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000502_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000502_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e990864466e5773e85443ca0f52c96684fa5af53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000502_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2413:0.06276583,3_2296:0.37001917):0.10170764,4_458:0.01907543):0.01307557,1_185:0.00705752,0_458:0.01616548);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000503_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000503_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20f80666e5a19e035b564e32c1a28725f37bb146
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000503_tree_id.txt
@@ -0,0 +1,2 @@
+((1_186:0.00692465,(4_459:0.00013235,0_459:0.00414665):0.00444935):0.19424055,3_2295:0.31457233,2_2412:0.16027367);
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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/OG0000507_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000507_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..152070ae4b76444d2f525c5c55356ee60a816924
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000507_tree_id.txt
@@ -0,0 +1,2 @@
+(4_463:0.00253711,((3_2290:0.25429733,2_2408:0.35435967):0.09290296,0_463:0.00578388):0.00311112,1_191:0.00589489);
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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/OG0000510_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000510_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e7a45388d40ae8fbc6a29d6104eba688589b5d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000510_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2286:0.18040373,(1_198:0.01461207,0_468:0.00375393):0.00330734):0.00581348,4_467:0.00038867,2_2403:0.00684233);
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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/OG0000511_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000511_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aecd33969662de7298ac6e4ee24dcd0af5ae351f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000511_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/OG0000512_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000512_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f8277cf696bda3f5a51926c655c3e377b145593
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000512_tree_id.txt
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+(1_200:0.00555965,((2_2401:0.17729117,3_2284:0.09976283):0.05616703,0_470:0.00611560):0.00665340,4_469:-0.00031065);
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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/OG0000513_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000513_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00ec27cf62c2a265010596f026398a72c12fefdd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000513_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/OG0000516_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000516_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7775e31660f6865e8d9a58e5688c6ae2aa446f64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000516_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/OG0000517_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000517_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6523eb7f943d714bbd4b5fff38469d49a11981ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000517_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/OG0000518_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000518_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff058c0c75d830abe794f4c3c9ed64864b8f864e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000518_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2394:0.23486750,3_2277:0.43067350):0.18589645,1_209:0.01718284):0.00728366,0_480:0.02421228,4_479:0.03500272);
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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/OG0000519_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000519_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28f007c6acea0e2e3b576636542f3c963855e6c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000519_tree_id.txt
@@ -0,0 +1,2 @@
+((4_480:0.00846663,(1_210:0.00588487,0_481:0.00672312):0.00464588):0.05286837,2_2393:0.04164788,3_2276:0.17359412);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000520_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000520_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46934dbd8a1cc8b16b4108c99a11538f622c6b7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000520_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2392:0.07262363,3_2275:0.09927037):0.06529788,(0_482:0.00177937,4_481:0.01095963):0.00436238,1_211:0.00699963);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000522_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000522_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..028fe0c73a10093adcb3e16a4fd9e8fdfdea9865
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000522_tree_id.txt
@@ -0,0 +1,2 @@
+((1_213:0.01296491,4_483:0.00753309):0.00423594,(3_2273:0.09418650,2_2390:0.06967550):0.11175097,0_484:0.02234394);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000528_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000528_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7823375eb2441dda073ff2e71a0120bc68529b40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000528_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2256:0.01257582,((4_499:0.01381650,0_499:0.00872750):0.00921862,1_230:0.01874237):0.00266863,2_2374:0.03527918);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000532_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000532_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4377591af3fb81cdc8d2c7e81209555261af8c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000532_tree_id.txt
@@ -0,0 +1,2 @@
+((0_507:0.04528963,(1_237:0.03270138,4_507:0.02923663):0.01304587):0.04733538,2_2369:0.14546287,3_2250:0.39294012);
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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/OG0000533_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000533_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ecd3bc07a7300c10496ef2aee8906e21d1fb7d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000533_tree_id.txt
@@ -0,0 +1,2 @@
+(0_508:0.00411038,(4_508:0.00291188,(2_2368:0.01267763,3_2249:0.13897538):0.01897412):0.00206163,1_238:0.00579662);
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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/OG0000535_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000535_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..461dfb54ede0c2747e6116ed364e428255109a84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000535_tree_id.txt
@@ -0,0 +1,2 @@
+(1_240:0.01060350,((3_2247:0.40307725,2_2366:0.21222875):0.15974325,0_510:0.01096075):0.01810225,4_510:0.01753750);
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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/OG0000536_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000536_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ad27b8abf4751542cb8986e2900bb95f8b65981
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000536_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/OG0000537_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000537_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c734966bf7245e7f6f304ccae8e9c43d439eca7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000537_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/OG0000538_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000538_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e608acf08923b951739f6713cf6e4972f45a8c7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000538_tree_id.txt
@@ -0,0 +1,2 @@
+(4_517:0.00000000,((2_2359:0.04551000,3_2241:0.24172600):0.04234150,1_247:0.01179950):0.01805350,0_514:0.00000000);
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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/OG0000540_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000540_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7137d98ec80d702ceee019d8b8b1be38a8cd59dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000540_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/OG0000549_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000549_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2191882a7ea52237b8db74efaf95cb370adf719b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000549_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_527:0.00000000,4_530:0.00000000):0.00000000,1_261:0.00000000):0.07011650,3_2227:0.18917950,2_2343:0.05705350);
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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/OG0000550_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000550_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81bdc44a4e728928e801ed35b4b5cb652a14138f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000550_tree_id.txt
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+(1_262:0.00000000,((2_2341:0.06287033,3_2225:0.12121967):0.07670351,4_531:0.00053254):0.00115546,0_528:0.00000000);
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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/OG0000551_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000551_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b634ea565226c59990009b6acae2b82020d0b579
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000551_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/OG0000552_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000552_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81eed063431c6cf96df9a83254f92651a3a191b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000552_tree_id.txt
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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/OG0000554_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000554_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c36234f46be339d93fb35b6554f6862be629e13e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000554_tree_id.txt
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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/OG0000555_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000555_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..610b0fc073784b5574216433183e1ab95ad853e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000555_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/OG0000556_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000556_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37cb8606e8c3fcfbb7b79f568343824829b8595c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000556_tree_id.txt
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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/OG0000557_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000557_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..521259964c559920987f87da9c14a1dd5c0167fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000557_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/OG0000558_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000558_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2afeeb8cb3052be76f9f765a0188979c93e1c3fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000558_tree_id.txt
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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/OG0000559_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000559_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ece496a170b45223c1bf631c7151a380017760dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000559_tree_id.txt
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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/OG0000563_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000563_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80d96babf8c0937b51479f8b4647f9fad4c8e252
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000563_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/OG0000567_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000567_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45c50d3e535fd65a3c2578eb36dba21c036b3789
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000567_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/OG0000572_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000572_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c5e67320e60726169d3bdc154b04096c8ab2382
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000572_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2298:0.89455333,1_302:0.05820067):0.01579212,(4_561:0.07714417,0_560:0.05117983):0.05375429,3_2192:0.08459538);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000573_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000573_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9ab3a03e7de57d35d6cf57992c849a3f95d701f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000573_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_711:0.72207663,0_583:-0.09399262):0.13369188,1_1718:-0.09003537):0.24447437,2_2313:-0.06012612,2_710:0.61388313);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000575_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000575_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d94a53deb30776bddba00ff2833880c8cefa791
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000575_tree_id.txt
@@ -0,0 +1,2 @@
+((2_390:0.00000000,0_609:0.00000000):0.00000000,(2_735:1.80487100,4_572:0.09302400):0.01111300,3_2143:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000577_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000577_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1581c3c86e8da2b8e60abee5809c1dc60076438b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000577_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2139:0.12376625,(0_612:0.00000000,4_569:0.00000000):0.03111575):0.33931925,2_1952:0.01439625,4_860:0.13382275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce32aff26c3b725c2165d0e2b350c826509d8e4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2269:0.13870025,(1_363:0.00213475,0_617:0.00606825):0.00371125):0.00540625,4_587:0.00630525,3_2131:0.00601775);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000585_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000585_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..337f6323676b55ca43c745d47515897ad98cfe11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000585_tree_id.txt
@@ -0,0 +1,2 @@
+(0_626:0.00000000,((2_2261:0.01912217,3_2117:0.06475183):0.00621910,1_372:0.01002579):0.00424421,4_596:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000588_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000588_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec7f044456f0579c2a66694290f15952e90d7689
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000588_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_375:0.00000000,4_599:0.00000000):0.00000000,0_629:0.00000000):0.02135600,3_2114:0.07631500,2_2258:0.01001300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4fa5a236b8e41c623a2d20bafdcbaf4e76b3b09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt
@@ -0,0 +1,2 @@
+((4_601:0.00591275,(0_631:0.00000000,1_377:0.00000000):0.01308425):0.04661142,3_2112:0.46003083,2_2256:0.07841017);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000591_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000591_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b68b53aa4ccb8a0c4d0dabd44c4dc967cad5258b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000591_tree_id.txt
@@ -0,0 +1,2 @@
+((0_633:0.00346594,1_379:0.00308706):0.00022178,(2_2254:0.01334333,3_2109:0.14175067):0.01816129,4_603:0.00014467);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da6e138e64e470bc66550d4f8e9e6ffaa8780b81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt
@@ -0,0 +1,2 @@
+((1_380:0.00449426,0_634:0.00188074):0.02572757,(2_2253:0.08859500,3_2108:0.39900600):0.04193030,4_604:0.02304627);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000594_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000594_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3afe5ea9c3dbda1bd2ea0df9e932154d484e565
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000594_tree_id.txt
@@ -0,0 +1,2 @@
+((4_606:0.00910144,(0_636:0.00799913,1_382:0.00275787):0.00438519):0.09954698,2_2251:0.11848667,3_2106:0.44160433);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000595_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000595_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca86e6ed25ad0fd10c37320415bb0187893f5f8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000595_tree_id.txt
@@ -0,0 +1,2 @@
+(4_608:0.00059625,((2_2249:0.09560025,2_1195:2.82543175):0.06571800,0_638:0.03241250):0.03477050,1_384:0.00211575);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000596_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000596_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..925d1456b5c7cd3ca5cd8b5a6bec74291efd26d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000596_tree_id.txt
@@ -0,0 +1,2 @@
+((4_612:0.00343313,(1_388:0.00296362,0_642:0.00791838):0.01303037):0.04889937,2_2244:0.03213388,3_2105:0.20233813);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed949430988cfbf14da60e0fa3d318992354b570
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt
@@ -0,0 +1,2 @@
+((4_613:0.00281305,(1_389:0.00034193,0_643:0.00628207):0.00094866):0.00907307,3_2104:0.09246100,2_2243:0.01743800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000599_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000599_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc3efc9f1116613b0997457e9d3b4958c7e80600
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000599_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_391:0.00000000,0_645:0.00000000):0.00000000,4_615:0.00000000):0.07363650,2_2241:0.05833450,3_2102:0.22160950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000602_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000602_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cba9d0d8a2e84130d7709684dc3f3611db6c8fce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000602_tree_id.txt
@@ -0,0 +1,2 @@
+((4_618:0.00072695,(1_394:0.00281968,0_648:0.00224832):0.00089789):0.06039087,2_2238:0.15070933,3_2099:0.05348767);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000603_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000603_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b9ffb13c5aaf28d044e9104fcdd45b41fee2777
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000603_tree_id.txt
@@ -0,0 +1,2 @@
+((1_395:-0.00005650,(4_619:0.00000000,0_649:0.00000000):0.00343550):0.04351833,3_2098:0.31549250,2_2237:0.02108650);
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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/OG0000604_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000604_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57f584f994296ad0981e19b1332784eb6a0d2b91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000604_tree_id.txt
@@ -0,0 +1,2 @@
+((1_396:0.00000000,0_650:0.00000000):0.00650525,(2_2236:0.10987325,3_2097:0.41384575):0.12732275,4_620:0.00038275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000605_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000605_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd29e62c345033581baacccae933cc8015b28758
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000605_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_397:0.00000000,0_651:0.00000000):0.00000000,4_621:0.00000000):0.02917500,3_2096:0.17280400,2_2235:0.02405200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000606_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000606_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fad0710c0cc3cf329d03faf96c1772ec1bd7f79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000606_tree_id.txt
@@ -0,0 +1,2 @@
+(1_399:0.00252637,((2_2234:0.06122187,3_2094:0.11356712):0.06383087,0_653:0.00799912):0.00117588,4_623:0.00062163);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000608_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000608_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4248bd13678a853190426776b67641adcf606fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000608_tree_id.txt
@@ -0,0 +1,2 @@
+((1_401:0.00389725,0_655:-0.00031625):0.00077050,(2_2232:0.04445075,3_2092:0.22234025):0.02044000,4_625:0.00236500);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbe3852c09e104d189339f0484c365e933f3062c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_656:0.00000000,1_402:0.00000000):0.00000000,4_626:0.00000000):0.06008500,2_2231:0.03499500,3_2091:0.10620600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000610_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000610_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f2239023e6ba356c774ea4b05f89c46bef74b40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000610_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_627:0.00000000,1_403:0.00000000):0.00000000,0_657:0.00000000):0.09633450,3_2090:0.26577550,2_2230:0.12494450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f964862b0db2d9ef5b234df3b904b03c5929d16b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt
@@ -0,0 +1,2 @@
+((4_628:0.00235275,(1_404:0.00000000,0_658:0.00000000):0.00391425):0.08819425,3_2089:0.18216475,2_2229:0.06204125);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000612_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000612_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2285ebd9e2faddb471f8a1c66892fdb2e7a0de19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000612_tree_id.txt
@@ -0,0 +1,2 @@
+(1_405:0.00152737,((2_2228:0.15937067,3_2088:0.23186033):0.13553230,4_629:0.01032289):0.00640961,0_659:0.01951663);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000613_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000613_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..518f9ee25872c94bd366b141e706171a1440d773
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000613_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_630:0.00000000,0_660:0.00000000):0.00866100,1_406:0.00267500):0.19856800,2_2221:0.18445500,3_2087:0.21933700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000619_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000619_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02e9cdbb533f78949f2d0c1483ec50f0b1c9dbc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000619_tree_id.txt
@@ -0,0 +1,2 @@
+((0_667:0.00335920,(1_413:0.00326630,4_637:0.00554470):0.00244400):0.01822212,3_2080:0.16900200,2_2211:0.03546100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000621_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000621_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b550b8522c98642dc866b2bbf41dbcedbe3154e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000621_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_639:0.01283950,0_669:0.01999150):0.03563903,1_415:0.01911181):0.09769998,2_2209:0.18631783,3_2079:0.21164217);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cef7759365c2c56fd0b139a35f687f8c2afdef90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt
@@ -0,0 +1,2 @@
+(4_641:0.02771734,(0_671:0.04123828,(3_2077:0.51318300,2_2207:0.12844400):0.16522109):0.00785772,1_417:0.00792266);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000627_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000627_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86a358e9a243c372580b08ad46af343c5192020b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000627_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2202:0.22781962,3_2073:0.29543838):0.18822388,(4_646:0.01949912,1_422:0.02152788):0.04029887,0_679:0.07142462);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fefca0c006cd2a76b48e892a1b95535014e1ea84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt
@@ -0,0 +1,2 @@
+(0_680:0.00000000,((3_2072:0.04177375,2_2201:0.07185525):0.02345325,1_423:0.00283425):0.00012875,4_647:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000629_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000629_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..832028fdd8d7d7c6d2b545bfa7e307c5af279b29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000629_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2071:0.01568513,2_2200:0.18729888):0.00826088,0_681:0.02183812):0.00805737,4_648:0.01186762,1_424:0.01600837);
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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/OG0000630_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000630_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e3e4e54ab478549958a164d62030a984f3bf8bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000630_tree_id.txt
@@ -0,0 +1,2 @@
+((1_425:0.00380038,(3_2070:0.01409788,2_2199:0.16768712):0.00136812):0.00290613,0_682:0.00516987,4_649:0.00509312);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000631_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000631_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4d36b8ba12a3dcdca1025a9ad89799f92c3e519
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000631_tree_id.txt
@@ -0,0 +1,2 @@
+((0_683:0.00747538,(4_650:0.00606913,1_426:-0.00009312):0.01367812):0.24269962,2_2196:0.01119063,3_2068:0.01902037);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000633_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000633_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a83d9e5d14c6acadd99ff78de0ea8541d0c86eff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000633_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2065:0.07823083,2_2194:0.05163717):0.06431530,1_428:0.00460440):0.00382510,4_652:0.00003145,0_688:0.00637455);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000634_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000634_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cac20d3c176ebfaa7495d1a3a75813aecdae1334
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000634_tree_id.txt
@@ -0,0 +1,2 @@
+((0_689:0.00565349,(4_653:0.00329744,1_429:0.00007356):0.00440174):0.02733402,2_2193:0.03312217,3_2064:0.09657083);
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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/OG0000636_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000636_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da132430a63848ee6e9185aade1f40967516cd04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000636_tree_id.txt
@@ -0,0 +1,2 @@
+((1_431:0.00000000,4_655:0.00000000):0.00000000,(3_2062:0.53960850,2_2191:0.06099750):0.07053650,0_691:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000637_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000637_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba690a8987a1eb9ca9eaf555a2525814efe5ff9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000637_tree_id.txt
@@ -0,0 +1,2 @@
+((1_432:0.00893158,(4_656:0.00000000,0_692:0.00000000):0.01137842):0.03442803,2_2190:0.03744550,3_2061:0.15880050);
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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/OG0000638_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000638_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9618e7c7ce90d2c5198a7d4f8a396f410bcf18d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000638_tree_id.txt
@@ -0,0 +1,2 @@
+((1_433:-0.00003863,(3_2060:0.04588563,2_2189:0.01191637):0.00162312):0.00003863,4_657:0.00370663,0_693:-0.00003863);
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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/OG0000639_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000639_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f36c35bc8807d51c1037bb6d079b1103dfa221b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000639_tree_id.txt
@@ -0,0 +1,2 @@
+(0_694:0.00000000,((3_2059:0.12972325,2_2188:0.01981175):0.03020525,4_658:0.00155025):0.00286975,1_434:0.00000000);
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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/OG0000641_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000641_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ec3289240104cf5ef4161b5ab137b98c9ddeccc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000641_tree_id.txt
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+(1_436:0.00000050,(0_696:-0.00017875,(3_2057:0.10699775,2_2186:0.02382225):0.02110925):0.00318525,4_660:0.00000050);
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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/OG0000642_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000642_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9302920b9336ce57685e760a81c88c7c6d6f8a47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000642_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/OG0000643_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000643_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c94285e2d35f10e688f8908870789f6c8be2e03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000643_tree_id.txt
@@ -0,0 +1,2 @@
+((1_438:0.00000000,0_698:0.00000000):0.00000000,(3_2055:0.57902450,2_2184:0.10305450):0.12413350,4_662:0.00000000);
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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/OG0000644_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000644_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3119a4fe8069c4a0a38050c37a69a897044e2728
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000644_tree_id.txt
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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/OG0000646_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000646_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a851558d1c2bd4d9e8c158db9eb505c78e06034
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000646_tree_id.txt
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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/OG0000649_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000649_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7ab58fff32594b7080eecdc4e1f01401cab073e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000649_tree_id.txt
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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/OG0000650_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000650_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c876da2c34c3c4fe9276ef119b93aba9e64a22a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000650_tree_id.txt
@@ -0,0 +1,2 @@
+(0_706:0.00000000,((2_2171:0.03998033,3_2046:0.11831367):0.02301098,4_670:0.00117493):0.00073207,1_446:0.00000000);
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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/OG0000654_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000654_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1950a3ff3e5977f719471bc97d67deba7aa6d1c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000654_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2144:0.08223633,3_2042:0.35580267):0.08221433,1_450:0.02769899):0.01530101,0_710:0.01186527,4_674:0.01818573);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000655_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000655_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc833b21dfb36db70fa3e470c8495a1b51063c45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000655_tree_id.txt
@@ -0,0 +1,2 @@
+(0_711:0.00000000,((3_2041:0.62585325,2_2143:0.18253075):0.14725125,4_675:0.00952475):0.00391725,1_451:0.00000000);
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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/OG0000656_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000656_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb521e4b1a0a6bc4c11118eec38dc02322ad2987
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000656_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/OG0000659_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000659_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cf28f9002322cc52d750265d9336aec790f033a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000659_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/OG0000660_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000660_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9bd6046838a19de89734bc9034b0e383185c518
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000660_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2033:0.01844975,2_2136:0.05423225):0.00291575,(1_457:0.00355667,4_682:-0.00068267):0.00389989,0_717:0.00832178);
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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/OG0000662_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000662_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4046ff853fe68cbb42002663ee07730c8d16062a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000662_tree_id.txt
@@ -0,0 +1,2 @@
+((0_719:0.00000000,3_2031:0.00000000):0.00000000,(2_2134:0.01072500,1_459:0.00764800):0.00148400,4_684:0.00000000);
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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/OG0000664_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000664_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1a3689f59a0dd230d8a0f30f305adcce99a84d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000664_tree_id.txt
@@ -0,0 +1,2 @@
+(1_463:0.00297175,(4_688:0.00229275,(2_2130:0.03550350,3_2024:0.15939450):0.01406925):0.00199475,0_724:0.00559325);
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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/OG0000666_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000666_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e63a097dc38d12c8357db6c604eb121918d752a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000666_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/OG0000668_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000668_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13cdc851307fe644c4f4ad48a33740f473d7decf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000668_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/OG0000669_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000669_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5133bc34a04eae6992bd3a402b4f8b40c9910cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000669_tree_id.txt
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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/OG0000670_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000670_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed38c0ae29a3253e7451acc4b9628c8dda641287
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000670_tree_id.txt
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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/OG0000674_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000674_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..187fb53d566f55a5c8f659cf4c39c58156829a04
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000674_tree_id.txt
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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/OG0000676_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000676_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67659a0ac68c3797f941f6ea2ca35680194c7974
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000676_tree_id.txt
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+(1_476:-0.00034693,(0_737:0.00604348,(3_2011:0.27774667,2_2116:0.18160833):0.17102083):0.00711702,4_701:0.00903993);
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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/OG0000677_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000677_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f94af96f3e745554e6cf63004d0a9a5e5af6aa6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000677_tree_id.txt
@@ -0,0 +1,2 @@
+(0_738:0.00000000,(4_702:0.00617925,(3_2010:0.17454325,2_2115:0.07133675):0.07146425):0.00261275,1_477:0.00000000);
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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/OG0000680_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000680_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dded82c9e704a11bca7968c7d0c2653916caee5b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000680_tree_id.txt
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+(0_743:0.00469212,((2_2111:0.15029312,3_2006:0.13690888):0.11154712,1_483:0.01243637):0.00744363,4_707:0.02143587);
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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/OG0000684_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000684_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c30898474ef85180113eb4fe06d6782521892149
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000684_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/OG0000686_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000686_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c31c2493ba7097a1ec7aeaba912902f710f36d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000686_tree_id.txt
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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/OG0000690_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000690_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..315155b8a5b5ae8d12e61b4d5f90fa684378dc8b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000690_tree_id.txt
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+(2_2101:0.02241450,((0_753:0.00282575,1_493:0.00255925):0.01646225,4_720:0.00794875):0.01031475,3_1994:0.20324750);
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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/OG0000692_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000692_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fb98a068490ba2f607f46ca5a611a19c22fe083
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000692_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/OG0000698_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000698_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..faedd5f8c3098922475899577f01345c33c3a430
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000698_tree_id.txt
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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/OG0000702_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000702_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e237304eb168afe7b05e40a0e4820e6dcefc84e2
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000702_tree_id.txt
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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/OG0000704_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000704_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27c76d1595967007cd3e514d84ac1e39fe71a26b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000704_tree_id.txt
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+((4_735:0.00329739,(1_508:0.00000000,0_768:0.00000000):0.00030661):0.02829330,3_1979:0.06084817,2_2087:0.01167483);
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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/OG0000706_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000706_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b40f94ca96796396cfa7b8a0398bc4f802095539
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000706_tree_id.txt
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+(3_1977:0.11424208,(0_770:0.00421200,(4_737:0.00000000,1_510:0.00000000):0.01046400):0.00422300,2_2085:0.01384892);
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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/OG0000707_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000707_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c79b7f0bf2a159d1fc0dae6027251260349f1110
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000707_tree_id.txt
@@ -0,0 +1,2 @@
+((0_771:0.00817612,(4_738:0.00906537,1_511:0.02229363):0.02140737):0.17286737,3_1976:0.95127388,2_2084:0.21298213);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000713_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000713_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..acc2acf472084863709fc7ed457658d2225014de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000713_tree_id.txt
@@ -0,0 +1,2 @@
+(1_517:0.01270312,((2_2077:0.18494112,3_1969:0.32023187):0.09973113,0_777:0.02956137):0.01003013,4_744:0.00626188);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000714_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000714_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d51d8cf6810288d0bc7270825528270f8b067b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000714_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2076:0.02203450,3_1968:0.18880150):0.09049506,4_745:0.02151267):0.00646233,0_778:0.00000000,1_518:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000718_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000718_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..223f66ff1b97696822e11a96894525ea8b99f482
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000718_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1961:0.28171550,2_2071:0.06140850):0.05663850,1_524:0.00000000):-0.00000000,4_752:0.00000000,0_783:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000720_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000720_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07527ac43e1577d5c1ae096abd130c18127ada95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000720_tree_id.txt
@@ -0,0 +1,2 @@
+(1_526:0.00000000,((2_2069:0.05163517,3_1959:0.11769683):0.12214614,0_785:0.00869991):0.01429109,4_754:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000726_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000726_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01007ef07b28f326373ce877f5b233408e15b562
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000726_tree_id.txt
@@ -0,0 +1,2 @@
+((4_760:0.00064028,0_791:0.00184572):0.00270149,(3_1953:0.10825483,2_2063:0.13377017):0.22586495,1_532:0.00433322);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9d68bc2f1d6f3e0c2d3a34c3bfe9ecc5053e81d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt
@@ -0,0 +1,2 @@
+(1_535:0.00000000,((3_1950:0.12645350,2_2060:0.04497650):0.05715000,4_763:0.00518500):0.00289900,0_794:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd94f80331d5288c90895b0889925029fe7ba72f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt
@@ -0,0 +1,2 @@
+((4_764:0.00705508,(0_795:0.00000000,1_536:0.00000000):0.01392292):0.10763569,3_1949:0.35563667,2_2059:0.11105233);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000732_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000732_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..544d31416e90e75e2cc407ba15d74e173fc77acb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000732_tree_id.txt
@@ -0,0 +1,2 @@
+((1_538:-0.00009350,4_766:0.00683350):0.00078025,(2_2049:0.10337275,3_1947:0.34516225):0.11565225,0_797:0.03110875);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cd062aa14bed541e0b2b0b9d46706683828318b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt
@@ -0,0 +1,2 @@
+(0_798:0.00000000,(4_767:0.00382962,(3_1946:0.03408650,2_2048:0.06986950):0.02734537):0.00200938,1_539:0.00000000);
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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/OG0000734_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000734_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce12a709cc7ffb364759d1c4e91ff4a043ca158b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000734_tree_id.txt
@@ -0,0 +1,2 @@
+((1_541:0.04059794,(3_1975:0.38915083,2_2083:0.39491017):1.28920881):0.02789606,4_769:0.05887862,0_800:0.01434738);
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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/OG0000736_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000736_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45f73a34aee0e6ee9a95f3da6d76f6f231ebce7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000736_tree_id.txt
@@ -0,0 +1,2 @@
+((0_802:0.00000000,1_543:0.00000000):0.00000000,(4_772:0.00571800,3_1944:0.07942600):0.00061100,2_2046:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de891607cc40a54bedea1034caf27b89508c9cac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt
@@ -0,0 +1,2 @@
+(4_774:0.00000000,(0_804:0.00446375,(2_2044:0.02649725,3_1942:0.17497575):0.02802175):0.00072825,1_545:0.00000000);
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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/OG0000739_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000739_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49c7ac402e1068c258e64b64ded0d07a19436184
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000739_tree_id.txt
@@ -0,0 +1,2 @@
+(4_776:0.00000000,(1_548:0.00096652,(3_1941:0.15488550,2_2042:0.03719250):0.04165001):0.00040148,0_817:0.00000000);
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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/OG0000742_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000742_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e59c40b227108d70f8d3186a88e5286dc21a76f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000742_tree_id.txt
@@ -0,0 +1,2 @@
+((0_820:0.01648575,(2_2039:0.03844725,3_1938:0.11350075):0.02119875):0.03153925,1_551:0.00000000,4_779:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..742a8761aea622430f37bd38025741d79946be95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt
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+(4_781:0.00000000,((3_1930:0.05157050,2_2036:0.02268250):0.01772050,0_822:0.00316700):0.00810100,1_553:0.00000000);
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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/OG0000748_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000748_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f627fd320fcf6cde76b1d384f57f9b9472b5af3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000748_tree_id.txt
@@ -0,0 +1,2 @@
+(0_828:0.00284375,(4_787:0.00260050,(2_2031:0.07858000,3_1924:0.13044600):0.04507750):0.00538250,1_559:-0.00019475);
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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/OG0000753_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000753_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2acdd150e60611a362e5e3774344f2292eaa2380
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000753_tree_id.txt
@@ -0,0 +1,2 @@
+(4_792:0.00715157,((2_2026:0.07216100,3_1919:0.22734700):0.13282424,1_564:0.00532572):0.00073428,0_833:0.01844243);
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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/OG0000754_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000754_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f082cabb9c4680b52ab0d3f85fcb500e3310ebd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000754_tree_id.txt
@@ -0,0 +1,2 @@
+(4_793:0.00424463,(0_834:0.00845287,(3_1918:0.20251612,2_2025:0.04589987):0.03729913):0.00079712,1_565:0.00616638);
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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/OG0000757_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000757_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..691491a530e92f3ebc7cb46ac2991dd26c241494
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000757_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/OG0000760_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000760_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8625bbecf80616f468676d578bbf7436f546513
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000760_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/OG0000763_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000763_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8426d0641ccda3d4347a00715b1dc41f6011fa8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000763_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/OG0000767_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000767_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ce24eb188b236fc75b1d5140da4c7632c99b118
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000767_tree_id.txt
@@ -0,0 +1,2 @@
+(0_847:0.00271075,(1_578:0.00599850,(3_1905:0.18196950,2_2012:0.05762850):0.05574350):0.00151450,4_806:0.00983425);
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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/OG0000771_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000771_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d560300d466968d765d9807e3b99f367a5d0f56c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000771_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/OG0000772_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000772_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08c5cf1278dd574147ff9307690b8be720ed3e48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000772_tree_id.txt
@@ -0,0 +1,2 @@
+(1_594:0.00249050,((3_1897:0.43842275,4_814:0.69237925):0.22126400,2_2000:0.19048050):0.12593600,0_863:0.00540750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000773_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000773_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f8ceffb07fd5a96b35c92b67450e8e38ff5888e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000773_tree_id.txt
@@ -0,0 +1,2 @@
+((4_815:0.00707738,0_864:0.00881963):0.00093363,(3_1898:0.30025687,1_595:0.02006413):0.00547212,2_2001:0.00849688);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000774_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000774_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dbc6fde290da08b7339ef9dd4864ba97ea728dff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000774_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1998:0.04025088,4_816:0.05843213):0.00675762,1_596:0.06421937):0.13023312,0_867:0.10475413,3_1895:0.07512688);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e013a67fa8c2d644de1a836e29c3b0ccea07edd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt
@@ -0,0 +1,2 @@
+((4_820:0.00000050,1_600:0.00000050):0.00100100,(2_1994:0.05556900,3_1891:0.07000800):0.00319150,0_872:0.01928350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9004beb5ccd90440eba9421fd877e13ed4e54fce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_601:0.00000000,4_821:0.00000000):0.00000000,0_873:0.00000000):0.01012000,2_1993:0.00295200,3_1890:0.08909600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000781_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000781_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6efbb7a35a2e6a08f4d7b4e0228574ad4b92416f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000781_tree_id.txt
@@ -0,0 +1,2 @@
+((1_603:0.00359050,(0_875:0.00000050,4_823:0.00000050):0.00139200):0.06929900,2_1991:0.03401950,3_1888:0.15866450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000783_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000783_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75309f03e6364b516e75dda0008d8dc492f78cd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000783_tree_id.txt
@@ -0,0 +1,2 @@
+((4_825:0.00946688,1_605:0.00816512):0.00670587,(2_1989:0.16783687,3_1886:0.31335813):0.09176188,0_877:0.00737662);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000784_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000784_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b8a174525377f64eadccb59047c3d3c7b516b6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000784_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_826:0.00000000,1_606:0.00000000):0.00000000,0_878:0.00000000):0.10016350,3_1885:0.63590150,2_1988:0.21598850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000789_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000789_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd5f3407a76e6b8826cc0fa4fcf6f5f860bd9284
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000789_tree_id.txt
@@ -0,0 +1,2 @@
+((1_611:0.01072810,4_831:0.00878690):0.00702420,(2_1983:0.20774650,3_1880:0.28932250):0.13082225,0_883:0.00916831);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000790_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000790_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..961c08bd50bfd3cf6adde8785630b11fc595f94e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000790_tree_id.txt
@@ -0,0 +1,2 @@
+(0_884:0.02303418,((3_1879:0.36094983,2_1981:0.11070617):0.11236573,1_612:0.01086968):0.00513332,4_832:0.02193582);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..848981385e6f9e0784b4177be1cde3e2cbbb8294
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_613:0.00000000,0_885:0.00000000):0.00431600,4_833:0.00288100):0.03204600,3_1878:0.22871600,2_1980:0.04571300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffe617bd203ec3ae7cae908f69defe309f1ebe57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt
@@ -0,0 +1,2 @@
+((1_617:0.00376151,(0_889:0.00911918,4_837:0.00081282):0.00734999):0.05485501,2_1976:0.09841083,3_1874:0.16711217);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000796_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000796_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f6ce86a0b6033ea22b2f63774f2ac8c6cf5ace4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000796_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1873:0.26134100,2_1975:0.05778600):0.03670275,(1_618:0.00391100,0_890:0.00058600):0.00231425,4_838:0.00898225);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000799_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000799_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ad8e200fb2b7372f9720bc0678a5cabbf7db07f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000799_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1870:0.51781867,2_1972:0.10147233):0.15955392,1_621:0.01498077):0.00426523,4_841:0.00000000,0_893:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000803_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000803_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..384d43144af5d931545150aeecd415c2222c8bf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000803_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_846:0.00000000,1_625:0.00000000):0.00000000,0_897:0.00000000):0.01467050,3_1864:0.35122950,2_1967:0.14397250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000804_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000804_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b906b97e90546c47be9d65ceadb6a47d74fccb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000804_tree_id.txt
@@ -0,0 +1,2 @@
+((1_626:0.00000000,4_847:0.00000000):0.00000000,(3_1861:0.05505550,2_1966:0.00270650):0.00522350,0_898:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4908b9355a52c6563809bde7a6064c6f1cac8de2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt
@@ -0,0 +1,2 @@
+((0_901:0.00160425,(1_629:0.00000000,4_850:0.00000000):0.00421175):0.01956775,2_1962:0.02031675,3_1858:0.07291725);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000808_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000808_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4699821f7646c61314db5de9a4fcf5d39976c42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000808_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1961:0.00574050,((3_1857:0.26760650,0_902:0.00763350):0.00485798,4_851:-0.00091555):0.00406205,1_630:0.01340350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12a6ea2f00d2560edd9f047ed02c301c2c98e2d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1856:0.57813525,(4_852:0.01069875,2_1960:0.01720825):0.00208725):0.00419425,1_631:0.01512875,0_903:0.02425125);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14fd90f465c4634c23ee7f892b55f44dd0e58908
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt
@@ -0,0 +1,2 @@
+((1_633:0.01539663,3_1854:0.32477137):0.00609562,(4_854:0.02005887,2_1958:0.44078013):0.00897313,0_905:0.00597288);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000814_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000814_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49efe9d61ebbb879b45e285abf93410530ae115e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000814_tree_id.txt
@@ -0,0 +1,2 @@
+((1_636:0.00812300,0_908:0.00325000):0.00205600,(3_1851:0.03999475,2_1954:0.12589025):0.01051000,4_857:0.00662250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec0aa14ed93403af3a5bd442d279f13a6506fe19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt
@@ -0,0 +1,2 @@
+((4_867:0.00605012,(3_1841:0.05748113,2_1890:0.08917788):0.01118837):0.00255888,0_921:0.00215663,1_643:0.00642838);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68cc28c13656c509038b78c5c172d08e3f76cab5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt
@@ -0,0 +1,2 @@
+(4_870:0.01431513,((3_1838:0.20213337,2_1888:0.36999862):0.07924763,1_646:0.00558338):0.00399962,0_924:0.00430687);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000824_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000824_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..235e1f204add1d22be9731174734e415980c8f5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000824_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1828:0.21659950,2_1881:0.07060350):0.07773807,(1_652:0.00906266,4_876:0.00801934):0.00179907,0_930:0.00612934);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69dab15b5fb9a58c0bdd4c7f1ecf49745e6d593a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1822:0.14199267,2_1876:0.03698733):0.00884169,1_660:0.00412507):0.00184293,4_880:0.00549190,0_937:0.00706210);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..336c1ac4c7eb63437b0142dc95ad35e62eeeca5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt
@@ -0,0 +1,2 @@
+((0_938:-0.00048525,(3_1821:0.07851425,2_1875:0.00589475):0.00225975):0.00674525,1_661:0.00000000,4_881:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000831_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000831_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..236e0215160eaad361bc77192994154adf7c77e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000831_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_883:0.00000000,1_663:0.00000000):0.00000000,0_940:0.00000000):0.02795950,3_1819:0.03928950,2_1873:0.01467850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..303341eb39aa363df10f049abf7d18edf83e27df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1815:0.00469712,(4_886:0.00127862,2_1869:0.14504138):0.00110338):0.00176688,1_666:0.00171487,0_943:0.00164213);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a777ab59314acd1caf4056211885e0ae45a848dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt
@@ -0,0 +1,2 @@
+(0_944:0.00000050,((2_1868:0.17405925,3_1814:0.00469575):0.00328625,1_667:0.00390025):0.00208125,4_887:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e93532ac8698a4fea1adcff55c285aa7cc3c9709
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_947:0.00085275,4_890:0.00417425):0.00748575,3_1811:-0.00041825):0.00039275,2_1865:0.01025625,1_670:0.00391375);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ce34172a35ed8ac08c33152cfeb356c16460a0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt
@@ -0,0 +1,2 @@
+((4_892:-0.00001188,(1_672:0.00536387,0_949:-0.00001187):0.00001188):0.00388187,3_1809:0.00327487,2_1863:0.00507312);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000841_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000841_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..801e6ebebc6fe6d97e511e966c15b9907564e0b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000841_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_893:0.00000000,0_950:0.00000000):0.00138114,1_673:0.00184286):0.02277679,2_1862:0.01656983,3_1808:0.01165717);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8abfc5fd12d8e5e7ab20af1ff0470baa53103f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt
@@ -0,0 +1,2 @@
+((1_674:0.00390109,4_894:0.00160891):0.01112305,(2_1861:0.03080433,3_1807:0.00968067):0.01612777,0_951:0.00438916);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000844_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000844_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6df591af3b8eaff7ad0ce3808d073760af06de36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000844_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1803:0.09738163,2_1857:0.01585737):0.01060337,(1_678:0.00253988,4_898:0.00361712):0.00074388,0_955:0.00310912);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000848_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000848_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a2bbbc180bfaf016b64b5fd2b292f3f82fa03e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000848_tree_id.txt
@@ -0,0 +1,2 @@
+((1_683:0.00000050,0_960:0.00000050):0.03563686,(2_1853:0.23462833,3_1780:0.25053867):0.21569055,4_903:0.05926864);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000849_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000849_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22a84b431e016454489335310533181127ee08ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000849_tree_id.txt
@@ -0,0 +1,2 @@
+((1_684:0.00000000,(3_1779:0.03479050,2_1852:0.01061850):0.01049050):0.00000000,4_904:0.00000000,0_961:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e31286af4058c54a4a61cfc9d1c7b60bbba54f0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt
@@ -0,0 +1,2 @@
+((1_685:0.00000000,(4_905:0.00000000,0_962:0.00000000):0.00000000):0.00000000,2_1851:0.00000000,3_1778:0.06414400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2c2e6454acf8cefcd6323081faf85d491e3e6fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_906:0.00000000,1_686:0.00000000):0.00000000,0_963:0.00000000):0.04330900,2_1850:0.02265800,3_1777:0.11183800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000852_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000852_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cf921b7de97b544e6ef788141db7a730e2872bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000852_tree_id.txt
@@ -0,0 +1,2 @@
+(4_907:0.00866540,(0_964:0.00267248,(3_1776:0.19475483,2_1849:0.05048917):0.06749933):0.00334952,1_687:0.00266360);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000853_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000853_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22ce32d08fefeba33144dd64b90a44694b91f382
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000853_tree_id.txt
@@ -0,0 +1,2 @@
+((4_908:0.00204503,(3_1775:0.22290550,2_1848:0.05612550):0.04717184):0.00813547,0_965:0.00001268,1_688:0.00058432);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000854_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000854_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..711fa5aafd2b5cc37a1e2cf3486f981f00a12b87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000854_tree_id.txt
@@ -0,0 +1,2 @@
+((4_909:0.01557800,(1_689:0.00000000,0_966:0.00000000):0.00186200):0.07518467,2_1847:0.07159933,3_1774:0.31055467);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae3f34eb2ce4587ffefcaaddf3e69eb1960ac351
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1846:0.03943983,3_1773:0.18597517):0.01749494,(0_967:0.00000000,1_690:0.00000000):0.00402067,4_910:0.02258333);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000856_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000856_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72c5d2bce30cdd37abf5fe0e23616303a22b91a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000856_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1845:0.05741900,3_1771:0.10204900):0.04540400,(1_691:0.00000000,0_968:0.00000000):0.00979650,4_911:0.00501850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000857_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000857_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55e68aa9e82c498b62a48477244778689f041be6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000857_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_692:0.00000000,0_969:0.00000000):0.03559709,4_912:0.01466491):0.15648714,3_1770:0.32748817,2_1844:0.21317583);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000858_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000858_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6bee8b0e00fa0d0ddf142a38b801ec7fcd163056
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000858_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1206:2.79150900,2_1838:0.01188900):0.00616450,1_696:0.00262900):0.00186750,0_973:0.00000050,4_916:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000861_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000861_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f7dbda88aec9775e2eee9dfcb64baf800a7ec53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000861_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1832:0.15029250,3_1723:0.47130650):0.10093137,(1_701:0.01284529,0_978:0.02154671):0.01106231,4_922:0.00810904);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..971601fb782fb3b4bd1d5e209a08dffc31f38b1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt
@@ -0,0 +1,2 @@
+((1_706:-0.00357250,(4_926:0.05242450,0_982:0.00001350):0.01328050):0.11994750,3_1721:0.24688175,2_1829:0.09799025);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000866_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000866_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4af4379cf97df379801a0ebce78537219070ecdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000866_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1825:0.02289262,4_927:-0.00057263):0.00057263,0_983:-0.00057263):0.00057263,1_707:-0.00057263,3_1714:0.06833562);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000867_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000867_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebb8aab9f2837777549fd19713e1056ba21f3d4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000867_tree_id.txt
@@ -0,0 +1,2 @@
+((1_708:-0.00057312,(0_984:0.00214712,4_928:-0.00057312):0.00057313):0.04785713,2_1824:0.01765512,3_1713:0.28055487);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee7bd889087c54a5b7cb753de6df585a3779d283
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt
@@ -0,0 +1,2 @@
+(0_985:0.00000000,((2_1823:0.01146300,3_1712:0.07448800):0.00619175,4_929:0.00268626):0.00150474,1_709:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000869_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000869_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa857b86e251469f6bfd5ecd9ffdce620677791d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000869_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1708:0.06369850,2_1822:0.02616250):0.02872625,(0_986:0.00365775,1_710:0.00399925):0.00227775,4_930:0.00231625);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000871_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000871_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5112835311a1059293488328460ba34d653d9a10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000871_tree_id.txt
@@ -0,0 +1,2 @@
+((1_715:0.02924945,(3_1703:0.01910275,2_1814:0.01933925):0.00612125):0.02717538,4_935:-0.00059383,0_991:0.00264883);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000873_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000873_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a095c9ef80449b839d66ae58c16d3ed76eb349f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000873_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_717:-0.00005563,0_995:0.00891963):0.00420138,4_937:0.00580113):0.00030438,2_1812:0.01279338,3_1701:0.00048162);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000874_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000874_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24df190fb9f0e858f9a9dbd12f0ac2bc5c04f811
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000874_tree_id.txt
@@ -0,0 +1,2 @@
+((4_938:0.00120414,(3_1700:0.02472429,2_1811:0.01354371):0.00328309):0.00824808,1_718:0.00445767,0_996:0.00043133);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2d3d51d226b4198ec98738923e80ffcaed1b81b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt
@@ -0,0 +1,2 @@
+((4_940:0.00582075,(0_998:0.00686475,1_720:0.00721425):0.02997875):0.14865575,3_1699:0.22657900,2_1810:0.05311500);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18699682670fcc10a01fabfbb62a71624da9f6da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt
@@ -0,0 +1,2 @@
+(2_525:0.45230463,((1_724:0.01112837,4_943:0.00551862):0.24686787,0_1002:0.28395612):0.10703488,3_1697:0.78252138);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000878_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000878_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3cc51f9d8ffd9fb3f4c4f125fed57effdbf10e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000878_tree_id.txt
@@ -0,0 +1,2 @@
+(1_726:0.00939047,(4_945:0.00337901,(3_1694:0.12114350,2_1808:0.14452450):0.05053650):0.00085699,0_1004:0.00428253);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000879_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000879_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb24e255a0e17eaacb09ee77a06d9e5219c43d32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000879_tree_id.txt
@@ -0,0 +1,2 @@
+((1_727:-0.00012037,(4_946:0.00091363,0_1005:0.00093237):0.00178288):0.05013537,3_1693:0.03880787,2_1806:0.04699113);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d188179490568c85552d192d5bf8ad98186d1f7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1007:0.01997214,(4_948:0.00710866,1_729:0.00502934):0.00722247):0.07408773,2_1804:0.06203583,3_1691:0.21388517);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000884_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000884_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5acc5a13dfcacf847aa8cceb01eeedc814feb2b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000884_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1010:0.00041550,4_951:0.00120150):0.00679350,1_732:0.01115100):0.03275450,3_1688:0.12261300,2_1799:0.04407600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000890_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000890_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f4171e6335483b038aa34e1e8f1d3ce6bc69c0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000890_tree_id.txt
@@ -0,0 +1,2 @@
+((4_963:0.00790837,(0_1016:0.00024663,1_744:0.00918737):0.00880712):0.02461462,2_1793:0.06519938,3_1682:0.16773963);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000892_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000892_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbf91341ec2befd37cb6670fadfe8a3a435380b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000892_tree_id.txt
@@ -0,0 +1,2 @@
+(4_965:0.02062375,((2_1791:0.29362225,3_1680:0.24905275):0.12976425,1_746:0.01222375):0.00889625,0_1018:0.01183525);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27728b688a37f0c64e8385422dd94d7bbe3d0d85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_968:0.00000000,1_749:0.00000000):0.00357701,0_1021:-0.00022101):0.07641983,2_1789:0.07171583,3_1677:0.16207417);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0a6c747d101a833ff08467854dfde69d76f207b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1033:0.00000000,1_761:0.00000000):0.00000000,(3_1674:0.08782600,2_1788:0.00300300):0.00300300,4_982:0.00000000);
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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/OG0000896_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000896_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86438ac8fa8b7f144cf10e09eac189b9a2f9e660
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000896_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_984:0.00000000,1_763:0.00000000):0.00432250,0_1035:0.00277950):0.02015300,3_1672:0.09406750,2_1786:0.05781850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000900_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000900_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a5826f28a37c373c8e94276de018932c281047a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000900_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1039:-0.00183675,(1_767:0.00000000,4_988:0.00000000):0.00667975):0.11414175,2_1781:0.12898675,3_1668:0.42343025);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2767611659e1dce44841138b0e1b061b2811d91e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt
@@ -0,0 +1,2 @@
+((4_990:0.00097927,1_769:0.00073173):0.00397965,(3_1666:0.08844633,2_1779:0.02223767):0.01905884,0_1041:0.00500896);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d3ebd96ade6df846ee4ce91efc866f570d8381b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_991:0.00000000,1_770:0.00000000):0.01627750,0_1042:0.01106350):0.02298200,2_1778:0.02690800,3_1665:0.25370600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70e2301b6a4cb2b6645c91a33477b8e8b06ebc4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1045:0.00138374,1_773:-0.00036674):0.00281334,(3_1662:0.04713950,2_1774:0.27810650):0.04140064,4_994:0.00009840);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f9e7c671813ee7981a6d8b830db923dafba3a91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1773:0.04667225,3_1661:0.07707775):0.04465550,0_1046:0.00406050):0.00166900,4_995:0.00212300,1_774:0.00307700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74b730a25b93afebcf90d35efc0624eafa320939
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt
@@ -0,0 +1,2 @@
+((4_996:0.00000000,1_775:0.00000000):0.00000000,(2_1772:0.07254850,3_1660:0.19647250):0.05998350,0_1047:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000910_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000910_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2c1827cda638447529899ab45a56ee941c7aed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000910_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_998:0.00000050,1_777:0.00000050):0.00000000,0_1049:0.00000050):0.17185500,3_1658:0.37162250,2_1769:0.15704450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000912_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000912_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03e5d88c1fc77bf35334eef51d473d63d1e3e05a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000912_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1656:0.12819900,2_1767:0.11860600):0.05612400,1_779:0.00000000):-0.00000000,0_1051:0.00000000,4_1000:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e28c8971fa4775287b616fd7a9f7031877b27ee5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1052:0.00000000,4_1001:0.00000000):0.00000000,1_780:0.00000000):0.07633650,3_1655:0.11338950,2_1766:0.06326650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000914_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000914_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f2b048eabc63c678aa3e482e6b02faa2e559d75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000914_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1002:0.05351177,(2_1765:0.02372183,3_1654:0.14152317):0.09222576):0.00864823,0_1053:0.00000000,1_781:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94083ecbf2ab7b531ad8a096a1a00a3f688a5c06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1054:0.00935674,1_782:0.01730726):0.00687721,4_1003:0.02198008):0.10995747,3_1653:0.28380283,2_1764:0.08894717);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000916_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000916_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..743dc5cbfa5992729c3cc35badce5ab14a890241
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000916_tree_id.txt
@@ -0,0 +1,2 @@
+(1_783:0.00288162,(0_1055:0.00579437,(2_1763:0.04023963,3_1652:0.16754938):0.04305012):0.00206412,4_1004:0.00719137);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94d3651f59387b3cf57a55e20d0d563abc749d05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt
@@ -0,0 +1,2 @@
+(1_787:0.00000000,((3_1648:0.48208783,2_1758:0.11571517):0.13306176,0_1059:0.00390378):0.00388722,4_1008:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000922_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000922_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1019017a39b93314299d27881b6acb7639a64615
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000922_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1063:0.01300590,(1_791:0.00000000,4_1012:0.00000000):0.02384110):0.09043347,2_1752:0.16946783,3_1644:0.49749817);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d7e24b76f99c2c1432ecddd091cd751dfef0d00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1064:0.02579295,(3_1643:0.90143300,2_1751:0.34818900):0.29099098):0.00628005,1_792:0.00000000,4_1013:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a596ece51c34abaf62cd951dea2745393426dd31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1068:0.00247184,(4_1018:0.00118125,1_796:0.00058875):0.00186349):0.01438484,2_1748:0.02010200,3_1640:0.09550600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000926_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000926_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63bbb25d80fda00069c94bc1267ec0feaf21d9ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000926_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1747:0.01502896,(4_1019:0.00000000,1_797:0.00000000):0.00268504):0.00319399,0_1069:0.00611933,3_1639:0.21563367);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1cafaa9dd8b9c88982da4fa5eb09a3f8d2f97800
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1746:0.02943450,3_1638:0.18469950):0.00191150,0_1070:0.01195077):0.01279723,1_798:0.00000000,4_1020:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85325a5f8901ce82b254f9a750ab685d60315b10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1029:0.00060137,((3_1629:0.13964662,2_1736:0.03997037):0.03171388,1_807:0.00223513):0.02142637,0_1079:0.00140763);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000935_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000935_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e05fff45c6032f017c72659c364f20cc630f6066
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000935_tree_id.txt
@@ -0,0 +1,2 @@
+(1_808:0.00048549,((2_1735:0.04671783,3_1628:0.16592117):0.06526791,4_1030:0.00062123):0.00482427,0_1080:0.00247351);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4024088af174af5099818a25152c9b04f436c11c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1032:0.00000000,0_1082:0.00000000):0.00000000,1_810:0.00000000):0.02922400,3_1626:0.19309200,2_1733:0.02594400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000938_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000938_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40670dd0665e73c9abcd7dcd5a5ce0636a196530
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000938_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1083:0.00000000,4_1033:0.00000000):0.00000000,1_811:0.00000000):0.02479350,3_1625:0.07660650,2_1732:0.01935350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000940_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000940_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6e68aa8a587992737ab40671f159a509c4f4de0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000940_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1035:0.00037200,(0_1085:0.00000050,1_813:0.00000050):0.00252650):0.04272100,3_1623:0.19615050,2_1730:0.05258050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c7c9ccced12e3191293ec4eadf21294a0bc3284
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1725:0.07717775,3_1618:0.30464525):0.05033325,(1_818:0.00000000,0_1090:0.00000000):0.00304625,4_1040:0.00773675);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e115321089b554d9f00cb711fb09c5519d2c5195
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1617:0.31232350,2_1724:0.06627650):0.03281350,1_819:0.00000000):0.00000000,0_1091:0.00000000,4_1041:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..051f46500c5884ad35a9f0b2b5640da2210fcfa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1042:0.00043725,1_820:0.00111275):0.00059575,0_1092:0.00095425):0.01103925,2_1723:0.01404500,3_1616:0.04225700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000952_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000952_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca6ed3d89682e05179eb1b88f6c54c337149cf6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000952_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1717:0.01429100,3_1611:0.06755800):0.00668300,(0_1097:0.00394175,1_825:0.00001125):0.00184550,4_1047:0.00162100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5520943e12b87f19fad8ace3bc39c6c6db00e55f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1098:0.01560618,(2_1716:0.12086983,3_1610:0.20624717):0.07689989):0.00813582,1_826:0.00000000,4_1048:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b38c09cca30f3632e633fa6e8a9452781fc41936
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1100:0.00859550,(2_1715:0.15511125,3_1608:0.50047375):0.15791900):0.01923850,4_1050:0.00985425,1_828:-0.00130325);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000956_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000956_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..123243c51f2473454f4967aaf648c89b8c554a07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000956_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1053:0.00000000,(0_1103:0.00204429,(2_1712:0.05995267,3_1605:0.26919033):0.03500643):0.00171871,1_831:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a7b276d028dd06bb0a83e93fa701440cc94cc0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1105:0.00215050,(1_833:0.00000000,4_1055:0.00000000):0.00366350):0.07581400,2_1710:0.22610050,3_1603:0.10141350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000959_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000959_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8c4f981d8b49fdf34194f9448a0ee5c0987913a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000959_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1107:0.00000000,4_1057:0.00000000):0.00000000,1_835:0.00000000):0.00864550,3_1601:0.01170950,2_1707:0.00864550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000960_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000960_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e3ce2e8e0a3f45bc5e480e987832b2aa7dace95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000960_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_836:0.00000000,4_1058:0.00000000):0.00000000,0_1108:0.00000000):0.06448650,2_1705:0.03734750,3_1600:0.18075350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7277aa2c5705f9a348d8e56ff3e250e39339ad6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt
@@ -0,0 +1,2 @@
+((1_843:0.00496332,(0_1115:0.00174177,4_1065:0.00292023):0.00321873):0.05050454,3_1594:0.10285483,2_1698:0.03938517);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000968_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000968_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2635b25e4960899a2a657e65060060f37882e480
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000968_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1068:-0.00022775,(3_1591:0.29281975,2_1695:0.19806425):0.11157225):0.00158575,1_846:0.00000000,0_1118:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c5c7d9994bf04d56ee55a6b358857c51009ec72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1693:0.03738600,3_1590:0.21217000):0.03734875,(1_847:0.00395600,0_1119:0.00224300):0.00421225,4_1069:0.00312275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4251ca46e9add79492cb8455d28fa1f6dbca5fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt
@@ -0,0 +1,2 @@
+(1_848:0.00000000,((2_1692:0.08480200,3_1589:0.07956900):0.08227450,4_1070:0.00321550):0.00321550,0_1120:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000973_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000973_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74e2aa3ea950e1696ab9ea782945beed9fbba70c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000973_tree_id.txt
@@ -0,0 +1,2 @@
+((1_851:0.00605025,(4_1073:0.00000000,0_1123:0.00000000):0.00106275):0.05862275,2_1689:0.06342175,3_1586:0.15619825);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000977_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000977_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32afa3ab62d7303965d433a00cfe4a065eb8f717
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000977_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1685:0.02264212,3_1582:0.17831288):0.01333837,(1_855:0.00271487,4_1077:0.00019213):0.00026687,0_1127:0.00155312);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000979_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000979_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..578d39d1764f604d2dc6dfdf2f329098b016d13a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000979_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_857:0.00207600,0_1129:0.00098600):0.00170225,4_1079:0.00887425):0.00299025,2_1683:0.01024950,3_1580:0.26897150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1caa80b61abe621b01980281dfd3346801fd5ddc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1081:0.00529375,(3_1578:0.34956825,2_1681:0.01034175):0.00728825):0.00078525,0_1131:0.00000000,1_859:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2385b9f27b133efe75fb66672cea6f6ff47604d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1577:0.28176625,2_1680:-0.00396225):0.00369375,(0_1132:0.00000000,1_860:0.00000000):0.02121650,4_1082:0.02527050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1c3ddd330093fed28c24537d01c6db1d775a8dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1675:0.11287038,3_1573:0.45003962):0.07649763,(4_1086:0.00421988,0_1136:0.00546212):0.00506962,1_864:0.00936987);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcfe0709d09c21b083e99e4af947b66495c06ade
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1087:0.00000000,0_1137:0.00000000):0.00000000,(3_1572:0.56200650,2_1674:0.11727250):0.06973650,1_865:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000989_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000989_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19a677f6c0a0ac15b69317bc9805576ffcef978e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000989_tree_id.txt
@@ -0,0 +1,2 @@
+((1_868:0.00885567,(0_1140:0.00000000,4_1090:0.00000000):0.00362133):0.14236839,2_1671:0.21153583,3_1569:0.35236317);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000990_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000990_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d43cdda72eec4556c1dbea590eb546d32ee9551
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000990_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1141:0.00000000,4_1091:0.00000000):0.00000000,(3_1568:0.10642400,2_1670:0.01585200):0.01237800,1_869:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..076a66654a98b6e299b4eecd10953273ac25276a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1567:0.18821919,(1_870:0.00200125,2_1669:0.02577875):0.00281825):0.00235581,0_1142:0.00000000,4_1092:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d1e511e109dd4dcb86ec8aa069cc55499b86499
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1093:0.00000050,((2_1668:0.06057625,3_1566:0.21117275):0.06079975,1_871:0.00743125):0.00271225,0_1143:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000993_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000993_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9b3dc8c1ace8ffdda4cc2d6548a7b778c1b20fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000993_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1144:0.00000000,4_1094:0.00000000):0.00463547,1_872:0.00504153):0.13844234,2_1667:0.06658017,3_1565:0.44134883);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000994_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000994_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f69df623dda7cea5eeff9ca021ae0716d8e35a83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000994_tree_id.txt
@@ -0,0 +1,2 @@
+((1_873:0.00885025,(3_1564:0.32406033,2_1666:0.08643467):0.09627242):0.00155625,4_1095:0.00407448,0_1145:0.00345552);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000995_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000995_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8bd51c149287fef1e7ca1d1e5f090f0628adf5d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000995_tree_id.txt
@@ -0,0 +1,2 @@
+((1_874:0.01142850,(0_1146:0.01133275,4_1096:0.00106925):0.00811950):0.11766500,3_1563:0.56858375,2_1665:0.09624225);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000999_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000999_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05e8080a85266bec9340f7d6a02c2c3a5b316405
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000999_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1104:0.00000000,1_879:0.00000000):0.00011119,(2_1660:0.05179567,3_1556:0.09935433):0.06313827,0_1150:0.00439681);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001004_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001004_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9bdbd2d41cba54060d5e3c717219714b5fb389c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001004_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1654:0.02698763,((0_1156:0.00529512,4_1113:0.01056388):0.04312087,1_884:0.02089463):0.02844437,3_1551:0.13158938);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001006_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001006_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5455d95c3939386db572097cb6bc7633624fe0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001006_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1158:0.01874891,((3_1549:0.17019450,2_1652:0.01793750):0.01648870,1_886:0.00754461):0.00263839,4_1115:0.00499709);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001010_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001010_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd8127a1477c3bd763eb999d28682c43fcccc8f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001010_tree_id.txt
@@ -0,0 +1,2 @@
+((1_890:0.00912662,(4_1119:0.01020262,0_1162:0.00561038):0.00476487):0.03436887,2_1648:0.03183663,3_1545:0.20835138);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cae1d872920f7022101fdc59b32a25e3b0f35fe6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1163:0.01021250,((3_1544:0.63744425,2_1647:0.08689275):0.06172600,1_891:0.01311350):0.00729100,4_1120:0.00120050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f710a7a7983a213085ae939fa920f052894f016
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1164:0.00000000,4_1121:0.00000000):0.01273290,(3_1543:0.14831417,2_1646:0.28594683):0.01397653,1_892:0.00925810);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddbd1402f87cd2f10b18595f434eadbf3e6748f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1169:0.00000000,(3_1538:0.09421550,2_1642:0.04738550):0.03105050):0.00000000,1_897:0.00000000,4_1126:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001018_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001018_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6013e74a93d001267dc97b41a2de1d32653969f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001018_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1171:0.00286475,(1_899:0.00330800,4_1129:-0.00005400):0.00643225):0.07458125,2_1640:0.08078450,3_1536:0.25010650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001021_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001021_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a1dfc8dc3f30b3bd2c7320decdeb4b2051c9831
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001021_tree_id.txt
@@ -0,0 +1,2 @@
+(1_902:0.00702305,((3_1533:0.11109217,2_1637:0.07324083):0.02874286,0_1174:0.00185807):0.00162943,4_1132:0.00695995);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001022_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001022_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1e3fd6bfb3f14a3f42c968865ad4560d93fc533
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001022_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1133:0.00594816,0_1175:-0.00053116):0.00053116,(2_1636:0.05334150,3_1532:0.41922450):0.05413862,1_903:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001023_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001023_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..416e747b7152a9b23e0fab65b6ac4a729d129a3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001023_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1135:0.00046577,1_905:0.00244823):0.00383651,(3_1531:0.06430667,2_1634:0.01334933):0.01492758,0_1177:0.00588041);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cca61287e3297d134078ad341b60ca6860b2fc2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1178:0.01043688,4_1136:0.00689012):0.01259963,(3_1530:0.38811212,2_1633:0.20950388):0.21976363,1_906:0.02223987);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a77ff312bcfa815a3316bc2f38263f046adc9d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt
@@ -0,0 +1,2 @@
+((1_907:0.00000000,2_1632:0.00000000):0.00000000,(3_1529:0.12464550,0_1179:0.01202750):0.01664450,4_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/OG0001026_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001026_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..766a0652f5ac5bc8eb7236a721eab4c6e9adf0e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001026_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1180:0.00367166,(4_1138:0.00000000,1_908:0.00000000):0.00679234):0.04699389,2_1631:0.04487267,3_1528:0.17784333);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5db4753b485f57805cbe570d8369359e32f9ef09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1140:0.00232651,1_910:0.02489249):0.08131761,0_1182:0.17744408):0.22233728,2_1629:0.38074717,3_1526:0.56233883);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001032_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001032_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fcc35d30b673c762a72493d37663a594b69f754
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001032_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1144:0.02012834,(1_914:0.02988696,0_1186:0.04022904):0.00795638):0.14357615,3_1522:0.23271067,2_1625:0.19215733);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001034_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001034_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..330cbf2af7539b85269b738cd6b056cb451271c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001034_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1146:0.00224284,(1_916:-0.00015695,0_1188:0.00393495):0.00043111):0.01696251,2_1623:0.02733617,3_1520:0.12576383);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa0063c595fedcf9797b286f3c7e625506c240c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt
@@ -0,0 +1,2 @@
+((1_919:0.00000000,(0_1191:0.00285736,4_1149:-0.00047936):0.00047936):0.04373418,2_1620:0.03120867,3_1517:0.17353333);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001038_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001038_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2116b82659555e7faf6970bfcfcad43082e2219
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001038_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1516:0.22728900,2_1619:0.04159200):0.10882950,(0_1192:0.00000000,4_1150:0.00000000):0.01132900,1_920:0.02800200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b64a007cf1327da04b4f0a3c00b41efbd66c72c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1193:0.00266937,4_1151:0.00004863):0.00284038,1_921:0.00125263):0.11677387,2_1618:0.08404612,3_1515:0.25292987);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001042_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001042_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63ca7fac1335e15dcf09c3e2e49e600f6778ecd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001042_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1154:0.00000000,0_1196:0.00000000):0.00000000,(2_1615:0.11342650,3_1512:0.34509150):0.10719050,1_924:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001047_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001047_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b45f58eef4a55ffc88c440faf0d004a12d29f902
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001047_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1159:0.00000000,((2_1609:0.04009450,3_1506:0.11280750):0.03654150,0_1201:0.00493900):0.00033600,1_929:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001050_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001050_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1f61bc3e9f9389f03e0af87d71aa14ec3f50d6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001050_tree_id.txt
@@ -0,0 +1,2 @@
+((1_932:0.00000000,4_1162:0.00000000):0.01006450,(2_1606:0.11092700,3_1503:0.36782300):0.10469000,0_1204:0.01660650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a644335a05ee04dcab97273d4d733229f6353a48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1501:0.31808205,(0_1206:0.02208825,2_1604:0.11077975):0.01924575):0.01390628,1_934:0.01161933,4_1163:-0.00175033);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54293b9257ecd4e1195d8a1c5090f29d0b7fa8d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1499:0.95352800,2_1602:0.19198400):0.33738000,1_936:0.00000000):-0.00000000,4_1165:0.00000000,0_1208:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2ad63da5e97e51b97181d56f0a3f64d6259f2c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1170:0.00000000,((3_1494:0.09946167,2_1597:0.17131933):0.13109947,0_1213:-0.00009958):0.00189558,1_941:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72a6e7de1938c2e72caa3f3eab8c8b2b2fccc3b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1171:0.00000000,0_1214:0.00000000):0.00000000,1_942:0.00000000):0.09178900,2_1596:0.15955600,3_1492:0.09953400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..053ee08475818c0b1b6ace1c58d528980b02ef41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_944:0.01507775,4_1173:0.00072525):0.00364800,0_1216:0.02044600):0.09127950,3_1490:0.31889925,2_1593:0.12453575);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21c2438ed884932854b7dff8f3c4bd85f0965ffd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1218:0.01771859,(1_946:0.00000000,4_1175:0.00000000):0.01044641):0.09934036,2_1591:0.06706417,3_1486:0.15710983);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8a9450f58432438ec212cd4ef40da09ad6b2155
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1176:0.00000000,1_947:0.00000000):0.01418550,0_1219:0.01216650):0.14630700,2_1590:0.16940450,3_1485:0.43596550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a66b5c756630dc3ecae2ca63913df223747c365
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1220:0.01194274,(4_1177:0.00000000,1_948:0.00000000):0.01320126):0.02626108,3_1484:0.15560250,2_1589:0.04390550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001066_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001066_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5de254eac6362e8b59d5940e6680c5e9c0d5bf31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001066_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1588:0.05042150,3_1483:0.22276450):0.03774950,1_949:-0.00000000):0.00000000,4_1178:0.00000000,0_1221:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60172bab3c9504ee789c23a5357cef0ca5056d84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1179:0.00000000,1_950:0.00000000):0.01217197,(3_1482:0.21250550,2_1587:0.11575450):0.06130418,0_1222:0.01394803);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001068_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001068_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51fd5b8bafcf87d22124812affaa3915c839ce4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001068_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1481:0.57742862,2_1586:0.14038138):0.16015538,1_951:-0.00160188):0.00160188,0_1223:0.00771788,4_1180:-0.00160188);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c82f45579ae9175c466784c7ff9f014b58dd96f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1182:0.00000000,1_953:0.00000000):0.00152725,0_1225:0.00097275):0.07117075,2_1584:0.06495425,3_1479:0.19282475);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001070_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001070_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08414aa011e950ba70f164635ea99a4ffcc2ae33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001070_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_954:0.00000000,4_1183:0.00000000):0.00345517,0_1226:0.00429683):0.04000594,3_1478:0.25122467,2_1583:0.09782233);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001076_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001076_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93caf099b12bf48da389459eae476528b0a7b524
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001076_tree_id.txt
@@ -0,0 +1,2 @@
+(1_960:0.00372750,((2_1576:0.37817250,3_1471:0.25079550):0.05978079,0_1232:-0.00060914):0.00185364,4_1189:-0.00000350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001083_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001083_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62d3edd91a2a3a6e23cf62083c5d040256f5ed11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001083_tree_id.txt
@@ -0,0 +1,2 @@
+(1_979:0.00000000,((3_1463:0.05731783,2_1567:0.01073217):0.01403470,4_1204:0.00056660):0.00083840,0_1247:0.00000000);
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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/OG0001084_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001084_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5e6b477220e85edf343a88b7286deef7dfb1649
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001084_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1566:0.03345250,3_1462:0.17850050):0.02752150,0_1248:0.00000000):0.00000000,4_1205:0.00000000,1_980:0.00000000);
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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/OG0001085_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001085_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb7b1b07f97a1a0dd5a77cafecdac22b6542111f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001085_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/OG0001089_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001089_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a09760efe216b9e06f561c105d2eb3acdbb743f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001089_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/OG0001090_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001090_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..665f6341aff7e2d2b690f6f8766defe98628da5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001090_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/OG0001092_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001092_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0dbeb2c515731607eb6cf0267624562ee943027
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001092_tree_id.txt
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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/OG0001093_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001093_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05a184cbd39a0a763f06915a9228f8e57adc44bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001093_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/OG0001094_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001094_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..610859ffc39968f0ae9673a9de2394283cd62947
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001094_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/OG0001095_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001095_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4943f806e6efdf36c61753f214bf57712a6dc23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001095_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/OG0001097_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001097_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b53c5c7bca4fa7b08af165fdebf579b55483e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001097_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/OG0001099_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001099_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..204e246c0c48b67c887b7469e2c5c910ec766e30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001099_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1446:0.10683000,(0_1264:0.00000000,2_1550:0.00000000):0.06305200):0.15413250,4_1221:0.00347600,1_996:0.00334300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001100_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001100_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f370a8c9ff0c6bf5c35609f8f9047bf5d30d38d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001100_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1265:-0.00010075,2_1549:0.00391175):0.05029925,(4_1222:0.00000000,1_997:0.00000000):0.11480650,3_1445:0.05331850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b747ea4863a37909e26f17f73d0c1dcaa7da5cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1546:0.00162800,((1_998:0.00118100,4_1223:0.00031000):0.08407225,3_1442:0.11189025):0.07057725,0_1268:-0.00013700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001102_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001102_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6965f78639df70bb2bda19a4f872955205d72643
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001102_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1269:0.00903340,(4_1224:0.00388622,1_999:0.00852678):0.02306122):0.03878381,3_1441:0.22083317,2_1545:0.05988683);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001104_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001104_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7b68d5d362358f00b7e5d2f88e99212790175d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001104_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1438:0.07535900,2_1542:0.02172900):0.00452603,(0_1271:0.01669751,1_1001:0.00193249):0.00097742,4_1226:0.00190040);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001105_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001105_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a656b63c4c9594664452c22616611e420c845e24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001105_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1437:0.20219450,2_1541:0.02182950):0.04574025,1_1002:-0.00118425):0.00118425,4_1227:0.01208725,0_1272:-0.00118425);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e99f12639f79e2dc455be20d3ca8b06f4d184a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1539:0.54167238,3_1435:0.84406063):0.34435512,(0_1274:0.00111462,4_1229:0.02092938):0.01774463,1_1004:0.03913787);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001108_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001108_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdee19f237ad34f850c7ecf21c1166df047af64c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001108_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1275:0.00000000,4_1230:0.00000000):0.00694481,(2_1538:0.06536850,3_1434:0.27088250):0.05334656,1_1005:-0.00038781);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e17e367fd6b7fedef89d32ccf0cd8b50a0879944
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1428:0.16884462,2_1532:-0.00006662):0.00006662,(1_1011:0.00741738,0_1281:0.00216262):0.00005862,4_1236:-0.00006663);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001115_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001115_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e07312561201dc4b095f77bcaeddf43b9b80882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001115_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1012:0.00260425,(0_1282:0.00000000,4_1237:0.00000000):0.00110875):0.00150325,2_1531:0.01420725,3_1427:0.07266475);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001116_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001116_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c922a9955e53b4c7d70f3358f8d68603b10aef2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001116_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1530:0.04783862,3_1426:0.32054937):0.06489363,1_1013:0.00327037):0.00072363,4_1238:0.00056512,0_1283:-0.00056512);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..765301d55a2ed80f7b399963686f81f2792af176
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1529:0.00000000,0_1284:0.00000000):0.00000000,1_1014:0.00000000):0.12119950,4_1239:0.11198850,3_1425:0.24804950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffc04e6f8d97ea6d320238d97cbd106f1946010d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1285:0.00000000,((4_1240:0.01302975,3_1424:0.09592925):0.00144975,2_1528:0.00547975):0.00133525,1_1015:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..003f68331bb9903b737587487a70580646f57871
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1243:0.00332052,0_1288:0.00552748):0.01038565,(3_1421:0.09038767,2_1525:0.01497333):0.01403794,1_1018:0.00162819);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0a7792df1c2e8760a8c05fe23610b7e902b1a4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1291:0.04475749,(4_1245:0.00000000,1_1020:0.00000000):0.01594251):0.12394600,2_1523:0.12608883,3_1419:0.35880317);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c119ec7b327aa5422e0afe8fdbd6d4566b063530
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1246:0.00119464,0_1292:0.00766536):0.00214572,1_1021:0.00020030):0.02377290,2_1522:0.03259050,3_1418:0.10369250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72022aa3fcf7a3262d3a6e0c22b7d21379913f7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1248:0.00000000,0_1294:0.00000000):0.00000000,(3_1416:0.07212000,2_1520:0.03359800):0.02451300,1_1023:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..420e1ee64f0b0920acf1b71aa81238ee869dceef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1295:0.00127348,((3_1415:0.07284133,2_1519:0.01558167):0.01177945,1_1024:0.00233336):0.00145414,4_1249:0.00103652);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d88da4bcae4645720b001430e7d072ac103ec250
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1297:0.00246900,(4_1251:0.00801216,(2_1517:0.09000383,3_1413:0.28246517):0.07214655):0.00465784,1_1026:0.00089800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001128_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001128_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..238c200b3b50194ee696005b2bc1862a6b7ed4aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001128_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1252:0.00432062,(1_1027:0.05078126,(3_1412:0.47199200,2_1516:0.30311000):0.14409075):0.06962574,0_1298:0.01822338);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001129_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001129_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20eb2c4af2f8def814b021a147295d53803155ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001129_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1253:-0.00143325,((2_1515:0.04291750,3_1411:0.26289150):0.07038375,1_1028:-0.00143325):0.00143325,0_1299:0.01598925);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e7e6bebd8483434bd9e105ef3c89ce2c11dbe59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1300:0.00544180,(4_1254:0.02137304,(2_1514:0.14944883,3_1410:0.30871017):0.09551851):0.02584396,1_1029:0.02749620);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001133_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001133_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8dc736c5b518e7112e5211b9d1772d626cac01b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001133_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1032:0.01729750,4_1257:0.01019850):0.00724100,0_1303:0.01248000):0.02938800,3_1407:0.05898250,2_1511:0.03723750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa007ebe8801c4d22cee202432b36eff4bb66db8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1510:0.25990033,3_1406:0.64720667):0.20042586,(1_1033:0.01986455,4_1258:0.01336145):0.00691893,0_1304:0.01623257);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001138_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001138_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..544581089acbe4ead86d4c5cef3f9efea1efc510
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001138_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1262:0.00353475,1_1037:0.00379825):0.00186700,0_1308:0.00846400):0.05271050,2_1506:0.05862525,3_1402:0.12339575);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df00c14a2d9be9068a759a8d7c37dd6b30c2e8ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1310:0.00294122,(1_1039:0.00371236,(2_1505:0.32603383,3_1400:0.10807917):0.05990329):0.00296114,4_1264:0.00024978);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b7e809ee4c8bdec69eb0b1a466291a38da68c4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1265:0.00381591,0_1311:0.00634909):0.00844093,(2_1504:0.10668350,3_1399:0.23639250):0.08489663,1_1040:0.02225430);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f787c83c6a57fe708ff87bbc5d73be2cc9ba13f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1266:0.00107979,0_1312:-0.00019179):0.00668308,(3_1398:0.33083333,2_1503:0.08501267):0.05357252,1_1041:0.00288971);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001144_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001144_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2b1e349d65c09d828b55875089453b7ac0be8c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001144_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1315:0.00000000,((3_1395:0.09675075,2_1500:-0.00074875):0.00694575,1_1044:-0.00136975):0.00136975,4_1269:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58ee046175ae507c430a4192f91b9212856d8310
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1316:0.00000000,1_1045:0.00000000):0.00000000,4_1270:0.00000000):0.21475050,2_1499:0.21633850,3_1394:0.66610350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001146_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001146_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db51cf1cda9bbea4b58d76edd3b68ed4d915c897
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001146_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1317:0.00341600,1_1046:0.00333000):0.00315475,(3_1393:0.36644975,2_1498:0.10831925):0.12209625,4_1271:0.00699375);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4eaa8d5ddf325178cd97aae5424cea2793c6e6d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1049:0.01138689,(4_1274:0.00440449,0_1320:0.00783951):0.01407149):0.08099513,3_1390:0.51877533,2_1495:0.14452567);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79a9b7238ab060bc1d34d975d6b45bfadba5846d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1387:0.11721825,2_1491:0.06399775):0.01595775,1_1052:0.03480725):0.01431275,4_1277:0.00633425,0_1323:0.00334575);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001154_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001154_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5dd5950f817bf4677ad5eed7054dd6ed71e72ba1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001154_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1488:0.05452600,3_1383:0.21063100):0.07396250,(1_1055:0.00002500,4_1280:0.00204200):0.00881950,0_1326:0.03351250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95d0dd30c07dc408beeaf441152161a4004d2be9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1058:0.01620012,((2_1485:0.08386688,3_1380:0.43615112):0.06970162,4_1283:0.01064837):0.00437613,0_1329:-0.00040212);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001159_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001159_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fc25490a97c4e586ecb0fb8f7060acac2934212
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001159_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1331:0.00412650,(4_1285:0.00000000,1_1060:0.00000000):0.00860950):0.02672000,2_1483:0.10575900,3_1378:0.34208400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da666918247c599947a20ac054e9844eedeb5804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1332:-0.00057236,(3_1377:0.20035833,2_1482:0.01647067):0.01982921):0.00057236,1_1061:0.00588400,4_1286:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cae777b01b0da71b8df586fc3d60a5a13b046f47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1364:0.33557550,2_1457:0.02730350):0.04093450,4_1313:0.00193400):0.00159100,0_1364:0.00000000,1_1104:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff1b55ecd5c114ab8eeacffcf5f562db9088e66c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1456:0.02030200,3_1363:0.05587000):0.03436650,1_1105:0.00300350):0.00200550,4_1314:0.00363450,0_1365:0.00086650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001169_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001169_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e64057813330cfaad2d58376cb7be9f57c073c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001169_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1106:0.00340038,((2_1455:0.02211662,3_1362:0.01388337):0.01920963,4_1315:0.00004038):0.01155062,0_1366:0.00400363);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef3d3d8e112356195e0cb9fce7a2fb03d2cca9f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1316:0.00211350,0_1367:0.00923050):0.00309125,1_1107:0.00661325):0.00712625,2_1454:0.01443125,3_1361:0.02962775);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cda0995b89e3ff30eb955fb63a5b2d1774c4f85f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1109:0.00787925,((3_1360:0.28057400,4_1318:0.03787700):0.02579275,0_1369:0.02727525):0.01339625,2_1452:0.01399675);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001174_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001174_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d939b158fac6d788121a5ce12d130ff29a8cda72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001174_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1112:0.00000000,4_1321:0.00000000):0.01415200,0_1372:0.01156200):0.03657150,3_1357:0.20519150,2_1449:0.05504150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..972a44f132ed27e3272b987f9c3bbd7cfa47cbc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1373:0.02880137,(4_1322:0.00916037,1_1113:0.00245662):0.03215113):0.16738912,2_1448:0.12924712,3_1356:0.19240688);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..813b2b0f52a85aacccd7d27f2aa4bbe4ac267845
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1119:0.00347187,(2_1443:0.03095688,3_1350:0.09068512):0.02328112):0.00344513,0_1378:0.00295087,4_1327:0.00128413);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001182_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001182_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df4d2efd6d17416523e688c2049583ae658c3047
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001182_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1329:0.02566262,((2_1441:0.15959713,3_1348:0.50445587):0.13454013,0_1380:0.07094587):0.04111563,1_1121:0.00413737);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d25be9d3e0429b01830ee98631cf60cdf0ebe606
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1332:0.00404287,(1_1124:0.00142063,0_1383:0.00288338):0.00335463):0.07637463,2_1437:0.09069563,3_1345:0.20367638);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001187_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001187_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1134519292af8558c4865a16d2fcfcaa33701544
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001187_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1334:0.00923049,(0_1385:0.00632438,1_1126:0.00566762):0.00258057):0.09433591,3_1343:0.16526317,2_1435:0.06252283);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..832930f25a66ac74464cadeaa67cc6158daabede
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1127:0.00643811,((2_1434:0.04711400,3_1342:0.09391400):0.03415392,4_1335:0.00626676):0.00092774,0_1386:0.00643389);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd1120c3b807b91abba151581a35b6b5da2bf9b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1340:0.00889477,(1_1132:0.00050390,0_1391:0.00131810):0.00871816):0.05128019,2_1429:0.04776917,3_1337:0.29706083);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001194_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001194_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9316a1d35096e2998f6f65d608bf004b2a50c5bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001194_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1394:0.02286500,(1_1135:0.00460925,(2_1427:0.13288750,3_1331:0.25287150):0.12383475):0.00258025,4_1343:0.01308700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001195_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001195_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..444f2ee9151eb785b9672b3b7c8196596d8cf537
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001195_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1395:0.05860762,((3_1330:0.19535900,2_1426:0.08615900):0.08069435,1_1136:0.01433405):0.01322345,4_1344:-0.00067862);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d75588fcfd7bf2c1de86a43b03f242135ead4b4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1397:0.00000000,((2_1424:0.11793875,3_1328:0.39673725):0.09666775,4_1346:0.06809775):0.01889925,1_1138:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001198_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001198_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3b98ee9f9145ee1659988e16427e42a7162a742
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001198_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1348:0.02214683,0_1399:0.02970617):0.27411792,(1_1140:0.30267565,3_1326:0.15953135):0.02588437,2_1422:0.08791675);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001200_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001200_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddc6e3a0c666ccde2a81f034f8e7b6168dd7fd23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001200_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1351:0.00000000,0_1402:0.00000000):0.00000000,1_1143:0.00000000):0.01248450,2_1420:0.00822050,3_1323:0.02936250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001202_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001202_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..311637a632a41566c1b8e1477ed0b722df18b311
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001202_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1418:0.03001650,(4_1353:0.00000000,0_1404:0.00000000):0.05135750):0.01309250,1_1145:0.02225747,3_1321:0.09035553);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001203_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001203_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c16d10bc4cee640477f6bd7302efa4378aab79f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001203_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1354:0.00000000,1_1146:0.00000000):0.02381910,0_1405:0.00014990):0.71272763,3_1320:0.76038800,2_1417:0.07449300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001207_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001207_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12eab4bca51bae25e5f9f92f2f1751150a898aec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001207_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1150:0.00545285,(0_1409:0.00728263,4_1358:0.00014337):0.00682875):0.06328598,3_1316:0.42944883,2_1413:0.14807217);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5765f3b75aca53038129875dd6520a433437670c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1412:0.00000000,4_1361:0.00000000):0.00779575,(3_1313:0.54536025,2_1410:0.31051775):0.27198775,1_1153:0.01380325);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001211_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001211_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f26c215fbf6dd725e7eec01872db33127efcd33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001211_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1413:0.00726090,((2_1409:0.24946483,3_1312:0.56396817):0.14891080,1_1154:0.00916190):0.01101410,4_1362:0.00069210);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b677566f0092f0148f815e954adf26794bf0515
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1368:0.00000000,0_1419:0.00000000):0.01337450,1_1160:0.00682350):0.02050500,3_1305:0.08761000,2_1403:0.02679100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001217_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001217_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d779ea5a7c0bf04463b3032a3ebfe1cbe6b198a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001217_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1161:0.00880852,0_1420:0.02165248):0.01220014,4_1369:0.01623073):0.16044408,2_1402:0.12831333,3_1304:0.14847967);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66f54d8dfecbba7c8e622703af3f2dac054542e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1163:0.00025493,0_1422:0.00235807):0.00580513,4_1371:0.00244376):0.02819757,2_1400:0.03891450,3_1302:0.11742250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001220_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001220_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79117f5233dffd9b3fdfcc3d4024e4da6eb586cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001220_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1399:0.18292725,(0_1423:0.01478525,(1_1164:0.00250925,4_1372:0.00099575):0.00945825):0.00277825,3_1301:0.03079175);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001221_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001221_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..649fd5b9b2e4a765e821b5240f85bf2f212a3c54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001221_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1375:0.00000000,1_1167:0.00000000):0.00000000,0_1426:0.00000000):0.11632050,3_1298:0.17844350,2_1398:0.17586650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001226_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001226_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5124a653f414c7c449f0f3858ac382ff69944c52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001226_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1293:0.20444562,2_1393:0.02814737):0.04952363,(1_1172:0.00008088,4_1380:0.01183613):0.01391912,0_1431:0.04491937);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001228_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001228_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aba517282e5984670fff186ddc6acc08a2bf4116
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001228_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1382:0.00287663,1_1174:0.01581437):0.02534288,0_1433:0.03430463):0.16654737,2_1391:0.09520662,3_1291:0.47820538);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3791af72734142ac309fd68900afa3bf762a8977
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1176:0.00087259,4_1384:0.00086341):0.00233090,0_1435:0.00202020):0.03508110,2_1389:0.02019217,3_1288:0.48998883);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001231_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001231_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2441e4e427e6311545fc7354e900c772bc06c034
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001231_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1458:0.00560409,(4_1385:0.00451210,(3_1287:0.19604567,2_1388:0.05562233):0.04343737):0.00140290,1_1177:0.00004291);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001237_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001237_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28cf428c59a2646f2aeb2fc149c24bfc4f3c5673
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001237_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1465:0.01877050,(4_1392:0.00822450,1_1184:0.01263350):0.00601950):0.04116600,2_1381:0.14232050,3_1281:0.43234050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ade913e12c76cfcf995bdce54d9b8d4f0cc95cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1394:0.00486188,0_1467:0.00454112):0.00112687,(3_1279:0.31046987,2_1379:0.08591313):0.06403638,1_1186:0.00747913);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21eb56f67a2c3fe41206047fc7758243b9c10fd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1188:0.00879588,(4_1396:0.00681162,(3_1277:0.19615437,2_1377:0.04026562):0.04271037):0.00118738,0_1469:0.00841513);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001242_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001242_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98aa9c85298d56ca4c44b48847558ba78ea44b63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001242_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1470:0.00322700,(2_1376:0.03823250,3_1276:0.03181350):0.02169250):0.00034400,1_1189:0.00000000,4_1397:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaef291ccef2cc93193fc7312d20534762087415
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1374:0.03090550,(3_38:0.31090775,0_1472:0.01229525):0.00591900):0.00341400,1_1191:0.01364075,4_1399:0.00701425);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ed667512789db9bbfb391f4f4268eda849a69e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1400:0.00000000,(1_1193:0.00579425,(3_1265:0.39250075,2_1373:0.02095025):0.03695925):0.00813775,0_1473:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001249_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001249_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc0fd2c474437efc0c77371974141a561cea0e2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001249_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1404:0.00000000,0_1477:0.00000000):0.00072163,1_1197:0.00038037):0.04318662,3_1261:0.18072083,2_1369:0.06535117);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..765f07edc2caba70695aef00f67bccd1b3b444b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1405:0.00000000,0_1478:0.00000000):0.00000000,(3_1260:0.14061300,2_1368:0.05441700):0.04170900,1_1198:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a66cdafe923ab3fa9ee083c3f04724b77bee82f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1480:0.00000000,(1_1200:0.00137750,(2_1366:0.05243200,3_1258:0.15587300):0.06848700):0.00053150,4_1407:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001253_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001253_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55a03c8b00f4a4be3a66d67071a40676f36969a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001253_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1408:0.00430555,(1_1201:0.00139293,0_1481:0.00481007):0.00175376):0.08234527,2_1365:0.09397050,3_1257:0.23807450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001257_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001257_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c96874f5832f091cd1d7fa1ca7fa3bebe807fff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001257_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1413:0.00000000,((2_1360:0.12071950,3_1252:0.10775050):0.10149750,0_1486:0.00767400):0.00843500,1_1206:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001261_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001261_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c0a5021fffc27b5b8271f9204855ade7c465ceb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001261_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1210:0.00000000,0_1490:0.00000000):0.00284976,4_1417:0.00686224):0.04089591,2_1356:0.02815750,3_1248:0.15994350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08f072d8bc77b309228fdc6af316ec05175d3762
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1214:0.00184178,(4_1421:0.00061772,(3_1244:0.95279667,2_1352:0.16046433):0.13774057):0.01043328,0_1494:-0.00001178);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a3e523a7f2d18bece96b20a2f2e526dc993a260
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1349:0.20271400,3_1241:0.40724700):0.24916850,(0_1497:0.02351068,1_1217:0.01553232):0.02144015,4_1424:0.06879330);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001268_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001268_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccc6526e96eee966b69c90dfa2caf989ebc03158
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001268_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1425:0.00139144,((2_1348:0.10834817,3_1240:0.27458783):0.06785587,1_1218:0.02752612):0.01578688,0_1498:0.02833156);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16ff52da88d3803045de06c1c0d501ee0451cf46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1222:0.00465000,(4_1429:0.00000000,0_1502:0.00000000):0.00007100):0.07641300,3_1236:0.20320300,2_1344:0.09003200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..accc2e3aaa2a0e2b46b56512c4f744267f34c54c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1224:0.00696588,(4_1431:-0.00009051,0_1504:0.00417551):0.00213564):0.08315777,3_1234:0.09019050,2_1342:0.03034650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001275_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001275_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa7b04c41856d3ba13ddf6fca1d8aabd2760454d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001275_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1341:0.01827550,3_1233:0.05506350):0.01264548,(1_1226:0.00106092,0_1506:0.00535108):0.00158204,4_1433:0.00071496);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001278_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001278_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7a57d4e56c8af98663698aaa2f6fe8293c5a1bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001278_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1230:0.00277179,0_1510:0.00048921):0.00075651,(2_1337:0.05940983,3_1229:0.03216317):0.01409129,4_1437:0.00069354);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001281_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001281_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7e21c1719b8689e8409b2653dc61a77abccb8c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001281_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1440:0.00329875,2_1334:0.00521125):0.00017575,(1_1233:0.00000000,0_1513:0.00000000):0.00461875,3_1226:0.25187825);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1efe0d61423e2f6d2850dfb27032c7f885fa2f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1441:0.02834450,(3_1225:0.24393000,2_1333:0.02253100):0.01012350):0.02180250,0_1514:0.00000000,1_1234:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001285_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001285_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df819c0e4c19e85208c5b87caac536bb6b7d34bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001285_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1238:0.00669632,(3_1221:0.23955683,2_1327:0.04126717):0.05161094):0.01080018,0_1518:0.01609359,4_1445:0.00926541);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001287_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001287_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8aa3039540754c252b8e80eb0627e7f8118d3b3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001287_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1520:0.00127000,((2_1325:0.15776100,3_1219:0.22230300):0.13115175,4_1447:0.00677225):0.00151125,1_1240:0.00173300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0e1ac97995d64d5e71db3b9063b5ea6fa6eece1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1320:0.19763600,(4_1451:0.00076050,1_1244:0.00237150):0.00268100):0.00316000,0_1524:0.00373300,3_1214:0.01833800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43e443df27f9c8e60c8438dcce0c8026deb18e0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1526:0.01274158,(1_1246:-0.00071653,4_1453:0.00516553):0.01137795):0.00865949,2_1318:0.19491933,3_1212:0.00405967);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001294_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001294_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1f2ef9dc8cadfb99c9e456891227e2335517ad6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001294_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1209:0.40737483,2_1310:0.30091317):0.00273552,0_1533:0.00199806):0.00121794,1_1254:0.00257841,4_1460:-0.00000741);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1d845db88e3ab2a0e0f74a2883f12f092280600
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1464:0.02976462,(0_1537:0.00000000,1_1259:0.00000000):0.00619038):0.10691971,2_1275:0.10150450,3_1195:0.13807550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdb772d7f5d2b490c379086a6eb5bda55b31a5f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1190:0.02720618,((0_1541:0.01558350,2_1276:0.37701950):0.00546294,1_1263:0.01493432):0.00264618,4_1468:0.02091582);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58a980ca3a5e8d7aaa1ca5d856bcc64efc894c10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1543:0.00000050,((2_1273:0.05014033,3_1183:0.07167067):0.04849980,4_1470:0.00739041):0.00470609,1_1265:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..342d882566553f0077b8a4ef5c80b7d132d88ea3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1471:0.00395500,(0_1544:0.00000000,1_1266:0.00000000):0.02893000):0.03370800,2_1270:0.96905550,3_1180:-0.01446450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e3b45d00a0834c42d6642d88aaf78bccc8da935
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1267:0.00230375,4_1472:0.00506325):0.00093550,0_1545:0.00090600):0.01204700,2_1269:0.00230225,3_1179:0.00136775);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001302_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001302_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f65879d00f0ae9454392b230b51ad494602d17ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001302_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1546:0.00152683,(4_1473:0.00341104,1_1268:0.00312496):0.02889070):0.04857507,2_1268:0.01593850,3_1178:0.01493050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001303_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001303_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dd15ecad8ebbf5588662c8948405d0703334ae2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001303_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1475:0.00000000,0_1548:0.00000000):0.00354371,(2_1267:0.08203633,3_1176:0.01026167):0.01046443,1_1270:0.00023829);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20c74785b58584a42cffcaaa32958cc38005192a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1556:0.01401913,(4_1482:0.01351363,1_1277:0.00255237):0.00545587):0.00580788,3_1169:0.02368087,2_1263:0.10817613);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001306_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001306_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87d968372be1dda714c4a74f8047203ac0c89d7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001306_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1483:-0.00040263,1_1278:0.01004562):0.00133337,2_1262:0.02947612):0.00214488,0_1557:0.00797238,3_1168:0.01139262);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c0b382e7f218ad59560013ba3334e196d7a85a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1599:0.01839612,((0_1566:2.09328337,3_819:0.01396162):0.01207713,2_880:0.00802088):0.00705612,4_1820:0.01284887);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d48d0f5ff1d929ead8f01c808f6dfa007ba52a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1157:0.17615225,1_1288:0.14942375):0.00691075,(4_1501:0.00519700,0_1572:-0.00009300):0.10649012,2_1246:0.12001188);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001310_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001310_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5642a86d584d71995945a0523e8d1b78d5e38a62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001310_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1152:0.04409562,((0_1574:0.01235063,4_1503:0.01896238):0.04154387,1_1289:0.02473463):0.03130388,2_1243:0.15344937);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2c05ee04128e9b4e105cb5db589b9a3339df51b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1504:0.00527375,(1_1290:0.00568375,0_1575:0.01054425):0.00379775):0.09670575,2_1242:0.15831025,3_1151:0.30774975);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001313_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001313_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..324aedaa2cc3257e6b59274fb26301c2a61472ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001313_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1506:0.00537617,0_1577:0.00649683):0.01350840,1_1292:0.00807105):0.05245641,2_134:1.30570933,2_1240:0.01810567);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..272496e4a2a8a262edd71efaa199e2964e4fb021
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1293:0.00751613,((3_1148:0.07540812,2_1238:0.03902188):0.01544587,0_1578:0.00764363):0.00306238,4_1507:0.00676988);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3820cc4b145d97b0a35da10445a751f80287277a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1580:0.00244600,((3_1146:0.14345850,2_1236:0.16395250):0.11123675,1_1295:0.01179975):0.00216625,4_1509:0.00808300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..481bfd03757e0a4dd5adab212dcce191cc696cd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1510:0.00000000,0_1581:0.00000000):0.00396675,(2_1235:0.21265825,3_1145:0.08971775):0.09937775,1_1296:0.02334925);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001319_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001319_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0eeedb8874b32a9480a21bc11e5f6a76c92b817
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001319_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1299:0.00000050,(4_1513:0.00416725,(2_1232:0.02745725,3_1142:0.04214075):0.02786175):0.00002225,0_1584:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001321_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001321_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34d6a775f10771ec83eb443a6c6e4f5afcca5bf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001321_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1301:0.00642204,(0_1586:-0.00023443,4_1515:0.00340443):0.01624939):0.07744027,3_1140:0.23991783,2_1230:0.10573217);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6152459d62e526cb93a44d55d37723fa44ae18c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1517:0.00650984,((3_1139:0.55716867,2_1229:0.09794933):0.10324691,1_1302:0.01568974):0.00412076,0_1587:0.00275116);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d23932bbbde8f09f391886a0e1b7c48aa02a316
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1589:0.02457637,((3_1137:1.53434438,2_1225:0.47291862):0.09680487,1_1304:0.01465962):0.05383187,4_1519:0.00492963);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e45c2f375e6e8c4f99b219b6e56a4028a16280a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1590:0.00841522,4_1520:0.00550578):0.00495123,(3_1136:0.24530650,2_1224:0.04895650):0.02136260,1_1305:0.01562860);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06b03c2fd21ebfd2e3af1fde78bfb1ef4123597d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1223:0.08973525,3_1135:0.49385375):0.07311350,0_1591:0.00269400):0.01073050,1_1306:0.00738400,4_1521:0.00353000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..926698e195119e3f2fe561b182c0ce8fcd4ec4a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1312:0.00741700,(4_1527:0.00186375,0_1597:0.01110225):0.00559150):0.12305050,2_1217:0.10736725,3_1129:0.26214175);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001334_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001334_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fdc078d5c9c5ff89bdbe52d13f01643feef689a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001334_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1215:0.01421050,3_1127:0.05828150):0.01839260,(4_1529:0.00014551,1_1314:0.00033449):0.00486400,0_1599:0.00567722);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a9069c77e5ab6db089de61407fece246308aa19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1530:0.00090563,((3_1126:0.11959963,2_1214:0.05932238):0.05268113,0_1600:0.00644987):0.00216763,1_1315:0.00195137);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..309192b1b3a22fb6b95f04688fdebe26cc49f267
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1320:0.00704978,((2_1210:0.04588300,0_1605:-0.00051800):0.00303700,4_1535:0.00655600):0.00050650,3_1122:0.00503522);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ada493a3d045363f37c395817ea56f6c35f6b4a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1121:0.00439500,(2_1209:0.13985550,4_1536:0.00469750):0.00204800):0.00366250,0_1606:0.00872075,1_1321:0.00434125);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001340_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001340_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60ea5ef84e527d39a1d7a8376f0934c1051afb7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001340_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1538:0.00579900,(2_1207:0.16844541,1_1323:0.02491659):0.00827628):0.00881046,0_1608:0.02197983,3_1119:0.06661217);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001341_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001341_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a268163df38652bc83b2f6f21bcd3c474a11fb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001341_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1206:0.49835937,3_1118:0.54120163):0.04603013,(0_1609:0.01843788,1_1324:0.00914513):0.00359362,4_1539:0.01706438);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95b9db4648f19dce360e33d486bd1a444c10c4b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1540:0.00428944,(0_1610:0.00337400,1_1325:0.00823200):0.00247387):0.20502440,2_1205:0.06540700,3_1117:0.11450800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72456bec892e1fbeb7959ffa842400432e88827a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1541:0.00373761,((3_1116:0.12505317,2_1204:0.03759183):0.03713480,0_1611:0.01162990):0.00044810,1_1326:0.00322239);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1be103cc22299ab7522097de2be1485281eccfd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1613:0.02678000,(3_1114:0.30563350,2_1202:0.06778950):0.05011450):0.01249300,4_1543:0.00000000,1_1328:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d687e96a2379c4ca39a5e1d7a3383387a3d07796
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1329:0.00783400,(0_1614:0.00702296,4_1544:0.00705604):0.00369900):0.05547250,2_1201:0.10530583,3_1113:0.09830017);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001349_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001349_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..155ae808134fa511ebe9f89240ff21cb061886b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001349_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1618:0.00309847,1_1333:0.00980453):0.00388739,4_1548:0.00601390):0.03663091,3_1110:0.22180367,2_1181:0.02780533);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001350_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001350_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d08ba3f97995ce235a1f1442d2c4adfc7ce31bc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001350_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1619:0.00078601,1_1334:0.00920799):0.02034947,(2_1180:0.05671917,3_1109:0.32597783):0.04698196,4_1549:0.01713358);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001351_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001351_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..73451e3f5aa89a29cc4e5b177bc6e1855f74cb82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001351_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1179:0.14141117,3_1108:0.37031483):0.10669625,(1_1335:0.00943163,0_1620:0.00896437):0.00982898,4_1550:0.00643394);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001353_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001353_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0c6d94cd357c3dd90ed35c0f379152bae45e9fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001353_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1106:0.19473075,2_1177:0.03326425):0.02481425,4_1552:0.00251475):0.00146125,1_1337:0.00000000,0_1622:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9410d0c7b743cf0969ff21e60560c11214d57c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1623:0.00422587,1_1338:0.00193413):0.02507563,4_1553:0.01317837):0.11699063,3_1105:0.55185038,2_1176:0.15657263);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e27aa81f648e4ccee034169ae040344507ac04de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1554:0.00308700,(1_1339:0.00000000,0_1624:0.00000000):0.00470500):0.02162000,2_1175:0.04257300,3_1104:0.10491400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d3503e787816bfc9470707bdaa6b24b3eb50ec8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1344:0.00446664,(0_1630:0.00025504,4_1559:0.00169196):0.00489911):0.20446971,2_1169:0.19418650,3_1100:0.11949150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001360_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001360_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..626c2535a94f4babf39c47a1bfd96128dc6117b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001360_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1561:0.00025753,(0_1632:0.00004770,1_1346:0.00288230):0.00204244):0.02189205,2_1167:0.02188050,3_1098:0.10139050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001362_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001362_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b3200fcd57fa25d320625eca8e3c425a96eda0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001362_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1564:0.00000000,0_1635:0.00000000):0.00541351,(2_1164:0.03746650,3_1095:0.03712250):0.01472033,1_1352:0.00453649);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e337f2f2e383763f70498cc40b94be5b3e633dfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1355:0.00008650,(4_1567:0.00000000,0_1638:0.00000000):0.00583250):0.03686150,3_1092:0.05905000,2_1161:0.05581600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001366_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001366_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bf3df4cf1b6094e2289e1c211c23c31be61e3a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001366_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1639:0.00214887,(3_1091:0.04709983,2_1160:0.00258617):0.01179279):0.00098113,4_1568:0.00161355,1_1356:0.00308145);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b1336442aa5432d4d49534b588f7ce899ad4820
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1155:0.02894400,3_1086:0.11284200):0.05330873,(1_1361:-0.00032212,4_1573:0.00759612):0.00724643,0_1644:0.00403469);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001373_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001373_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43906186a2801a3e31ef50704666963ee810bc69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001373_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1363:0.00000000,((3_1084:0.07815250,2_1153:0.02228050):0.03258479,4_1575:0.00343388):0.00698512,0_1646:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6eb92f3bc92ed08de2286f7a1ba377fb11cd242
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1364:0.00000000,0_1647:0.00000000):0.00000000,4_1576:0.00000000):0.00993450,2_1152:0.00594950,3_1083:0.07819650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001375_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001375_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..892348500d95215dfba3b706664207a2a1959ede
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001375_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1365:0.00000000,0_1648:0.00000000):0.00000000,(2_1151:0.01052350,3_1082:0.08060250):0.01745150,4_1577:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3778adb7e9b59ecabe1958687f3b88c55f78d58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1650:0.00545000,(2_1149:0.01755550,3_1080:0.02192350):0.00103450):0.00107400,4_1579:0.00000000,1_1367:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c820ae68221fa0a1b15d616601ce60f3d29b1ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1075:0.01475250,(4_1584:0.00000050,1_1372:0.00000050):0.00000000):-0.00000000,0_1655:0.00000050,2_1144:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001387_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001387_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3a4a80f3b18161e98ad6c9bd488b92103090068
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001387_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1377:0.00000000,(3_1070:0.02436900,2_1139:0.00000000):0.00000000):0.00000000,4_1589:0.00000000,0_1660:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..647bd99f836456f170e4295834b033b4f00bce38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1068:0.01271600,(0_1662:0.00000000,1_1379:0.00000000):-0.00000000):0.00000000,4_1591:0.00000000,2_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/OG0001391_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001391_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bec4a808af6866203cf1b43cf089c648f13a6da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001391_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1664:0.00000000,1_1381:0.00000000):0.00000000,(2_1135:-0.00137650,3_1066:0.03073250):0.00768450,4_1593:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bd929ac2b09000c816582f98b9e81259285f0ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1383:0.00000000,(2_1133:0.00000000,0_1666:0.00000000):0.00000000):0.00000000,4_1595:0.00000000,3_1064:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9939922d53bf1f9679cb8a55cd30d5db9614ee4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1389:0.00000000,((3_1058:0.00416650,2_1127:0.00416650):0.00626150,0_1672:0.00207050):0.00207050,4_1601:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da8d06f05f26ecbe97d63011cee1a2ab5cb7d1bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1673:0.00000050,4_1602:0.00000050):0.00083925,(2_1126:0.01388575,3_1056:0.04022525):0.00964375,1_1390:0.00114825);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001401_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001401_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6633426cd5723bb2ec1c62d492d44bfd90d15898
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001401_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1125:0.01355250,3_1055:0.02741550):0.00850850,0_1674:0.00000000):0.00000000,4_1603:0.00000000,1_1391:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..348c33c0eb536795057a442b3413e331cc631083
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1675:0.00130463,4_1604:-0.00130463):0.00130462,(2_1124:0.00507462,3_1054:0.08220337):0.02922263,1_1392:-0.00130462);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09e477f4ef41d285b9d51ba75ac6c169886837f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1679:0.01857445,(4_1608:0.01818023,1_1396:0.01031177):0.02203291):0.05614001,3_1050:0.19848333,2_1120:0.10176867);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001413_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001413_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a8fe697736d434eefc4395a74d6a0f7ac98716b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001413_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1615:0.00140513,((2_1112:0.18631087,3_1042:1.03789413):0.15991363,0_1686:-0.00047163):0.00591262,1_1403:0.00402087);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001414_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001414_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8b221604cfde7f3fcb54f5e262aee335d375956
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001414_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1687:0.00000000,1_1404:0.00000000):0.00534956,4_1616:0.00099144):0.05044948,2_1111:0.08563433,3_1041:0.26948567);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001415_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001415_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61094fa3684ad07088b47c86e544194028de4664
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001415_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1405:0.00000000,0_1688:0.00000000):0.00000000,4_1617:0.00000000):0.05425900,3_1040:0.16812700,2_1110:0.05485700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001419_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001419_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f75b145ab4402f87bb42c30af41caeeef4d6dcde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001419_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1409:0.00000000,0_1692:0.00000000):0.00984800,(2_1106:0.10555500,3_1035:0.37592800):0.07302600,4_1621:0.00131600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001420_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001420_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e4d5227fe6292ef338206c3fb8117cc91b7fa38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001420_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1622:0.00000000,1_1410:0.00000000):0.00000000,0_1693:0.00000000):0.08373750,3_1034:0.20395050,2_1105:0.05840850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001423_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001423_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13c6d60d8ad54c37f265cdd1c39ac11fbd10eb69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001423_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1625:0.02964489,(0_1696:0.00000000,1_1413:0.00000000):0.00698911):0.06344313,2_1102:0.07145217,3_1028:0.30189083);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001424_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001424_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..907b2f3f9ddf3806b08ba25ccc2d3e3296c622e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001424_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1697:0.00000000,((3_1027:0.08527550,2_1101:0.05837450):0.04845724,4_1626:0.00376922):0.01712678,1_1414:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001427_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001427_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..680d87a1a98012a6f6e58a9dabf82cc718656bda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001427_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1629:-0.00085175,(0_1700:0.00000000,1_1417:0.00000000):0.00980075):0.02323175,2_1098:0.05101625,3_1024:0.18248475);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001429_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001429_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..011fcaa0f54aac9ec0c412c7073de9a2d7e8cefa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001429_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1702:0.00000000,(4_1631:0.01602899,(2_1096:0.07416150,3_1022:0.21609750):0.05434816):0.01999801,1_1419:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001434_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001434_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7faa5e2eca7778498d2e75953e6b4c195ddddaad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001434_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1636:0.00997448,((3_1017:0.30426033,2_1091:0.06212167):0.05904184,0_1707:0.02715151):0.00319749,1_1424:0.01973552);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db62dfcee5b1836334ebb4e5b86f58207cdcea46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1427:0.00043800,0_1710:0.00458600):0.00048800,4_1639:-0.00048800):0.00999900,3_1015:0.09113575,2_1088:0.00016025);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001437_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001437_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e1374c34e9f6797c8bfd55bf8517df25db1bc6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001437_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1640:0.00000000,1_1428:0.00000000):0.00718787,0_1711:0.01789213):0.06430354,3_1014:0.41381950,2_1087:0.09650150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4399b9582e931abd6d5806e383d4ba94ffe58625
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1429:0.01036112,((3_1013:0.20945913,2_1086:0.04323987):0.06900587,0_1712:0.00963613):0.00164588,4_1641:0.00334288);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001441_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001441_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..049fbeeefeb8c262a52935a8842c23e1285ad4e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001441_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1716:0.01457049,((3_1008:0.06157750,2_1082:0.05616950):0.03651411,4_1645:0.00993083):0.00908217,1_1433:-0.00005649);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f015105fefc54a14099cfad31f5390c9571cd40f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1717:0.00093517,1_1434:0.00352583):0.00700272,(2_1081:0.11628917,3_1006:0.17113383):0.03911215,4_1646:0.00472205);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7767d018373c497cb4ab7c0fd11a5fd501d3f7ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1647:0.00155843,1_1435:0.00118757):0.00448174,(3_1005:0.15973633,2_1080:0.05462467):0.05288295,0_1718:0.00433573);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001447_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001447_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53b8a376fad6e33af234a3d23932b8c86922b9f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001447_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1074:0.02309550,3_998:0.04153950):0.01294766,4_1654:0.00924948):0.00066052,0_1725:-0.00037276,1_1442:0.00110276);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001448_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001448_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bafba96bde61b958fe22e427cfff598d78a4800e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001448_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1726:0.00045663,(4_1655:0.00400537,1_1443:0.00568863):0.00147387):0.01809787,2_1073:0.03286888,3_997:0.10806912);
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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/OG0001450_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001450_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b53ea22e8b1f6fca9eeaa6aca563fc205f95b93f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001450_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1728:0.00545275,(2_1068:0.02048250,3_995:0.25843050):0.01114175):0.00168075,1_1446:0.00265025,4_1658:0.00062175);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0c3e316db98ef7ea2e82dbc107e34493e9c3724
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1739:0.00365490,4_1659:0.00797110):0.00108137,1_1447:0.00385276):0.03426492,3_993:0.20869650,2_1057:0.05233950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001452_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001452_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d1be6a075ce9b05b06ea93803a59c2512dcf1b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001452_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1448:0.00024933,4_1662:0.00658067):0.00099514,(2_1053:0.01740983,3_990:0.07261117):0.02461429,0_1740:0.00029003);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f8da4a9865cdb7ca5dc368b7f1221e6bf88fe3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1743:0.00639331,((3_987:0.22318083,1_1451:0.01680217):0.02778268,2_1050:0.00859455):0.00724045,4_1665:0.00376869);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001456_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001456_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9d10cc6e3a8bbb0ea5d549a282be7e374a9f72b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001456_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1049:-0.00085375,1_1452:0.00693275):0.22317400,3_986:0.23064650):0.09494600,4_1666:0.03241675,0_1744:0.06169625);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001459_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001459_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50de0906402e594fa2bf33c0095b648907639d79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001459_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1459:0.00471607,0_1751:0.02167193):0.04062063,(2_1043:0.21625100,3_979:0.76260500):0.30127069,4_1673:0.00662881);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001461_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001461_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df71470444c98f881a8e846e8777456270990397
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001461_tree_id.txt
@@ -0,0 +1,2 @@
+((3_977:0.04660600,(4_1675:0.00000000,0_1753:0.00000000):0.00000000):-0.00000000,1_1461:0.00000000,2_1041:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001462_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001462_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ded2f61afc9350a7eb220ba7582a95201bcf9ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001462_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1676:0.00822750,0_1754:0.00725850):0.00172700,1_1462:0.00121200):0.04684150,3_976:0.17268400,2_1040:0.06442600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddb5fc7908335634371e4f144ef3c2f9c1469eb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1039:0.06631638,3_975:0.12762862):0.08351812,4_1677:0.00457138):0.00332763,0_1755:0.00449288,1_1463:0.00728013);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001464_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001464_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4946faf9422dc389a0ce89cea9d49e43892648c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001464_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1756:-0.00084760,(4_1678:0.00251040,(3_974:0.07717983,2_1038:0.02153517):0.01874130):0.00314710,1_1464:0.00879760);
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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/OG0001467_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001467_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5aa5e0d88eedfe76a9f3a647d6c3354cfc8e37e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001467_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1759:0.00365352,(1_1467:-0.00002336,4_1681:0.00304236):0.01231985):0.04469502,2_1031:0.03462733,3_970:0.14005067);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001468_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001468_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2619eb50c4448f41d676e3c9753781eabb2bbf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001468_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1760:0.00105800,(1_1468:0.00001850,4_1682:0.00831750):0.00090250):0.03051050,3_969:0.07699500,2_1030:0.02886200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001470_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001470_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63ab8a42dbd06cab027bf8a3d3a8cde437fff453
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001470_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1762:0.00000000,(1_1470:0.02847375,(2_1027:0.05605075,3_967:0.20053525):0.06692125):0.01575325,4_1684:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001471_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001471_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ee3986c88c4cf0dc74b3e946d3be5b4567afe54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001471_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1026:0.07732693,((4_1685:0.00000000,0_1763:0.00000000):0.04552850,1_1471:0.01392750):0.03932450,3_966:0.44189907);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001472_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001472_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..337890fae6be6c2ecf6aebd96cc6fba081ed9bb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001472_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1686:0.00593627,((2_1025:0.10802733,3_965:0.16415367):0.06075342,1_1472:0.01297325):0.00143175,0_1764:0.00864873);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001473_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001473_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7d39b7056f458b1f993c770c125ff2cc16300e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001473_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1687:0.02046500,1_1473:0.08547700):0.05924525,(2_1024:0.47103100,3_964:0.78417600):0.08193125,0_1765:0.04461775);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001474_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001474_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17b44de830e1058eb23e9514dc85c395a16613a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001474_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1766:0.01457733,4_1688:0.01519967):0.10230183,(2_1023:0.18910501,3_963:0.64136899):0.08112602,1_1474:0.02870748);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e45bad18586b907ed34c65d40325d0b95266522
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1773:-0.00003425,(4_1695:0.00273963,1_1481:-0.00007163):0.00277387):0.03135192,3_956:0.08412283,2_1015:0.02157617);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001486_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001486_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37780be4364288498b6de0cf0dcc049c1d9bb256
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001486_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1488:0.00000000,4_1702:0.00000000):0.02079163,0_1780:0.00756737):0.03204629,2_1008:0.04100583,3_950:0.15631717);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b8eaa78430c3eb47c4505c360f9a247fba9ae50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1783:0.00000000,((3_947:0.33021925,2_1005:0.12413475):0.06084175,4_1705:0.02464675):0.01489525,1_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/OG0001491_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001491_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03a7f4537916cccb6a653cd41f702b3cd7577dd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001491_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1709:0.00000000,0_1788:0.00000000):0.00000000,1_1495:0.00000000):0.03390600,3_943:0.39116500,2_1000:0.05333500);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001493_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001493_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f0e622b94a89b88217eda2c40998dba89a75316
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001493_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1497:0.00448038,(4_1711:0.00191663,0_1790:0.00071837):0.00279163):0.06399812,2_998:0.05605688,3_941:0.26839412);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001495_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001495_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02dbc04ebecf1f29700630169749986d323b4f6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001495_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1713:0.00590635,0_1792:0.00691565):0.00329727,1_1499:0.01480654):0.04652643,3_939:0.41452300,2_996:0.09246200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001496_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001496_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5bcaf7cecd759c3fa86c5ed34433ae871e96ef0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001496_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1715:0.00472075,1_1501:0.00656825):0.00134075,(2_994:0.18189325,3_937:0.16101475):0.13366875,0_1794:0.00394225);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ca9a05748e680b9f935a5bc2785f8a05e8e384c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1503:0.01741086,(4_1717:0.00000000,0_1796:0.00000000):0.01558214):0.10586079,2_988:0.17554783,3_933:0.48096717);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..703e15fa446009a5d91d2b03d3b2e9d1085de8ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1718:0.00201675,(1_1504:0.00563150,(2_987:0.05794800,3_932:0.05959400):0.06742600):0.00199400,0_1797:0.00273125);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001500_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001500_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4e20a71ac0fef10694695e0d5a93b5caddd0f3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001500_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1505:0.00395800,(0_1798:0.00336275,4_1719:0.00483425):0.00183450):0.03307400,2_986:0.05097750,3_931:0.17605450);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001503_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001503_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95561db75ca4aa10a6608e9f26b90bd1dc07477f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001503_tree_id.txt
@@ -0,0 +1,2 @@
+((2_982:0.14225562,(3_926:0.22751000,4_1722:0.06581000):0.06330250):0.04811038,1_1508:0.00000000,0_1801:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001504_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001504_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..220d1e378554a480c22ccc8ad976c603a4eaf337
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001504_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1802:0.02002000,4_1723:0.01593700):0.00997475,(2_978:0.17353775,2_1480:2.07843125):0.23912825,1_1509:0.03400275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001507_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001507_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a4c00920cade064143f1f2200cb550a4d1b5ee9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001507_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1805:0.02024933,(4_1726:0.06048162,(2_975:0.03795300,3_915:0.98351100):0.05771821):0.02027388,1_1512:0.05312967);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001509_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001509_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e056c484e6de84c49ef827b509c5cc9bb5a22e01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001509_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1514:0.00050187,(4_1728:0.00604288,0_1807:0.00081512):0.00342912):0.04249462,2_973:0.07092637,3_912:0.09348163);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001512_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001512_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34cce81d165c71e442365b77715fe42e7fc9a98b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001512_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1517:0.00000000,((2_970:0.09408583,3_909:0.24471017):0.04944974,4_1731:0.00128472):0.00074828,0_1810:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001515_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001515_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2682773099715ac1ff53105f9687dd464456a54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001515_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1813:0.01463612,1_1520:0.02561687):0.01552837,(3_905:0.73118938,2_967:0.16137463):0.09087887,4_1734:0.02591763);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001516_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001516_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04290e904d137827b40ee50163d42d50d6ccd888
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001516_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1814:0.00000000,((4_1735:0.01354417,2_966:0.00402583):0.07991523,3_904:0.53479920):0.07130180,1_1521:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001517_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001517_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ee1cd2ef4274d97bd117e0432c006eba6f6d931
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001517_tree_id.txt
@@ -0,0 +1,2 @@
+(2_965:0.26695575,(4_1736:0.02970700,(1_1522:0.01957950,0_1815:0.01314550):0.04535450):0.01682850,3_903:0.28890525);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001520_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001520_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..100c60eee5839f03f1f69ed49171e4c1c8c91fe0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001520_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1821:0.00000000,(4_1742:0.00805400,(2_958:0.11167300,3_899:0.41036000):0.11989900):0.01104800,1_1528:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001521_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001521_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbbb2782699235d78988c097fa505c6c3329f421
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001521_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1529:0.00842855,(0_1822:0.00603146,4_1743:0.01979754):0.01125197):0.07491798,3_895:0.35117683,2_956:0.04558117);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001522_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001522_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdd4daccddce46f6750c9f5087064f7402b07292
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001522_tree_id.txt
@@ -0,0 +1,2 @@
+(2_955:0.06531325,((4_1744:0.00000000,0_1823:0.00000000):0.09337575,3_894:0.25584125):0.02926925,1_1530:0.02741175);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa1761412a201bccb0da593f9f57733f2dcb5f03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1532:0.01925981,(4_1746:0.00000000,0_1825:0.00000000):0.01652919):0.11951660,2_953:0.11263033,3_892:0.24722067);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bfcbd75b525940577fd0a6083f021cbd7522ccd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_952:0.05519750,3_891:0.30084150):0.05141750,1_1533:0.01076541):0.08840759,4_1747:0.00000000,0_1826:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24b26b561f68c8b499059698c549eb316c16f5ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1749:0.00000000,0_1828:0.00000000):0.00287266,1_1535:0.00324334):0.04660578,2_950:0.03775567,3_889:0.14587433);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001528_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001528_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f539d47446c60df17dd95d4c056348e213b2d9e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001528_tree_id.txt
@@ -0,0 +1,2 @@
+((3_888:0.38509888,2_949:0.07660312):0.03918338,(1_1536:0.00739413,4_1750:0.00575187):0.03181587,0_1829:0.08435712);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001530_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001530_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b09e2ff586d23b27bb1107f702d3a6096191b2b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001530_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1538:0.01746260,(4_1752:0.00670814,0_1831:0.00359786):0.02227097):0.03499028,3_886:0.22569983,2_947:0.07700917);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001531_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001531_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97c9759fd4260be7f0c19b594509d28cbe890c18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001531_tree_id.txt
@@ -0,0 +1,2 @@
+((2_946:0.02094950,3_885:0.09390550):0.02218887,(4_1753:0.00082875,0_1832:0.00306125):0.00114827,1_1539:0.00330327);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bc333eb76471f5c1da3c987c5ad180f067bb0d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1757:0.00000000,(1_1543:0.00181250,(2_942:0.10244000,3_882:0.19389600):0.09316650):0.00423450,0_1836:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001535_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001535_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..174d068c49f030e3fcd1ec12b9510903eed0f2b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001535_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1548:0.02947275,(0_1841:0.00000000,4_1762:0.00000000):0.05404825):0.09520175,3_878:0.52081125,2_937:0.14734675);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001537_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001537_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84ac2a7229a20f04a852eb1fb73673457ebfb8b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001537_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1764:0.00815130,((2_935:0.05813133,3_876:0.19695867):0.07306322,1_1550:0.00620067):0.03471133,0_1843:0.01534970);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001538_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001538_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..73ee1e0781e2e0a21f2e98eb7fe27417bbdd1fca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001538_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1765:0.01963921,((3_875:0.47114917,2_934:0.18019183):0.12257314,0_1844:0.03356592):0.04846858,1_1551:-0.00113121);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001540_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001540_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6231cc8671a72f48d3a76d8d8fc3f6b3cfbe83bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001540_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1846:0.01508475,((2_932:0.15634050,3_873:0.55830150):0.30428700,4_1767:0.01322050):0.01865650,1_1553:0.01158325);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001543_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001543_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9890cb597ae0e9de1cd4d6f0606802f46c6881d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001543_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1849:0.00000000,(2_929:0.00000000,3_870:0.00000000):0.01336300):0.00000000,1_1556:0.00000000,4_1770:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001544_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001544_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e7308232846250917960acee415fcbb9862a728
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001544_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1771:-0.00004750,(2_928:-0.00004750,1_1557:0.01614050):0.00004750):0.00004750,3_869:0.01934050,0_1850:-0.00004750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0cd4b2a26ac0b16b3bedbd35e0fc64de924f2a2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1772:0.00402900,1_1558:0.00284400):0.00776325,0_1851:0.02372625):0.14690725,3_865:0.11676025,2_923:0.19099575);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001548_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001548_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3a97f0ca6f9204b992b1518022ab53b63c35d8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001548_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1860:-0.00044662,((2_920:0.07611338,3_856:0.32979063):0.03848713,4_1781:0.00318587):0.01287563,1_1567:0.00770662);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001553_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001553_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bde4b945c2d076f18e84d4ac889c67f8d851256f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001553_tree_id.txt
@@ -0,0 +1,2 @@
+(3_846:0.05771353,(2_914:0.00905800,(1_1574:0.00000000,4_1787:0.00000000):0.00901300):0.00584450,0_1867:0.00134547);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc164296ee3d0ded0c50d36838dbfc9daa4c4d4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1788:0.00897662,(1_1575:0.00457287,0_1868:0.01254113):0.00231188):0.11235887,2_911:0.12580513,3_844:0.26624387);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001557_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001557_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62b990d1cd56b8bdcb8d0354fbc5b7b44f4a992b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001557_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1872:0.01817870,((2_907:0.15110400,3_842:0.77592000):0.16756114,4_1792:0.00613942):0.00690158,1_1579:0.00262430);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001558_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001558_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..655038de1abe9e3047d83d38a0ba672756e1f17f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001558_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1793:0.00606091,(1_1580:0.00710987,0_1873:0.01832513):0.00481044):0.08990934,3_841:0.19951217,2_906:0.12761683);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001560_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001560_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8aa6042255232251b2210a9b027b1deb9c69e7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001560_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1875:0.00347412,(4_1795:0.00331538,(3_839:0.14589863,2_904:0.16532038):0.12471612):0.00149263,1_1582:0.00036288);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001562_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001562_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28d4ecec3761278cf86c2db9efc61a71beb02709
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001562_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1584:0.01229035,(3_837:0.17363600,2_902:0.08476800):0.07833478):0.00540665,4_1797:0.00000000,0_1877:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001563_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001563_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1fdd5933844a6a0feea40fcf0ff4ec58d25a7cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001563_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1878:0.00000000,((3_836:0.50766317,2_901:0.15119883):0.16028659,1_1585:0.00642928):0.00566672,4_1798:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001568_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001568_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a238005fab44176ce08fb26e1b65f44f42792e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001568_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1887:0.01152014,((2_891:0.45771967,4_1807:0.00480533):0.00296778,3_828:0.01528533):0.00581767,1_1592:0.02633286);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001569_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001569_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..079418bdfef54d238b85710db5cfd42b570f1141
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001569_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1593:0.00000000,3_827:0.00000000):0.00000000,0_1888:0.00000000):0.00568250,2_887:0.00175250,4_1812:0.05540550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001573_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001573_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61c396d8779126a96cfd0e35beeb728e9ad752cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001573_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1908:0.02458457,(1_1613:0.01074926,4_1835:0.02489174):0.00661797):0.00265314,2_871:0.01890800,3_813:0.41003600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..518833f054472c0fdc2bf761de1c633b7c4ec9dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1837:0.00525768,((3_811:0.34136100,2_869:0.01451400):0.01136032,1_1615:0.01109396):0.00217104,0_1910:0.00736232);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001576_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001576_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf82fdefa4f28e03cbba82cf4a4748d59c500c54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001576_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1911:0.01177363,(4_1838:0.00668012,1_1616:0.00260188):0.00903587):0.12754237,3_810:0.41977638,2_868:0.16536862);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9e7c551d8ba9adcc4e1dd2eacb5fe5d1373b085
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1844:0.00638800,2_861:0.45401000):0.00214450,(3_797:0.00000000,1_1622:0.00000000):0.00126000,0_1917:0.00555800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c91f4bf9ea464c1671e8f6cb114b2d457d30716
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1623:0.00661655,(0_1918:0.00418445,4_1845:0.00749955):0.00168157):0.00600286,2_860:0.24717083,3_796:0.01245217);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67a77cdfd747c41f483183f77ad32e1332a4ee4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1624:0.00579373,(4_1846:0.00000000,0_1919:0.00000000):0.00394627):0.01577274,3_795:0.01061617,2_859:0.23341883);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001582_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001582_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e7181981e1410bc994f3882519044b79158b5c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001582_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1920:0.00098409,(1_1625:0.00098176,4_1847:-0.00000576):0.00243667):0.00221785,3_794:0.00462750,2_858:0.31868150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001587_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001587_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14d17f3a4687cebefcb8bbe099791723a1c94f0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001587_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1928:0.05315751,(1_1633:0.05384963,4_1855:0.05428537):0.01659732):0.23251672,2_849:0.38730933,3_787:0.73147467);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67e44c08f0aac495489f63ab026d2f38809719eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_847:0.28093875,3_786:0.06493125):0.03399375,0_1930:0.00947825):0.00112275,4_1857:0.00728650,1_1635:0.00469050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..076913a5c176cc8a0da537712671f2ec60892d9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1858:0.00451412,(3_785:0.00900787,2_846:0.03374312):0.01511588):0.00434088,1_1636:0.00897363,0_1931:0.00655537);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0ddc7517efcd35e12bad8dc268d1be5600258de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1637:0.00103878,(2_845:0.05049733,3_784:0.02642567):0.01057559):0.00090872,0_1932:0.00538436,4_1859:0.00193464);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ec6e9e2bd3803d3350bd0fafcea49242e1c7f60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt
@@ -0,0 +1,2 @@
+((2_844:0.08288250,3_783:0.01792050):0.03289016,(4_1860:0.00076486,0_1933:0.00795514):0.00204537,1_1638:-0.00030314);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001593_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001593_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2c2c136e3dcc7d75783854b3bb5eb57adbca394
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001593_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1639:0.00908904,((2_841:0.01999567,3_780:0.03517233):0.19309446,0_1934:0.00180337):0.01014963,4_1861:-0.00054604);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001596_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001596_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4d7f18d5af5f1a2a7e3b6d146648585cabd5f87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001596_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1939:0.00000000,1_1644:0.00000000):0.00000000,4_1866:0.00000000):0.10594900,3_775:0.38324500,2_838:0.07236100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..736cf1b5f18bf1094dba2a317984f1455c78cce8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1943:0.00411497,(1_1664:0.00360001,4_1882:0.00389999):0.00613335):0.10093390,2_819:0.09229833,3_757:0.47094967);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001600_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001600_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0cbba2dca9c9635d3b665c817fd463a2212c4fea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001600_tree_id.txt
@@ -0,0 +1,2 @@
+((3_754:1.04441950,2_816:0.16003350):0.21341633,(4_1885:0.00338544,1_1667:0.01677656):0.01873165,0_1946:0.03176064);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bfd38e41b44cbfbdc3606a30931caf074ead7fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1891:0.00000000,1_1673:0.00000000):0.00319025,0_1952:0.00389775):0.05298875,3_748:0.10417525,2_810:0.07233275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001607_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001607_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3003fccb75cf23a48408078f923d432e51125b51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001607_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_787:0.04268450,4_1893:0.00306450):0.00168400,3_746:0.00423250):0.00198400,1_1675:0.00161300,0_1955:0.00230600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001611_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001611_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64d6933fef67506c085d89125cd0e4581dae80d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001611_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_741:0.00731600,2_780:0.06093300):0.00324375,0_1960:-0.00078875):0.00867525,1_1680:0.00077125,4_1898:0.00977375);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001612_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001612_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..927c73fea4ad7e491e658a2a3dbebfa643f13509
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001612_tree_id.txt
@@ -0,0 +1,2 @@
+((2_779:0.36923925,(3_740:0.03150350,4_1899:0.00614250):0.00120675):0.00223825,1_1681:0.01370350,0_1961:0.00694850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56198f4b30a714950d0b96e0cd383b7d4c427b51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1900:0.00357512,0_1962:0.00220988):0.00050346,(2_778:0.04009000,3_739:0.09436300):0.00621387,1_1682:0.00463585);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06325e2650a5e4b3a2d239cfc71074c2e703e1c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt
@@ -0,0 +1,2 @@
+(2_777:0.00360883,(1_1683:0.00258591,(0_1963:0.00472317,3_2039:0.55059383):0.00468114):0.00259959,4_1901:0.00117217);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1ece8f7c155f5ada228b4fd64c70295c513f760
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1964:0.01100611,(1_1684:0.03679155,4_1902:0.06821545):0.02774285):0.79400543,3_738:1.21360733,2_776:0.28134367);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e045757ade141d852c9bb5a0b207dcaaefb3972
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1972:0.00000000,4_1908:0.00000000):0.00000000,1_1690:0.00000000):0.03757050,2_769:0.01806150,3_1202:0.81214850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdf9d44259597d2ccef61dca32ab6844ca478f48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1692:0.00000000,0_1974:0.00000000):0.00432499,(2_763:0.01187267,3_730:0.01300833):0.03075600,4_1910:0.01119301);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001624_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001624_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8bd955b60b15755f66937ce6f818635c1e38a6b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001624_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1919:0.02243520,1_1701:0.01116580):0.00259225,0_1984:0.01059398):0.00830168,3_723:0.73938167,3_717:0.02134733);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..781dd749f06b1c996c1b58fc29b98d713e8a0b0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1992:0.01251890,(4_1927:0.01278232,1_1709:0.01251268):0.00304416):0.09669256,3_116:0.31952100,2_751:0.09585200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001629_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001629_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db5fe0dc054fb8e5b8dd1065ef8c5362fe3977aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001629_tree_id.txt
@@ -0,0 +1,2 @@
+((2_745:0.15979787,3_709:0.20540313):0.07587238,(0_1996:0.01175338,1_1713:0.01276462):0.02530437,4_1931:0.04108613);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001633_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001633_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64cccd05baebfa024c5339c363c526b2edb4d4fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001633_tree_id.txt
@@ -0,0 +1,2 @@
+(2_685:0.01249000,((0_2020:0.00000000,4_1959:0.00000000):0.00065300,3_596:0.00460300):0.00001300,1_1735:-0.00067400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001635_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001635_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0bea5929b0b22297ed77094382a1ebfc91f3b1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001635_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1738:0.00000000,(4_1962:0.00415400,(2_682:0.00561550,3_593:0.01248050):0.01409350):0.00035200,0_2022:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001636_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001636_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a662a2e3c03f07c6640945c3d7dabab6517711c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001636_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2023:-0.00001825,((3_592:0.00292800,4_1963:0.00588300):0.00221875,1_1739:-0.00001825):0.00001825,2_681:0.01180825);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001638_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001638_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3012f3fb34cf6cbaac7fe1bb2549ea0520eea7d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001638_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2025:0.00000050,1_1741:0.00000050):0.00323267,(3_590:0.00842883,2_679:0.00356817):0.00702011,4_1965:0.01125183);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001639_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001639_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ebc9408527224d5d54a651c1f4abb52eaa1e8b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001639_tree_id.txt
@@ -0,0 +1,2 @@
+(3_589:0.00694568,((0_2026:0.00000000,1_1742:0.00000000):0.00836650,4_1966:0.00530050):0.00152200,2_678:0.02433432);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001640_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001640_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9bbc462625dceaee7bec5f21410a0f8c0c031756
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001640_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2027:0.00000000,1_1743:0.00000000):0.01197575,(2_568:0.18934525,2_677:0.01025575):0.03507725,4_1967:0.01575925);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001641_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001641_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0343077c16e02b5cd363a6ad63a16b9b643eb122
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001641_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2031:0.01206062,(2_668:0.00552938,3_585:0.03993262):0.01436088):0.19721038,3_917:2.17161262,3_396:0.16952137);
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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/OG0001643_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001643_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e72c296f07fe159dd23b1e833c5b4758bf3a567
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001643_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1979:0.00244929,0_2038:-0.00018329):0.00018329,1_1756:0.00000000):0.05720661,3_577:0.17598933,2_662:0.06885567);
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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/OG0001646_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001646_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d1fd8549665e167190d0e868c8c84df2459e339
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001646_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1984:-0.00053956,(0_2043:0.00000050,1_1761:0.00000050):0.00232206):0.07560431,2_657:0.05817517,3_576:0.11076483);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..909eefdd6f2138cc03843a2e737aef25e1256e4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1763:-0.00024646,0_2045:0.00384046):0.00397323,4_1986:0.00348024):0.12618563,2_655:0.07233383,3_572:0.35605217);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001651_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001651_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84942a86401acf7bcca3f1b274f0f3f3e6acb952
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001651_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2049:0.00151390,((3_568:0.12932967,2_650:0.05769933):0.07614771,1_1767:0.00777313):0.00123337,4_1990:0.05276110);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4b1d9a18d5766bf8764a79ff54bd4a9fbe96104
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt
@@ -0,0 +1,2 @@
+((3_566:0.22799617,2_649:0.16537783):0.04257683,(1_1770:0.00909462,0_2052:0.00808838):0.00969240,4_1991:0.02258814);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ade3580a2527aab4f302ee3c803698839efc4502
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1992:0.01171975,0_2053:0.01775825):0.00837400,1_1772:0.03596050):0.07334350,3_565:0.29642675,2_648:0.08073725);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001657_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001657_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a4789dc9d0e336ca9cd23171e880c6af28fa011
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001657_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1777:0.00343961,((2_643:0.14772350,3_561:0.35096650):0.13588042,4_1997:0.02110376):0.05298274,0_2058:0.01104739);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a09762b9260ba35acb4005fd4997ad9803c7972
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1998:0.00000000,0_2059:0.00000000):0.00000000,1_1778:0.00000000):0.14673950,2_642:0.13225950,3_560:0.27281050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001660_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001660_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5e704cae7ab982f4cda6c41d2c8c1e2aa3e375a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001660_tree_id.txt
@@ -0,0 +1,2 @@
+(2_638:0.07640914,(3_557:0.00536300,(1_1781:0.00000000,4_2001:0.00000000):0.01509900):0.00178350,0_2062:0.01465986);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001662_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001662_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6fa0585a71960c85f3552ca41a9533a698784ea7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001662_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2065:0.00438617,(2_636:0.00877454,4_2004:0.01409046):0.00082954):0.00039777,1_1784:0.00045500,3_553:0.02766600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1cf4a4e8de5654ac680693f609d1aad3fc907a5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1786:0.00000000,(0_2067:0.00231775,(2_634:0.00263175,3_551:0.01164425):0.00770475):0.00051925,4_2006:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cea0eab3f00fd1b946d9f58e6297b1a3607f2d74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1788:0.00421883,4_2008:0.00320117):0.03513579,(0_2069:0.01901555,2_632:0.01757945):0.00381650,3_549:0.02401471);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001668_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001668_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b83a7e091a26640a98efc67c2047ecd47bd5495c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001668_tree_id.txt
@@ -0,0 +1,2 @@
+((2_630:0.02463600,3_547:0.02319300):0.01284850,(4_2010:0.00000000,0_2071:0.00000000):0.00976700,1_1790:0.01113800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001669_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001669_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a892ec0a9c1866162837917582bf6cf9aae97296
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001669_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2072:0.00457175,(1_1791:0.00521025,(2_629:0.03493275,3_546:0.05481725):0.01726775):0.00754575,4_2011:0.00176025);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001670_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001670_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b14045ba202518ad702ab9eeebd23f489cfd7dcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001670_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2073:0.01816740,(1_1792:0.00662666,4_2012:0.00959034):0.04405291):0.06087022,2_620:0.09031083,3_544:0.35967717);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001671_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001671_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c2484c8b52fac3b2e4276f63ae4c0e9f2233ee3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001671_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2014:0.00000000,1_1794:0.00000000):0.01059145,(2_618:0.03440617,3_543:0.22067283):0.02715502,0_2075:0.00190855);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001672_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001672_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b59ff3c7ef25abad8b0fb7e729f183070db8e185
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001672_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1795:0.00000000,0_2076:0.00000000):0.00000000,(2_617:0.06122550,3_542:0.13929450):0.03490350,4_2015:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001675_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001675_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed8c14e3e6d91817a5cc6c58f921df3d42a8ff1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001675_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2018:0.00194250,0_2079:-0.00010250):0.00010250,(3_539:0.25226925,2_614:0.01738575):0.05930300,1_1798:-0.00010250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001678_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001678_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..add26d3e803aeb033292a77c5d129e3b684758e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001678_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1801:-0.00002884,((0_2083:0.02257967,2_610:0.01098133):0.10934396,3_535:0.00676787):0.00627013,4_2021:0.00354784);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001679_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001679_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0beea6ad73ba0acad880a4afb7fa611d3a1d03ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001679_tree_id.txt
@@ -0,0 +1,2 @@
+((3_534:0.03303313,(0_2084:0.03093638,2_609:0.03815762):0.07459737):0.08249238,4_2022:0.00163338,1_1802:0.00439563);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001680_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001680_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b247932b0e2492182f87442fabadbc0766a47cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001680_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2023:0.00000050,1_1803:0.00000050):0.17886179,(2_608:0.75662975,0_2085:0.23624225):0.07517475,3_533:0.15422471);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01e73ba998443b5b4280218a778b50b4461480ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1815:0.00350728,4_2035:0.01152872):0.01773927,0_2091:0.01351600):0.20468681,3_517:0.09840717,2_592:0.18608583);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbafc1eccf8cc1aa2df3447c50f1a64b12561a99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1817:0.00394712,4_2037:0.00251088):0.00165987,0_2093:0.00718563):0.03257388,2_591:0.05146563,3_516:0.12564338);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001690_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001690_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86bb1c1d7fa5bd81af2efcb64757b82125699c12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001690_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1822:0.00178412,((2_581:0.26023550,3_504:0.32990050):0.11902182,4_2043:0.04172397):0.01762853,0_2098:-0.00001012);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001691_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001691_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fb7cb72f5a520800ee7eba88711d9d7e92be557
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001691_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1824:0.01592637,(4_2045:0.00000000,0_2100:0.00000000):0.00619163):0.21912496,3_502:0.80033650,2_578:0.44009250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001693_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001693_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfc0f5b961f35a95c511ca3b36f504b9683d87c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001693_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_499:0.47950200,2_575:0.16358600):0.20369600,0_2103:0.02838650):0.02724250,4_2049:0.00000000,1_1828:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001694_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001694_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f40de32e4a7ea23060331221deb86df760642783
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001694_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2106:0.00440563,((2_567:0.10695787,3_495:0.14318812):0.03944138,4_2052:0.03014213):0.00966538,1_1831:0.00823937);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001695_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001695_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55e02ebea2c66c0cc29144eb38aaaf12f96bb2b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001695_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1833:0.01505500,(0_2108:0.02027075,(2_565:0.24994600,3_492:0.41420400):0.18213975):0.01023625,4_2054:0.01387600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001698_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001698_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45427f5152b01dab358dbe0179182e8c7e58784b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001698_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2114:0.00704688,(1_1839:0.00159887,4_2060:0.00073413):0.00272013):0.10134713,2_559:0.21661712,3_487:0.12273687);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001699_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001699_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..931e01a5a5974f6d046e8f376b44e18eb3966562
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001699_tree_id.txt
@@ -0,0 +1,2 @@
+((3_486:0.23971367,2_558:0.31327733):0.24825330,(1_1840:0.01506082,4_2061:0.00000918):0.00244349,0_2115:0.00319138);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001700_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001700_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45dc889d067475ef2997cb6a3358c607e7b69946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001700_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2116:0.02182112,(1_1841:0.01164037,4_2062:0.01526163):0.01748538):0.17073437,2_557:0.29149888,3_485:0.29687712);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001702_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001702_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa68c8aa96c1910b97561d5bbabfd3d11c07a334
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001702_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2118:0.00088087,1_1843:0.00336213):0.00722562,4_2064:0.00237187):0.02484763,2_555:0.04896762,3_483:0.25893138);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001703_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001703_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..085b816e68bd7e146ada9be4fa0cd808b8aedaa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001703_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2119:0.00088530,(4_2065:0.02390698,(2_554:0.09031550,3_482:0.38157650):0.07967649):0.01058002,1_1844:0.01092170);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001704_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001704_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edbea4ac271c2c91d881c13210db1b71fe1c95e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001704_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1845:0.00421663,(0_2120:0.01221137,4_2066:0.00745263):0.00264038):0.07760738,3_479:0.22825487,2_551:0.10898913);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001706_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001706_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8eaeb42af10fdeeacd33876de4b7cdc89879af3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001706_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_2068:0.00551639,0_2122:0.02146761):0.01078963,1_1847:0.01623253):0.37248530,2_549:0.41403367,3_475:0.66437433);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001707_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001707_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5c050b9de095578ea089f4084b887f614e0c060
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001707_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_547:0.18619875,3_473:0.35888325):0.20882125,4_2070:-0.00205675):0.00867975,0_2124:0.00000000,1_1849:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001709_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001709_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..297b05950d192bf0e7f99b66d0f95ff5c934ac1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001709_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1853:0.00000000,(4_2074:-0.00067906,(3_467:0.30319967,2_539:0.03004233):0.07905331):0.00201006,0_2128:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001710_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001710_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6617b4f39ade6a4b5a2bb1d9fdb9629257c3d5d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001710_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2129:0.00620608,(1_1854:0.00266508,4_2075:0.01054192):0.00223730):0.13873184,3_466:0.39247933,2_536:0.12019567);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001712_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001712_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e12fa4856a83a0e60a247a95f968bfa023e35f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001712_tree_id.txt
@@ -0,0 +1,2 @@
+((2_531:0.02205138,(0_2134:0.00769087,4_2079:0.00194613):0.00667812):0.01796713,3_461:0.49659838,1_1858:0.05375062);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001713_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001713_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58902787d8f4a443942c4ce4653f9d26bae63a69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001713_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1859:0.02429200,2_530:0.02871000):0.00531876,(0_2135:0.00000000,4_2080:0.00000000):0.00478871,3_462:0.92974329);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001714_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001714_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8a9f4686970f277c6df857022c77b5b6a7e1dc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001714_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_2081:-0.00036487,2_529:0.03754988):0.00036487,0_2136:-0.00036487):0.00036487,1_1860:-0.00036487,3_463:0.86290587);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ced1ffb79f9bb5b297e57073b1a30abef2eb316
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2137:-0.00023237,((2_527:0.24927963,3_464:0.39471637):0.09430637,4_2082:0.00527363):0.00288037,1_1861:0.01000637);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001716_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001716_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc419c36a03aefb7d10527fa22309b831c72747b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001716_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1863:0.00000000,0_2139:0.00000000):0.00000000,4_2084:0.00000000):0.21667050,2_524:0.17585450,3_1750:2.08756950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001718_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001718_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9450ed3b8ace92ad3c158d880428e71e943e5761
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001718_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_455:0.56280350,2_523:0.15097850):0.08226600,1_1865:0.00000050):-0.00000000,4_2086:0.00000050,0_2141:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001720_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001720_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e49d3af85b8d8d2b4b79c1a5ce74241fb411ae88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001720_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1871:0.00000000,4_2092:0.00000000):0.02164699,0_2147:0.00849401):0.03926734,3_451:0.61386600,2_519:0.07229300);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e99d92a9b923bc2296254dd4e2c85f99489b4a10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1882:0.01410062,(4_2098:0.00651737,0_2158:0.00080062):0.01615487):0.42534287,2_509:0.37485938,3_448:0.43250362);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001723_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001723_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb36574283425da975925fe1fea78d19d2a0c7e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001723_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2159:0.01118925,(4_2099:0.00843275,1_1883:0.01043625):0.01114025):0.24416675,2_497:0.12686075,3_445:0.14688425);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001724_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001724_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f35930f4ee1ad1650746ca164fd624389a437535
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001724_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2178:0.01218600,4_2111:0.00475300):0.00210777,(1_1891:0.00246048,2_488:0.05568552):0.00128651,3_425:0.00566888);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001728_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001728_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c22a441cc4059664c676c0506c90187b5fe52d5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001728_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_494:0.65616750,2_482:0.07662550):0.06879750,0_2184:-0.00000000):0.00000000,1_1897:0.00000000,4_2117:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001731_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001731_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27bb29a955e96dc1065485be436b8f59833a85c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001731_tree_id.txt
@@ -0,0 +1,2 @@
+((3_414:0.00468500,2_458:0.01643500):0.00468500,(4_2126:-0.00001800,0_2194:0.00815800):0.00001800,1_1905:-0.00001800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48e266cb327ec82ecadd7c25823fd48cef0d4cd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1927:0.00040387,(0_2225:0.00147262,(3_387:0.37740737,2_433:0.02742563):0.01042537):0.00064037,4_2165:0.00523812);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001740_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001740_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b45878c7b2d65ff1cbf2a7d19c528bcd2e828525
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001740_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_431:0.03184075,3_384:0.15076125):0.01790725,0_2228:0.00514875):0.00200725,4_2169:0.00000000,1_1931:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001741_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001741_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff0fa9798b4348b72b8e6dd6e2f7155ef12da9c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001741_tree_id.txt
@@ -0,0 +1,2 @@
+((3_383:0.00684900,(0_2229:0.00000000,1_1932:0.00000000):0.00000000):-0.00000000,4_2170:0.00000000,2_430:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c56941accd1cbb4e6059385b6332e2873d54d51f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2230:0.00291250,1_1933:0.00518450):0.00552825,4_2171:0.00761975):0.02350275,3_382:0.15153125,2_429:0.08200775);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5d5c1818919a69af3591c5b1a6f6962560a8501
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1939:0.00631282,((2_422:0.02076583,3_376:0.07166917):0.01179948,0_2235:0.00469395):0.00095355,4_2177:0.00003118);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..399037b18d440c412cef35f55ad9fb1cc901a95e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1947:0.00000000,4_2185:0.00000000):0.00000000,(3_368:0.08789800,2_415:0.01643900):0.04794000,0_2243:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001752_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001752_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ea72b526873cef871a9d3dfed942e3c68012368
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001752_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1949:0.01164288,(0_2245:0.00581112,4_2187:0.00188488):0.00251113):0.02999063,3_366:0.11030287,2_412:0.02950512);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf96fc2ce069ccb5eaa355e01f0efe1fa68c6bb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2246:0.00659232,4_2188:-0.00016832):0.00321032,(2_411:0.04208900,3_365:0.27210400):0.02941191,1_1950:-0.00090801);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001755_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001755_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac3748fe9fb5646af20700733c2d9e2613a44ef7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001755_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2248:0.00423500,((4_2190:0.00432300,1_1952:0.00209800):0.02793900,3_363:0.12728050):0.01900250,2_409:0.02311500);
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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/OG0001757_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001757_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff7044170438e1d675d48f6fdcadd517cb48a64f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001757_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_407:0.08010533,3_361:0.54122967):0.02494413,0_2250:0.02690239):0.01875061,1_1954:0.00000000,4_2192:0.00000000);
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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/OG0001759_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001759_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..380ae8cea1dd8ed0beea98f7fba70f1ef5ce1409
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001759_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_223:0.50294616,2_2379:0.50863484):0.46067902,1_193:1.02832763):0.69255934,3_2262:0.30879833,4_493:0.15231867);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..815b4e077fe4990a6dd439711c5ad86b88dc7ff8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt
@@ -0,0 +1,2 @@
+((1_313:0.00000000,(1_352:0.00000000,1_1071:0.27663000):0.00000000):0.00000000,1_1917:0.00000000,1_1965:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1958c9a0866b891b7d444a61922fb9cfdca768c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2080:0.00000000,((2_80:0.57140400,3_126:0.56293900):0.85303624,2_253:0.03027973):0.01105027,4_121:0.00000000);
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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/OG0001766_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001766_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e5af86499188a2153b9ac611036d67ff7c458e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001766_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2154:0.00000050,(2_510:1.08314484,(2_496:0.07857667,3_438:0.08773533):0.10301195):0.07320166,4_210:0.00000050);
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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/OG0001767_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001767_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b191a45bbf49560d7e844dde7af17806fd79f605
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001767_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1827:0.68660497,((3_1722:0.52609750,2_140:0.98777750):0.06394264,3_1715:1.08250943):0.05565557,3_1728:1.13443003);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001769_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001769_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..041147a22d189d533b824573841d735292a81b61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001769_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_793:0.66937148,2_2335:1.10963452):0.26651190,2_500:1.17096610):0.65739453,2_926:0.04373650,3_867:0.13184750);
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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/OG0001771_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001771_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..25f4a1dfe801d3d9282bf1e20bcb5cf54378cfdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001771_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2114:2.23307975,4_32:-0.00978275):0.01638025,1_2001:-0.00657925,0_37:0.02748625);
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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/OG0001774_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001774_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..889283e9cbf273af91f172c44beb89381d5ce7f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001774_tree_id.txt
@@ -0,0 +1,2 @@
+(0_48:0.00970095,(4_43:0.00372600,2_336:0.11137000):0.00244300,1_2012:0.00086305);
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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/OG0001775_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001775_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0668557f84d3959ccac989f0b10433311af7f914
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001775_tree_id.txt
@@ -0,0 +1,2 @@
+((2_321:0.48904825,0_55:-0.00471225):0.00819775,4_50:0.01898750,1_2019:0.00487150);
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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/OG0001776_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001776_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cbdc547c9cc0f362f62f9c427ba5d3a0db2d535
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001776_tree_id.txt
@@ -0,0 +1,2 @@
+(3_247:1.17722025,(4_63:0.01581625,0_69:0.03343275):0.02008475,1_2033:0.04048775);
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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/OG0001779_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001779_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10b679ec4220b0356b20386bef66b5af7fc7956d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001779_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2077:0.00000000,(3_187:0.29194350,0_113:0.01665650):0.01062350,4_118:0.00000000);
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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/OG0001780_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001780_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f7c8af9379abb4bdf91958d0bcd0b2a909554ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001780_tree_id.txt
@@ -0,0 +1,2 @@
+((0_115:0.00390975,4_123:0.00700425):0.06340775,2_251:0.47729041,3_186:0.23413359);
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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/OG0001781_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001781_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6efdd0f23ff3278632e69bce82364fb78945f95c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001781_tree_id.txt
@@ -0,0 +1,2 @@
+(0_124:-0.00527300,(4_132:0.00000000,1_2089:0.00000000):0.02901600,2_243:0.25866600);
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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/OG0001784_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001784_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb31fb2c0b2db4265938289db558a6ef88f195f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001784_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2112:-0.23607031,(4_160:0.30639100,0_147:0.36481700):0.21370000,3_1439:0.97686831);
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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/OG0001786_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001786_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5109148fecec6b80fda5325c095d318ee3411bbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001786_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2138:0.01452500,2_184:0.28936100):0.02925000,0_191:0.00000000,4_194:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ff39ce452cd4ad70376c53f10f247c3d0d112b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt
@@ -0,0 +1,2 @@
+((0_192:0.27051025,2_179:0.28131275):0.11365825,3_135:0.18282662,3_115:1.96253738);
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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/OG0001790_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001790_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db410a4f2d1abfecf34427d7bb1371f1dc3c41bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001790_tree_id.txt
@@ -0,0 +1,2 @@
+((2_151:0.14407600,4_212:0.01270800):0.00773750,0_211:0.00834762,1_2156:0.00140038);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001791_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001791_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ae93a19c170d9c836baafdefad87d3d36b159bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001791_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2183:-0.00031650,3_101:0.02093050):0.00031650,4_220:0.00485150,0_219:-0.00031650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..304674a0ddc6752de1aa0e6e9b5e7954513ab149
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2197:0.01001325,4_234:0.00468175):0.01221625,0_234:0.06490196,2_118:0.03447604);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001793_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001793_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63073cf1481c356df5025b050d594c71e13acbcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001793_tree_id.txt
@@ -0,0 +1,2 @@
+((4_238:0.00711850,0_238:0.00746150):0.00560950,1_2201:0.00651664,3_82:0.19843336);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63366a7644b1991c97af9866e9ecc38f53707fd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt
@@ -0,0 +1,2 @@
+((4_243:0.00080825,2_109:0.02497175):0.00132975,1_2206:0.00316259,0_243:0.01938441);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001795_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001795_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc917bf0f8c1afa52a17c2ed9a2452999952c722
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001795_tree_id.txt
@@ -0,0 +1,2 @@
+((0_244:0.00670250,2_107:0.01051950):0.00093150,1_2207:0.00000000,4_244:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8bdf22a3f6c28195ff592db45a4a271242e24c3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt
@@ -0,0 +1,2 @@
+((3_39:0.37975425,4_282:0.01117275):0.00676325,1_2249:0.00934425,0_276:0.02557275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001804_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001804_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d3038c03394055d0884fe410cc3fae94f9c07e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001804_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2:0.05145150,0_315:0.00041650):0.00454000,4_322:0.00000050,1_40:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001807_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001807_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c3cb8a48071ef7e1734cc41ba389c71307bfb3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001807_tree_id.txt
@@ -0,0 +1,2 @@
+(0_366:0.01246850,(4_372:0.02915750,1_99:0.04540050):0.00550200,3_2385:0.01684950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82129b77bd4cd3141e9f563e46bc3e64cd107d2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2510:0.46451425,0_369:-0.00191525):0.00191525,1_102:0.00000000,4_375:0.00871800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001811_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001811_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b621aa78c85ef529e36452eab21231b1eebedf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001811_tree_id.txt
@@ -0,0 +1,2 @@
+((1_168:0.00622375,4_441:0.00130625):0.00057125,0_441:0.00132309,3_2313:0.40452191);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001813_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001813_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5311bad138f4252877ebf6078d0884219971421
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001813_tree_id.txt
@@ -0,0 +1,2 @@
+((4_486:0.03859475,3_2270:0.72132225):0.00408025,0_487:0.03959575,1_216:0.04451525);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc92bed43a7bfd6ca621857cfade98a560cd153e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt
@@ -0,0 +1,2 @@
+((0_500:0.00649675,4_500:0.00311225):0.20750275,3_2255:0.18966105,2_2373:0.19734895);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0fa3eaf754ca04a4d2ede95c0422c242f0288e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt
@@ -0,0 +1,2 @@
+((4_516:0.00000000,1_246:0.00000000):0.00102850,2_2360:0.19059550,0_513:0.06693850);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001816_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001816_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfdbb2404faed3e24724c9f46e5295a7cc6add9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001816_tree_id.txt
@@ -0,0 +1,2 @@
+(1_278:0.03294700,(3_2206:0.23141800,0_545:0.07538200):0.02164900,4_547:0.03949200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cc6f3c54c29caf12971c3885cd0a05b4678011a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt
@@ -0,0 +1,2 @@
+(0_553:0.00000000,(4_554:0.00280575,1_294:-0.00013475):0.00013475,2_2304:0.00213900);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001820_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001820_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42d43d07c928bf85d5ed7a75c02593855cc1d4f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001820_tree_id.txt
@@ -0,0 +1,2 @@
+((0_557:0.28887325,1_299:0.04302775):0.17537225,4_558:0.09324192,2_2300:0.56156008);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c8f1fee1cae612829f9f0c0688c461fb57546a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt
@@ -0,0 +1,2 @@
+(2_734:0.51688750,(0_613:0.00000000,4_568:0.00000000):0.03569250,0_599:-0.00025050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001823_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001823_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8cd54e9f61ce0c7eb01e42c472f1b9ede39e02d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001823_tree_id.txt
@@ -0,0 +1,2 @@
+(4_578:0.00618175,(2_384:0.01315225,0_603:0.00356075):0.00023725,3_2149:-0.00002575);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001824_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001824_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83391a2adb90f544b81b325687f9975a4fbeec5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001824_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2148:0.00677025,4_577:-0.00090625):0.00029725,2_385:0.01474400,0_604:0.00295400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001827_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001827_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0f39a6946d01e232cd86f07e28040162f09f621
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001827_tree_id.txt
@@ -0,0 +1,2 @@
+(4_583:0.00197125,(0_614:0.01502275,3_2134:0.01547325):0.00287525,1_360:0.00513375);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8695f5508482462a21bc33ccccd3f94032344488
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt
@@ -0,0 +1,2 @@
+(2_2266:0.26310150,(1_367:-0.00069675,0_621:0.00553975):0.00349825,4_591:-0.00038350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31d3e866bddadb437545b542fa88a4eb22c75ce7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt
@@ -0,0 +1,2 @@
+(2_2246:0.15759900,(1_386:0.00000000,0_640:0.00000000):0.00524500,4_610:0.00205800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001834_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001834_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e02abff225c70cb70971748851e5155fdad93590
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001834_tree_id.txt
@@ -0,0 +1,2 @@
+((0_652:-0.00012400,4_622:0.00762700):0.00928200,3_2095:0.31163300,1_398:0.01102000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001835_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001835_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad25270fd4b359c2e2ae7d36a43c9203e15489e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001835_tree_id.txt
@@ -0,0 +1,2 @@
+((4_642:0.01518950,1_418:0.00710250):0.00261550,2_2206:0.35273942,0_672:0.01246558);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001837_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001837_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f7a2c061d93d44d3ad1e34a51d527bcf1846fac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001837_tree_id.txt
@@ -0,0 +1,2 @@
+(0_759:0.00000050,(4_726:0.02082200,3_1988:0.48028100):0.02227250,1_499:0.00000050);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001839_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001839_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05548f2b704f0507b93044cc0b6e4c2194142fd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001839_tree_id.txt
@@ -0,0 +1,2 @@
+((1_556:0.01005725,3_1927:0.25844175):0.00682175,4_784:0.00274725,0_825:0.00471675);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0182cee22716c77cb37679d5a3e5f1437e79d41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1070:0.96883955,(0_912:0.00846525,1_640:0.00678775):0.09919725,2_1949:0.08394245);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001843_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001843_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e5da0aa2fd4b235063ceeaa534aff23cfa908d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001843_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1842:0.03104200,(0_970:0.00000000,1_693:0.00000000):0.04768500,4_913:0.01975100);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001845_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001845_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e466828633c011281fd4f32b7fae57188019e8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001845_tree_id.txt
@@ -0,0 +1,2 @@
+((4_919:0.00223575,2_1836:0.00848225):0.00000775,1_698:0.00224852,0_975:0.00394648);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001846_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001846_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8059aa84aedc72f731b87c9dd34c7ef13c2c60a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001846_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1679:0.23792200,(1_747:0.00877100,0_1019:0.00067400):0.00496450,4_966:0.00247600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fca607e2eb08c6e859fcd84979559424c957dbc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2177:0.08296900,1_750:0.00179100):0.01290700,0_1022:0.01556450,4_969:-0.00104150);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001849_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001849_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4fbef1163d9e4bc1695f1697ce39184037a35b50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001849_tree_id.txt
@@ -0,0 +1,2 @@
+((4_981:-0.00000000,2_2272:0.36750000):0.00000000,0_1032:0.00000000,1_760:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001850_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001850_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e6dbc32f4bb3876f158c8ee12fb13287880838e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001850_tree_id.txt
@@ -0,0 +1,2 @@
+(1_793:0.00406801,(3_1642:0.29763075,4_1015:0.06446625):0.17821125,0_1065:0.00718899);
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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/OG0001851_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001851_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77c25c92eda4729eae9c6872d0f4069b0abca9b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001851_tree_id.txt
@@ -0,0 +1,2 @@
+(1_794:0.00114050,(4_1016:0.00225300,0_1066:-0.00035900):0.00809000,2_1750:0.07013650);
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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/OG0001852_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001852_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dec99df958ee343d5c31c73ea5ca0753f3e6eb44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001852_tree_id.txt
@@ -0,0 +1,2 @@
+((1_827:0.00000000,4_1049:0.00000000):0.04658450,3_1609:0.62300850,0_1099:0.04627750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001855_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001855_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ebfb9646a01fd3eb2308710a71bdf8dd5ae7300
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001855_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1165:0.01476800,4_1122:0.00142900):0.00320900,1_893:0.00828580,3_1542:0.19773220);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001857_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001857_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be735559202dd486a5ef19101137bce2e3d90633
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001857_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1605:0.14826985,(1_933:0.02264050,0_1205:0.02355350):0.14217450,3_1502:0.47486115);
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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/OG0001860_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001860_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2dd946a7d4792e433f4d8bccdbe8866f664496ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001860_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2607:1.48548775,3_1443:-0.46743075):0.94140675,0_1267:0.00154825,2_1547:0.00451975);
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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/OG0001861_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001861_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49344d079309372d01b9fa106bb604aaee1b63b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001861_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1401:0.17033400,(4_1263:0.00000000,0_1309:0.00000000):0.00442200,1_1038:0.00455200);
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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/OG0001862_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001862_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49857ec257f2aac97c0b0e869bbd60e84c0d0f28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001862_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1288:0.00000050,(3_1850:0.54025100,1_1063:0.01392900):0.01122950,0_1334:0.00000050);
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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/OG0001865_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001865_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43110ab38041029aa25eb089fb3001ced25ed9fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001865_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1100:-0.08450850,4_1310:0.30496750):0.14310450,3_1367:0.62491000,0_1361:0.26477900);
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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/OG0001866_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001866_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3808c4f9856de295d77d4ab0f4243c6841bbaef9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001866_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1366:0.39109520,(0_1362:0.00456550,4_1311:0.00113750):0.06504000,1_1101:0.21655280);
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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/OG0001867_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001867_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb83ef833ceb2f39aa92d68f67fe225fc1925715
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001867_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1108:0.00000000,0_1368:0.00000000):0.00000000,2_1453:0.00418500,4_1317:0.00000000);
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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/OG0001868_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001868_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..947200bea0d6b820781f779a03fd8b59095a646d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001868_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1332:0.58046301,(0_1393:0.01436650,1_1134:0.02303150):0.00111450,4_1342:0.01938299);
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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/OG0001869_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001869_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8eab847fcd140777650470997d89a21d250740da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001869_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1350:-0.00209920,(3_1324:0.05228250,1_1142:0.00143650):0.00487950,0_1401:0.00629220);
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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/OG0001870_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001870_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aeaf277ca776a46c04c2aa3329f87ea58966b0c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001870_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1159:0.04013413,(4_1367:0.01988975,0_1418:0.02424225):0.02350125,3_1306:0.38503487);
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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/OG0001873_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001873_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cfd3369b213d180ddea3a14819f5242935abf5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001873_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1453:0.12875650,(3_1709:0.00000000,3_2184:0.00000000):0.08104050,3_623:0.24833250);
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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/OG0001875_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001875_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf4cd6f00f287f842efe9e0689671aa0ce3d2e2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001875_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1456:0.00403325,2_1314:0.00672775):0.00292775,0_1529:0.00241336,1_1250:0.02071164);
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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/OG0001879_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001879_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8451746f706f905a5b441702e49686788eeac2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001879_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1165:0.01254000,(1_1280:0.00411800,0_1560:0.00414700):0.00415900,2_1260:0.00971400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001880_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001880_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..552af02b334d02a7898d1a508e972222792825d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001880_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1500:0.16161726,(0_1571:0.01464500,1_1287:0.03518800):0.30823600,2_799:1.24802474);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6e12d1d6ef99177f8be69e5a3b81ef9c6975705
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1498:1.60618300,(1_1316:0.00013550,4_1531:0.00789950):0.01595850,0_1601:-0.00062600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001885_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001885_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f723b6ae18daab9a1157c01faf1d1f055d93419d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001885_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1426:0.00094150,0_1709:0.01092450):0.00333550,4_1638:0.00062150,2_1089:0.21206750);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..017bd6fb8beacc7882bb4fd0af88807e3bef809e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1485:0.00000000,(2_1011:0.22977150,0_1777:0.03235250):0.01728350,4_1699:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afb3c6b80236d7a75a35c00132444fda8ad7e963
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1001:0.15413326,(1_1494:0.00207700,0_1787:0.00184900):0.01183250,4_1708:0.00772274);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001890_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001890_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05de96c73ae0446777d395732d67d12c59a85c5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001890_tree_id.txt
@@ -0,0 +1,2 @@
+(3_900:0.84907775,(0_1818:0.00257825,1_1525:0.00635475):0.15571175,2_961:0.07054125);
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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/OG0001891_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001891_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c11497800c02b2d738ef0996218bc451ab51e54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001891_tree_id.txt
@@ -0,0 +1,2 @@
+((2_960:0.24586125,4_1740:0.02704975):0.00902825,1_1526:0.00631625,0_1819:0.00838075);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d1b18c1dfdafa57ef474e42646bd8afb9f7f44b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1540:0.01350598,(4_1754:0.00755450,0_1833:0.00862850):0.00537550,2_945:0.56566702);
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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/OG0001895_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001895_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f39166ba021aafc568e8cf7c88a1e2b10b6ee98e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001895_tree_id.txt
@@ -0,0 +1,2 @@
+(2_943:0.09357450,(4_1756:0.00000000,0_1835:0.00000000):0.01470150,1_1542:0.01217750);
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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/OG0001896_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001896_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20f3ac783792cfafb6c62e46d8ee1a6291c76d4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001896_tree_id.txt
@@ -0,0 +1,2 @@
+(2_941:0.45448600,(1_1545:0.00451000,0_1838:0.01220400):0.00448850,4_1759:0.00604600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e47ad8ad7fad6bfd1955e447601677b32bdd1e8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt
@@ -0,0 +1,2 @@
+(3_864:0.13131157,(4_1773:0.00249400,1_1559:0.00012600):0.00764950,0_1852:0.00944343);
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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/OG0001899_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001899_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7862a5843cb998f2178a8b27378165bd87f60455
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001899_tree_id.txt
@@ -0,0 +1,2 @@
+((3_862:0.47968400,0_1854:0.02171400):0.02896400,4_1775:0.00189000,1_1561:0.00152800);
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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/OG0001902_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001902_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4475f52d5e769858d0ef0bd9b758c544059506b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001902_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1791:0.00482879,(2_909:0.14964175,1_1578:0.00351625):0.00065475,0_1871:0.00757821);
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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/OG0001904_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001904_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3d8173b0870952280d6037888ca8d413f6f84bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001904_tree_id.txt
@@ -0,0 +1,2 @@
+((2_896:0.46372275,4_1806:-0.00140275):0.00140275,3_829:0.00576875,0_1886:-0.00140275);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac5220f44baea116da4d5d53cf02d3f4a128d7dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1842:-0.00065350,(0_1916:-0.00604600,2_862:0.18599100):0.05243950,1_1620:0.01500450);
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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/OG0001907_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001907_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e889ec5a8a7ac9f080c8e444a1fe2253a48a9b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001907_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1926:0.00000000,1_1631:0.00000000):0.00000000,2_851:0.00650900,4_1853:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001909_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001909_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78b408765a67bb928bb410c1935b91988d848a03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001909_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1936:0.01384275,3_778:0.89539525):0.00537075,1_1641:0.01503328,4_1863:0.02237472);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41a0de1205ed77f3c388021d03ff905ab5738fed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt
@@ -0,0 +1,2 @@
+((2_837:0.24113300,0_1940:0.02657400):0.01114850,1_1645:0.00750810,4_1867:0.00843890);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001911_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001911_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d263d9e4b76b11a3780b625bfddda9350618ba4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001911_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1971:0.00646475,(1_1689:0.00572475,2_770:0.01128425):0.00202325,4_1907:0.00901525);
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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/OG0001912_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001912_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b074576f0c9ebf291871e6965ec5442bb654a3eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001912_tree_id.txt
@@ -0,0 +1,2 @@
+(2_133:0.34344257,(0_1976:1.65810275,2_789:0.87957325):0.02769125,3_95:0.57820543);
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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/OG0001914_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001914_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..072fafddf1679793792a83cd66e003debad9d8a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001914_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1702:0.00634411,(0_1985:0.00664800,3_716:0.00568700):0.00179750,4_1920:0.01726389);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001918_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001918_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..503a175f915f2af64b35105a6c1edf273a64fd03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001918_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2370:0.80321300,3_2384:2.49188800):0.68816825,3_2170:0.02568925,0_2001:-0.01852525);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5206af1caee218c345aaa4b6dd4b1979d8beb229
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt
@@ -0,0 +1,2 @@
+(2_670:0.01566919,(3_587:0.01433050,0_2029:0.00525750):0.01540600,1_1748:0.00564581);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40195ce250a365a527301d145224b7fac6f4b0c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2036:0.04131250,(4_1977:0.00230300,1_1754:-0.00043200):0.01958950,2_664:0.22516350);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fd3d8fbae996b712819dc7a3809c96efdb3e4b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt
@@ -0,0 +1,2 @@
+(2_652:0.06423200,(0_2047:-0.00040675,4_1988:0.02693075):0.00393375,1_1765:-0.00002400);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c9d1e98f7f5ea9b5cde87a9b6f57d3fea0c9bd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1793:0.00000000,(2_619:0.02236600,0_2074:0.01087600):0.02127400,4_2013:0.00000000);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001930_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001930_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f6725ae5da8617f37afd87eee9f9e50794e60b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001930_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2110:0.00192842,4_2056:0.00565058):0.10822375,3_490:1.38099575,1_1835:0.03881625);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001932_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001932_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0658b2e8b475abf050dda4652d30a65b140880ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001932_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2126:0.04266025,(4_2072:0.00929275,1_1851:0.00814925):0.01225125,2_544:0.37297375);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001934_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001934_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d86ea1132d99123d9dc606a56ec48b27d50d0ca4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001934_tree_id.txt
@@ -0,0 +1,2 @@
+(2_532:0.06440779,(0_2131:0.01790850,4_2076:0.04085150):0.02872500,1_1855:-0.00125379);
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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/OG0001935_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001935_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b1d7095942e47794eee92b59154b993c300cc8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001935_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1856:0.05357536,(4_2077:0.00879850,0_2132:0.00978650):0.00616200,2_535:0.56655164);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a99b26d344be1e8a6411943f5ad9644938fb640
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1866:0.00000000,4_2087:0.00000000):0.00000000,0_2142:0.00000000,2_522:0.19952200);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001937_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001937_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95fdf2580c40724651d32e2598b8cc70d0cfdca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001937_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2146:0.02528925,(1_1870:0.01611925,2_520:0.05093975):0.02713625,4_2091:0.00365475);
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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/OG0001940_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001940_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7312c0e5b71c30eb84f95b0710d721d4237c4db4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001940_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2153:0.01081950,(2_512:0.16496300,1_1877:0.01089200):0.00313450,4_2093:0.01081950);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001942_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001942_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4beabc8baa9fd3fb1ccd710d9913062f344adedc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001942_tree_id.txt
@@ -0,0 +1,2 @@
+(2_498:0.43679073,(4_2100:0.00476200,1_1887:0.00861900):0.00408350,0_2160:0.01832627);
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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/OG0001943_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001943_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..042fbda08144fb6964da687fc9e9542bc92a1ee9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001943_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2161:0.00038625,3_444:0.12959775):0.00078375,4_2101:0.00299448,1_1888:0.01135152);
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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/OG0001945_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001945_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e67b90c0a954811bbc7a912c191cb34f54c1b61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001945_tree_id.txt
@@ -0,0 +1,2 @@
+(3_683:0.40411850,(0_2198:0.00000000,4_2130:0.00000000):0.50890750,2_445:0.15344050);
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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/OG0001946_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001946_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9fc1c689f0fe739ee218dc08e157c53c631c2fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001946_tree_id.txt
@@ -0,0 +1,2 @@
+(3_411:0.06002051,(0_2202:0.00404200,1_1908:0.00577800):0.00676600,4_2134:0.01367449);
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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/OG0001947_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001947_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48a9cf09fde96abf26b144aeff3a3ef491403ebc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001947_tree_id.txt
@@ -0,0 +1,2 @@
+(3_393:0.99526023,(1_1914:0.16897775,2_442:0.05956125):0.26045275,0_2211:0.04912677);
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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/OG0001948_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001948_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd99975fbf5fe404582d0fc90cf6d1d583ce6507
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001948_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1915:0.01746873,(3_391:0.25709250,0_2212:0.02360250):0.00396600,2_441:0.02287527);
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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/OG0001952_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001952_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..009523d93cb91e705a5ba24a9fbbe1fa344f7122
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001952_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2239:-0.00000000,3_372:0.20721200):0.00000000,4_2181:0.00000000,1_1943:0.00000000);
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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/OG0001953_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001953_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bbe0e9299dbfd20bf40e276206f19d1a8827b8c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001953_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1746:0.01614724,2_672:0.00829676):0.76391400,2_757:0.82868150,1_82:0.61195450);
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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/OG0001954_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001954_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f0915fc733da6a1aeabc505d03442998c5597dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001954_tree_id.txt
@@ -0,0 +1,2 @@
+((4_811:0.25776600,2_1199:2.22695500):0.41934300,2_2384:0.22159118,1_224:0.18290082);
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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/OG0001955_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001955_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..299eed3e7a2c5789171aceb676cb7a78e2eb3e23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001955_tree_id.txt
@@ -0,0 +1,2 @@
+(1_241:0.04713997,(4_511:0.02466650,3_2246:0.09073950):0.02753000,2_2365:0.79846303);
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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/OG0001956_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001956_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c0f6cb2699a34c02d9f2fce79ae5a5d725f2f44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001956_tree_id.txt
@@ -0,0 +1,2 @@
+(1_243:0.00331986,(3_2244:0.39303775,2_2363:0.15553525):0.14190525,4_513:0.00641214);
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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/OG0001957_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001957_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..358a1b8b38817aafffed17d41f9a71f7853598d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001957_tree_id.txt
@@ -0,0 +1,2 @@
+(4_567:0.16083100,(2_2223:-0.00021925,3_1786:0.00898025):0.00021925,1_307:0.00000000);
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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/OG0001959_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001959_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5427316f8fd1742962e5688aaf7adb13896acdfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001959_tree_id.txt
@@ -0,0 +1,2 @@
+((2_884:0.00135250,3_824:0.00011350):0.03675950,4_1815:0.17795850,1_1595:0.00573650);
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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/OG0001960_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001960_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a471e6f7cc11e1c28b10d2b39c44471d18dd671
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001960_tree_id.txt
@@ -0,0 +1,2 @@
+((2_883:0.00000000,3_823:0.00000000):0.06812100,1_1596:0.00324400,4_1816:0.00674800);
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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/OG0001962_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001962_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee48d48c958856d265c68509f14b64794be0b443
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001962_tree_id.txt
@@ -0,0 +1,2 @@
+((3_821:0.55630325,1_1598:0.15143675):0.18199025,2_881:-0.00898225,4_1819:0.11769225);
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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/OG0001963_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001963_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70c61e2a6cd56ead8566c36544b3227d6fca7592
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001963_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1647:0.14741750,(2_835:-0.31227275,4_709:1.42230875):0.34358125,3_773:0.46324550);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14a2f82c119a4ecda48b744a75031ed0f5e93a33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt
@@ -0,0 +1,2 @@
+(4_710:1.31293673,(2_834:0.04286825,1_1648:0.06511975):0.74234875,3_772:-0.24892173);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001965_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001965_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48e5dd5b28f104630ab4d625b4018c5be58ca75e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001965_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1868:0.00000000,1_1650:0.00000000):0.01444400,2_832:0.01972500,3_770:0.12952800);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3329de87f4c55bf4d5807586ec3cee279d49ff35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt
@@ -0,0 +1,2 @@
+(3_767:0.21064200,(4_1871:0.00449500,1_1653:-0.00168600):0.20206500,2_829:0.32545600);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b911b7edd53b53c423b1d1c01d32ccad3bfc69b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1656:-0.00200600,4_1874:0.01096200):0.08876750,3_761:0.08032950,2_827:0.13296650);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd87efe45b976cd26f8560c31168168179244330
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt
@@ -0,0 +1,2 @@
+(2_826:0.18028650,(4_1875:0.00000000,1_1657:0.00000000):0.08118850,3_760:0.16595250);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001971_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001971_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..668b5302753eb82ee978d016e3853bf1fb99d9ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001971_tree_id.txt
@@ -0,0 +1,2 @@
+(3_759:0.33565940,(4_1876:0.05436975,1_1658:0.06877625):0.09327675,2_825:0.20684160);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001976_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001976_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5aae1c51d8c583b3b5db6e9cb48e9b8b0c463d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001976_tree_id.txt
@@ -0,0 +1,2 @@
+((3_138:0.02348225,4_191:0.02816675):0.14359825,3_580:1.44915099,2_186:0.17407301);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15897a41994e4f12b685f90abd5f8110f9e3fd77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt
@@ -0,0 +1,2 @@
+((3_404:0.32284625,2_694:0.31567275):0.19492775,3_703:0.02373453,3_680:0.00431447);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48ce6d059d212f7d6798d3eb5e1dba56fcb714b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt
@@ -0,0 +1,2 @@
+(3_398:0.13660700,(2_715:0.00000000,2_732:0.00000000):0.19025700,2_2277:0.06747700);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee25967cfa484da4e7730746971b56e1f28e5398
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt
@@ -0,0 +1,2 @@
+(3_296:-0.29496448,(3_392:1.18538150,3_638:1.26865750):0.25628450,3_1736:0.88935448);
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001985_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001985_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e839ec20c1e36e1bbc1d93773b01da0c8d501d6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001985_tree_id.txt
@@ -0,0 +1,2 @@
+(3_657:0.47781533,(3_2174:0.32871525,3_658:0.28834175):0.15902225,3_2173:0.23702667);
+